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Perrier S, Gauquelin L, Fallet-Bianco C, Dishop MK, Michell-Robinson MA, Tran LT, Guerrero K, Darbelli L, Srour M, Petrecca K, Renaud DL, Saito M, Cohen S, Leiz S, Alhaddad B, Haack TB, Tejera-Martin I, Monton FI, Rodriguez-Espinosa N, Pohl D, Nageswaran S, Grefe A, Glamuzina E, Bernard G. Expanding the phenotypic and molecular spectrum of RNA polymerase III-related leukodystrophy. NEUROLOGY-GENETICS 2020; 6:e425. [PMID: 32582862 PMCID: PMC7238899 DOI: 10.1212/nxg.0000000000000425] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022]
Abstract
Objective To expand the phenotypic spectrum of severity of POLR3-related leukodystrophy and identify genotype-phenotype correlations through study of patients with extremely severe phenotypes. Methods We performed an international cross-sectional study on patients with genetically proven POLR3-related leukodystrophy and atypical phenotypes to identify 6 children, 3 males and 3 females, with an extremely severe phenotype compared with that typically reported. Clinical, radiologic, and molecular features were evaluated for all patients, and functional and neuropathologic studies were performed on 1 patient. Results Each patient presented between 1 and 3 months of age with failure to thrive, severe dysphagia, and developmental delay. Four of the 6 children died before age 3 years. MRI of all patients revealed a novel pattern with atypical characteristics, including progressive basal ganglia and thalami abnormalities. Neuropathologic studies revealed patchy areas of decreased myelin in the cerebral hemispheres, cerebellum, brainstem, and spinal cord, with astrocytic gliosis in the white matter and microglial activation. Cellular vacuolization was observed in the thalamus and basal ganglia, and neuronal loss was evident in the putamen and caudate. Genotypic similarities were also present between all 6 patients, with one allele containing a POLR3A variant causing a premature stop codon and the other containing a specific intronic splicing variant (c.1771-7C>G), which produces 2 aberrant transcripts along with some wild-type transcript. Conclusions We describe genotype-phenotype correlations at the extreme end of severity of the POLR3-related leukodystrophy spectrum and shed light on the complex disease pathophysiology.
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Affiliation(s)
- Stefanie Perrier
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Laurence Gauquelin
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Catherine Fallet-Bianco
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Megan K Dishop
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Mackenzie A Michell-Robinson
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Luan T Tran
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Kether Guerrero
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Lama Darbelli
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Myriam Srour
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Deborah L Renaud
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Michael Saito
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Seth Cohen
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Steffen Leiz
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Bader Alhaddad
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Tobias B Haack
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Ingrid Tejera-Martin
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Fernando I Monton
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Norberto Rodriguez-Espinosa
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Daniela Pohl
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Savithri Nageswaran
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Annette Grefe
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Emma Glamuzina
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery (S.P., L.G., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, K.P., G.B.), McGill University; Child Health and Human Development Program (S.P., M.A.M.-R., L.T.T., K.G., L.D., M. Srour, G.B.), Research Institute of the McGill University Health Centre; Department of Pediatrics (L.G., L.T.T., K.G., L.D., M. Srour, G.B.), McGill University, Montreal, Quebec, Canada; Division of Clinical and Metabolic Genetics (L.G.), Division of Neurology, the Hospital for Sick Children, University of Toronto, Ontario, Canada; Department of Pathology (C.F.-B.), CHU Sainte-Justine, Université de Montreal, Quebec, Canada; Division of Pathology and Laboratory Medicine (M.K.D.), Phoenix Children's Hospital, AZ; Department of Human Genetics (L.T.T., K.G., L.D., G.B.), McGill University, Montreal, Quebec, Canada; McGill University (K.P.), Brain Tumour Research Center Montreal Neurological Institute and Hospital, Quebec, Canada; Department of Neurology (D.L.R.), Department of Clinical Genomics, Department of Pediatrics, Mayo Clinic, Rochester, MN; Department of Pediatrics (M. Saito), University of California Riverside School of Medicine, Riverside Medical Clinic, CA; Department of Pediatrics (S.C.), Beaver Medical Group, Redlands, CA; Division of Pediatric Neurology (S.L.), Department of Pediatrics, Klinikum Dritter Orden, Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics (T.B.H.), University of Tübingen, Germany; Department of Neurology (I.T.-M., F.I.M., N.R.-E.), Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain; Department of Neurology (D.P.), Children's Hospital of Eastern Ontario, University of Ottawa, Ontario, Canada; Department of Pediatrics (S.N.) and Department of Neurology (A.G.), Wake Forest School of Medicine, Winston-Salem, NC; Adult and Paediatric National Metabolic Service (E.G.), Starship Children's Hospital, Auckland, New Zealand; and Division of Medical Genetics (G.B.), Department of Specialized Medicine, Montreal Children's Hospital and McGill University Health Centre, Quebec, Canada
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Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction. Nat Neurosci 2020; 23:718-729. [PMID: 32367065 PMCID: PMC7269834 DOI: 10.1038/s41593-020-0627-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 03/19/2020] [Indexed: 01/06/2023]
Abstract
DNA forms conformational states beyond the right-handed double-helix; however, the functional relevance of these non-canonical structures in the brain remains unknown. We show that, in the prefrontal cortex of mice, the formation of one such structure, Z-DNA, is involved in the regulation of extinction memory. Z-DNA is formed during fear learning, and reduced during extinction learning, which is mediated, in part, by a direct interaction between Z-DNA and the RNA editing enzyme Adar1. Adar1 binds to Z-DNA during fear extinction learning which leads to a reduction in Z-DNA at sites where Adar1 is recruited. Knockdown of Adar1 leads to an inability to modify a previously acquired fear memory and blocks activity-dependent changes in DNA structure and RNA state; effects that are fully rescued by the introduction of full-length Adar1. These findings suggest a novel mechanism of learning-induced gene regulation dependent on both proteins which recognize DNA structure, and the state.
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Hiraide T, Kubota K, Kono Y, Watanabe S, Matsubayashi T, Nakashima M, Kaname T, Fukao T, Shimozawa N, Ogata T, Saitsu H. POLR3A variants in striatal involvement without diffuse hypomyelination. Brain Dev 2020; 42:363-368. [PMID: 31932101 DOI: 10.1016/j.braindev.2019.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/26/2019] [Accepted: 12/27/2019] [Indexed: 11/27/2022]
Abstract
BACKGROUND Biallelic variants in POLR3A encoding the largest subunit of RNA polymerase III cause POLR3-related (or 4H) leukodystrophy characterized by neurologic dysfunction, abnormal dentition, endocrine abnormalities and ocular abnormality. Recently, whole-exome sequencing enabled the discovery of POLR3A variants in cases lacking diffuse hypomyelination, the principal MRI phenotype of POLR3-related leukodystrophy. Homozygous c.1771-6C > G variants in POLR3A were recently suggested to cause striatal and red nucleus involvement without white matter involvement. CASE REPORT Here, we report three cases in two families with biallelic POLR3A variants. We identified two sets of compound heterozygous variants in POLR3A, c.1771-6C > G and c.791C > T, p.(Pro264Leu) for family 1 and c.1771-6C > G and c.2671C > T, p.(Arg891*) for family 2. Both families had the c.1771-6C > G variant, which led to aberrant mRNA splicing. Neuropsychiatric regression and severe intellectual disability were identified in three patients. Two cases showed dystonia and oligodontia. Notably, characteristic bilateral symmetric atrophy and abnormal signal of the striatum without diffuse white matter signal change were observed in brain MRI of all three individuals. CONCLUSIONS Striatum abnormalities may be another distinctive MRI finding associated with POLR3A variants, especially in cases including c.1771-6C > G variants and our cases can expand the phenotypic spectrum of POLR3A-related disorders.
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Affiliation(s)
- Takuya Hiraide
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan; Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuo Kubota
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan; Division of Clinical Genetics, Gifu University Hospital, Japan
| | - Yu Kono
- Department of Neurology, Fuji City General Hospital, Shizuoka, Japan
| | - Seiji Watanabe
- Department of Pediatric Neurology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Tomoko Matsubayashi
- Department of Pediatric Neurology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Toshiyuki Fukao
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan; Division of Clinical Genetics, Gifu University Hospital, Japan
| | - Nobuyuki Shimozawa
- Division of Clinical Genetics, Gifu University Hospital, Japan; Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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Ng HM, Ho JCH, Nong W, Hui JHL, Lai KP, Wong CKC. Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica. BMC Genomics 2020; 21:208. [PMID: 32131732 PMCID: PMC7057501 DOI: 10.1186/s12864-020-6630-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 12/28/2022] Open
Abstract
Background Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-establishment of fluid and electrolyte homeostasis. The osmoregulatory plasticity of gills provides an excellent model to study the role of microRNAs (miRs) in adaptive osmotic responses. The present study is to characterize an ex-vivo gill filament culture and using omics approach, to decipher the interaction between tonicity-responsive miRs and gene targets, in orchestrating the osmotic stress-induced responses. Results Ex-vivo gill filament culture was exposed to Leibovitz’s L-15 medium (300 mOsmol l− 1) or the medium with an adjusted osmolality of 600 mOsmol l− 1 for 4, 8 and 24 h. Hypertonic responsive genes, including osmotic stress transcriptional factor, Na+/Cl−-taurine transporter, Na+/H+ exchange regulatory cofactor, cystic fibrosis transmembrane regulator, inward rectifying K+ channel, Na+/K+-ATPase, and calcium-transporting ATPase were significantly upregulated, while the hypo-osmotic gene, V-type proton ATPase was downregulated. The data illustrated that the ex-vivo gill filament culture exhibited distinctive responses to hyperosmotic challenge. In the hyperosmotic treatment, four key factors (i.e. drosha RNase III endonuclease, exportin-5, dicer ribonuclease III and argonaute-2) involved in miR biogenesis were dysregulated (P < 0.05). Transcriptome and miR-sequencing of gill filament samples at 4 and 8 h were conducted and two downregulated miRs, miR-29b-3p and miR-200b-3p were identified. An inhibition of miR-29b-3p and miR-200b-3p in primary gill cell culture led to an upregulation of 100 and 93 gene transcripts, respectively. Commonly upregulated gene transcripts from the hyperosmotic experiments and miR-inhibition studies, were overlaid, in which two miR-29b-3p target-genes [Krueppel-like factor 4 (klf4), Homeobox protein Meis2] and one miR-200b-3p target-gene (slc17a5) were identified. Integrated miR-mRNA-omics analysis revealed the specific binding of miR-29b-3p on Klf4 and miR-200b-3p on slc17a5. The target-genes are known to regulate differentiation of gill ionocytes and cellular osmolality. Conclusions In this study, we have characterized the hypo-osmoregulatory responses and unraveled the modulation of miR-biogenesis factors/the dysregulation of miRs, using ex-vivo gill filament culture. MicroRNA-messenger RNA interactome analysis of miR-29b-3p and miR-200b-3p revealed the gene targets are essential for osmotic stress responses.
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Affiliation(s)
- Hoi Man Ng
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon Tong, HKSAR, Hong Kong
| | - Jeff Cheuk Hin Ho
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon Tong, HKSAR, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Keng Po Lai
- Guanxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, 541004, People's Republic of China.
| | - Chris Kong Chu Wong
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon Tong, HKSAR, Hong Kong.
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Li X, Li C, Xu Y, Yao R, Li H, Ni W, Quan R, Zhang M, Liu L, Yu S, Ullah Y, Hu R, Li Y, Guo T, Wang X, Hu S. Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus. Funct Integr Genomics 2020; 20:563-573. [PMID: 32114660 DOI: 10.1007/s10142-020-00735-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022]
Abstract
Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes such as growth, development, and reproduction of animals. Here, we used RNA-seq technology to study the expression profile of lncRNAs in the anterior pituitary of sheep during estrus and anestrus. In this study, we identified a total of 995 lncRNAs, of which 335 lncRNAs were differentially expressed in two states (including 38 up-regulated and 297 down-regulated lncRNAs). RT-qPCR verified the expression levels of several lncRNAs. Target predictive analysis revealed that these lncRNAs can act in cis or trans and regulate the expression of genes involved in the regulation of sheep estrus. Target gene enrichment analysis of differentially expressed lncRNAs indicates that these lncRNAs can regulate sheep estrus by regulating hormone metabolism and energy metabolism. Through our research, we provide the expression profile of lncRNAs in the pituitary of sheep, which provides a valuable resource for further understanding of the genetic regulation of seasonal estrus in sheep from the perspective of lncRNAs.
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Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.,College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaseen Ullah
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaxin Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Tao Guo
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaokui Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
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Jin Y, Zhao JH, Zhao P, Zhang T, Wang S, Guo HS. A fungal milRNA mediates epigenetic repression of a virulence gene in Verticillium dahliae. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180309. [PMID: 30967013 DOI: 10.1098/rstb.2018.0309] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MiRNAs in animals and plants play crucial roles in diverse developmental processes under both normal and stress conditions. miRNA-like small RNAs (milRNAs) identified in some fungi remain functionally uncharacterized. Here, we identified a number of milRNAs in Verticillium dahliae, a soil-borne fungal pathogen responsible for devastating wilt diseases in many crops. Accumulation of a V. dahliae milRNA1, named VdmilR1, was detected by RNA gel blotting. We show that the precursor gene VdMILR1 is transcribed by RNA polymerase II and is able to produce the mature VdmilR1, in a process independent of V. dahliae DCL (Dicer-like) and AGO (Argonaute) proteins. We found that an RNaseIII domain-containing protein, VdR3, is essential for V. dahliae and participates in VdmilR1 biogenesis. VdmilR1 targets a hypothetical protein-coding gene, VdHy1, at the 3'UTR for transcriptional repression through increased histone H3K9 methylation of VdHy1. Pathogenicity analysis reveals that VdHy1 is essential for fungal virulence. Together with the time difference in the expression patterns of VdmilR1 and VdHy1 during fungal infection in cotton plants, our findings identify a novel milRNA, VdmilR1, in V. dahliae synthesized by a noncanonical pathway that plays a regulatory role in pathogenicity and uncover an epigenetic mechanism for VdmilR1 in regulating a virulence target gene. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
- Yun Jin
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China
| | - Jian-Hua Zhao
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China
| | - Pan Zhao
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China
| | - Tao Zhang
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China
| | - Sheng Wang
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China.,2 College of Life Sciences, University of the Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Hui-Shan Guo
- 1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China.,2 College of Life Sciences, University of the Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
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Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Mol Cell 2020; 77:475-487.e11. [PMID: 31759822 PMCID: PMC7014570 DOI: 10.1016/j.molcel.2019.10.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/20/2019] [Accepted: 10/13/2019] [Indexed: 12/15/2022]
Abstract
How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription factor C (TFIIIC) in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of AEs pre-marked by the activity-dependent neuroprotector homeobox Protein (ADNP) and located near cell-cycle genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone H3 lysine-18 (H3K18). This facilitates the contacts of AEs with distant CTCF sites near promoter of other cell-cycle genes, which also become hyperacetylated at H3K18. These changes ensure basal transcription of cell-cycle genes and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor regulates 3D genome folding and expression.
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Affiliation(s)
- Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chiara Di Vona
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - François Le Dilly
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Quilez Oliete
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Laura Jochem
- The Institute of Cancer Research (ICR), London, UK
| | - Erin Cutts
- The Institute of Cancer Research (ICR), London, UK
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alessandro Vannini
- The Institute of Cancer Research (ICR), London, UK; Human Technopole. Via Cristina Belgioioso, 171, 20157 Milano MI, Italy
| | - Martin Teichmann
- Université de Bordeaux, INSERM U1212 CNRS UMR 5320 146, Bordeaux, France
| | - Susana de la Luna
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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108
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A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21010302. [PMID: 31906285 PMCID: PMC6982300 DOI: 10.3390/ijms21010302] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.
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Holla S, Dhakshnamoorthy J, Folco HD, Balachandran V, Xiao H, Sun LL, Wheeler D, Zofall M, Grewal SIS. Positioning Heterochromatin at the Nuclear Periphery Suppresses Histone Turnover to Promote Epigenetic Inheritance. Cell 2019; 180:150-164.e15. [PMID: 31883795 DOI: 10.1016/j.cell.2019.12.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/29/2019] [Accepted: 12/04/2019] [Indexed: 01/09/2023]
Abstract
In eukaryotes, heterochromatin is generally located at the nuclear periphery. This study investigates the biological significance of perinuclear positioning for heterochromatin maintenance and gene silencing. We identify the nuclear rim protein Amo1NUPL2 as a factor required for the propagation of heterochromatin at endogenous and ectopic sites in the fission yeast genome. Amo1 associates with the Rix1PELP1-containing RNA processing complex RIXC and with the histone chaperone complex FACT. RIXC, which binds to heterochromatin protein Swi6HP1 across silenced chromosomal domains and to surrounding boundary elements, connects heterochromatin with Amo1 at the nuclear periphery. In turn, the Amo1-enriched subdomain is critical for Swi6 association with FACT that precludes histone turnover to promote gene silencing and preserve epigenetic stability of heterochromatin. In addition to uncovering conserved factors required for perinuclear positioning of heterochromatin, these analyses elucidate a mechanism by which a peripheral subdomain enforces stable gene repression and maintains heterochromatin in a heritable manner.
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Affiliation(s)
- Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ling-Ling Sun
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Ayoubi LE, Dumay-Odelot H, Chernev A, Boissier F, Minvielle-Sébastia L, Urlaub H, Fribourg S, Teichmann M. The hRPC62 subunit of human RNA polymerase III displays helicase activity. Nucleic Acids Res 2019; 47:10313-10326. [PMID: 31529052 PMCID: PMC6821166 DOI: 10.1093/nar/gkz788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 11/20/2022] Open
Abstract
In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3′-5′ DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα.
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Affiliation(s)
- Leyla El Ayoubi
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Hélène Dumay-Odelot
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- Correspondence may also be addressed to Hélène Dumay-Odelot.
| | - Aleksandar Chernev
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Fanny Boissier
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | | | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center, Robert-Koch-Strasse 420, 37075 Göttingen, Germany
| | - Sébastien Fribourg
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Martin Teichmann
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- To whom correspondence should be addressed. Tel: +33 5 5757 4647;
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Lawrimore CJ, Bloom K. Common Features of the Pericentromere and Nucleolus. Genes (Basel) 2019; 10:E1029. [PMID: 31835574 PMCID: PMC6947172 DOI: 10.3390/genes10121029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 12/20/2022] Open
Abstract
Both the pericentromere and the nucleolus have unique characteristics that distinguish them amongst the rest of genome. Looping of pericentromeric DNA, due to structural maintenance of chromosome (SMC) proteins condensin and cohesin, drives its ability to maintain tension during metaphase. Similar loops are formed via condensin and cohesin in nucleolar ribosomal DNA (rDNA). Condensin and cohesin are also concentrated in transfer RNA (tRNA) genes, genes which may be located within the pericentromere as well as tethered to the nucleolus. Replication fork stalling, as well as downstream consequences such as genomic recombination, are characteristic of both the pericentromere and rDNA. Furthermore, emerging evidence suggests that the pericentromere may function as a liquid-liquid phase separated domain, similar to the nucleolus. We therefore propose that the pericentromere and nucleolus, in part due to their enrichment of SMC proteins and others, contain similar domains that drive important cellular activities such as segregation, stability, and repair.
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Affiliation(s)
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA;
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Liko D, Mitchell L, Campbell KJ, Ridgway RA, Jones C, Dudek K, King A, Bryson S, Stevenson D, Blyth K, Strathdee D, Morton JP, Bird TG, Knight JRP, Willis AE, Sansom OJ. Brf1 loss and not overexpression disrupts tissues homeostasis in the intestine, liver and pancreas. Cell Death Differ 2019; 26:2535-2550. [PMID: 30858608 PMCID: PMC6861133 DOI: 10.1038/s41418-019-0316-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 01/18/2019] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase III (Pol-III) transcribes tRNAs and other small RNAs essential for protein synthesis and cell growth. Pol-III is deregulated during carcinogenesis; however, its role in vivo has not been studied. To address this issue, we manipulated levels of Brf1, a Pol-III transcription factor that is essential for recruitment of Pol-III holoenzyme at tRNA genes in vivo. Knockout of Brf1 led to embryonic lethality at blastocyst stage. In contrast, heterozygous Brf1 mice were viable, fertile and of a normal size. Conditional deletion of Brf1 in gastrointestinal epithelial tissues, intestine, liver and pancreas, was incompatible with organ homeostasis. Deletion of Brf1 in adult intestine and liver induced apoptosis. However, Brf1 heterozygosity neither had gross effects in these epithelia nor did it modify tumorigenesis in the intestine or pancreas. Overexpression of BRF1 rescued the phenotypes of Brf1 deletion in intestine and liver but was unable to initiate tumorigenesis. Thus, Brf1 and Pol-III activity are absolutely essential for normal homeostasis during development and in adult epithelia. However, Brf1 overexpression or heterozygosity are unable to modify tumorigenesis, suggesting a permissive, but not driving role for Brf1 in the development of epithelial cancers of the pancreas and gut.
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Affiliation(s)
- Dritan Liko
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Louise Mitchell
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Kirsteen J Campbell
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Rachel A Ridgway
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Carolyn Jones
- MRC Toxicology Unit, Hodgkin Building Lancaster Road, Leicester, LE1 9HN, UK
| | - Kate Dudek
- MRC Toxicology Unit, Hodgkin Building Lancaster Road, Leicester, LE1 9HN, UK
| | - Ayala King
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Sheila Bryson
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - David Stevenson
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Karen Blyth
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Douglas Strathdee
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Jennifer P Morton
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Thomas G Bird
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - John R P Knight
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - Anne E Willis
- MRC Toxicology Unit, Hodgkin Building Lancaster Road, Leicester, LE1 9HN, UK
| | - Owen J Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK.
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113
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Petrie JL, Swan C, Ingram RM, Frame FM, Collins AT, Dumay-Odelot H, Teichmann M, Maitland NJ, White RJ. Effects on prostate cancer cells of targeting RNA polymerase III. Nucleic Acids Res 2019; 47:3937-3956. [PMID: 30820548 PMCID: PMC6486637 DOI: 10.1093/nar/gkz128] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
RNA polymerase (pol) III occurs in two forms, containing either the POLR3G subunit or the related paralogue POLR3GL. Whereas POLR3GL is ubiquitous, POLR3G is enriched in undifferentiated cells. Depletion of POLR3G selectively triggers proliferative arrest and differentiation of prostate cancer cells, responses not elicited when POLR3GL is depleted. A small molecule pol III inhibitor can cause POLR3G depletion, induce similar differentiation and suppress proliferation and viability of cancer cells. This response involves control of the fate-determining factor NANOG by small RNAs derived from Alu short interspersed nuclear elements. Tumour initiating activity in vivo can be reduced by transient exposure to the pol III inhibitor. Untransformed prostate cells appear less sensitive than cancer cells to pol III depletion or inhibition, raising the possibility of a therapeutic window.
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Affiliation(s)
- John L Petrie
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Caroline Swan
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Richard M Ingram
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Fiona M Frame
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Anne T Collins
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hélène Dumay-Odelot
- Université de Bordeaux, ARNA Laboratory, F-33076 Bordeaux, France INSERM, U1212 - CNRS UMR 5320, ARNA Laboratory, F-33000 Bordeaux, France
| | - Martin Teichmann
- Université de Bordeaux, ARNA Laboratory, F-33076 Bordeaux, France INSERM, U1212 - CNRS UMR 5320, ARNA Laboratory, F-33000 Bordeaux, France
| | - Norman J Maitland
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
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114
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Gourvest M, Brousset P, Bousquet M. Long Noncoding RNAs in Acute Myeloid Leukemia: Functional Characterization and Clinical Relevance. Cancers (Basel) 2019; 11:cancers11111638. [PMID: 31653018 PMCID: PMC6896193 DOI: 10.3390/cancers11111638] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022] Open
Abstract
Acute Myeloid Leukemia (AML) is the most common form of leukemia in adults with an incidence of 4.3 per 100,000 cases per year. Historically, the identification of genetic alterations in AML focused on protein-coding genes to provide biomarkers and to understand the molecular complexity of AML. Despite these findings and because of the heterogeneity of this disease, questions as to the molecular mechanisms underlying AML development and progression remained unsolved. Recently, transcriptome-wide profiling approaches have uncovered a large family of long noncoding RNAs (lncRNAs). Larger than 200 nucleotides and with no apparent protein coding potential, lncRNAs could unveil a new set of players in AML development. Originally considered as dark matter, lncRNAs have critical roles to play in the different steps of gene expression and thus affect cellular homeostasis including proliferation, survival, differentiation, migration or genomic stability. Consequently, lncRNAs are found to be differentially expressed in tumors, notably in AML, and linked to the transformation of healthy cells into leukemic cells. In this review, we aim to summarize the knowledge concerning lncRNAs functions and implications in AML, with a particular emphasis on their prognostic and therapeutic potential.
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Affiliation(s)
- Morgane Gourvest
- Cancer Research Center of Toulouse (CRCT), UMR1037 INSERM-Université Paul Sabatier Toulouse III-CNRS ERL5294, 31037 Toulouse, France.
| | - Pierre Brousset
- Cancer Research Center of Toulouse (CRCT), UMR1037 INSERM-Université Paul Sabatier Toulouse III-CNRS ERL5294, 31037 Toulouse, France.
| | - Marina Bousquet
- Cancer Research Center of Toulouse (CRCT), UMR1037 INSERM-Université Paul Sabatier Toulouse III-CNRS ERL5294, 31037 Toulouse, France.
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115
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Haack F, Trakooljul N, Gley K, Murani E, Hadlich F, Wimmers K, Ponsuksili S. Deep sequencing of small non-coding RNA highlights brain-specific expression patterns and RNA cleavage. RNA Biol 2019; 16:1764-1774. [PMID: 31432767 DOI: 10.1080/15476286.2019.1657743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
With the advance of high-throughput sequencing technology numerous new regulatory small RNAs have been identified, that broaden the variety of processing mechanisms and functions of non-coding RNA. Here we explore small non-coding RNA (sncRNA) expression in central parts of the physiological stress and anxiety response system. Therefore, we characterize the sncRNA profile of tissue samples from Amygdala, Hippocampus, Hypothalamus and Adrenal Gland, obtained from 20 pigs. Our analysis reveals that all tissues but Amygdala and Hippocampus possess distinct, tissue-specific expression pattern of miRNA that are associated with Hypoxia, stress responses as well as memory and fear conditioning. In particular, we observe marked differences in the expression profile of limbic tissues compared to those associated to the HPA/stress axis, with a surprisingly high aggregation of 3´-tRNA halves in Amygdala and Hippocampus. Since regulation of sncRNA and RNA cleavage plays a pivotal role in the central nervous system, our work provides seminal insights in the role/involvement of sncRNA in the transcriptional and post-transcriptional regulation of negative emotion, stress and coping behaviour in pigs, and mammals in general.
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Affiliation(s)
- Fiete Haack
- Institute for Genome Biology, Functional Genome Analysis Research Unit, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Nares Trakooljul
- Institute for Genome Biology, Genomics Research Unit, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Kevin Gley
- Institute for Genome Biology, Functional Genome Analysis Research Unit, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Eduard Murani
- Institute for Genome Biology, Genomics Research Unit, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Frieder Hadlich
- Institute for Genome Biology, Functional Genome Analysis Research Unit, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute for Genome Biology, Genomics Research Unit, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
| | - Siriluck Ponsuksili
- Institute for Genome Biology, Functional Genome Analysis Research Unit, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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116
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Ahmed W, Xia Y, Li R, Bai G, Siddique KHM, Guo P. Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops. Genomics 2019; 112:1419-1424. [PMID: 31430515 DOI: 10.1016/j.ygeno.2019.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/03/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Abstract
Brassica crops face a combination of different abiotic and biotic stresses in the field that can reduce plant growth and development by affecting biochemical and morpho-physiological processes. Emerging evidence suggests that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), play a significant role in the modulation of gene expression in response to plant stresses. Recent advances in computational and experimental approaches are of great interest for identifying and functionally characterizing ncRNAs. While progress in this field is limited, numerous ncRNAs involved in the regulation of gene expression in response to stress have been reported in Brassica. In this review, we summarize the modes of action and functions of stress-related miRNAs and lncRNAs in Brassica as well as the approaches used to identify ncRNAs.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China.
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117
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Ciesla M, Skowronek E, Boguta M. Function of TFIIIC, RNA polymerase III initiation factor, in activation and repression of tRNA gene transcription. Nucleic Acids Res 2019; 46:9444-9455. [PMID: 30053100 PMCID: PMC6182151 DOI: 10.1093/nar/gky656] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/10/2018] [Indexed: 01/09/2023] Open
Abstract
Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC directly competes with Pol III for chromatin occupancy as demonstrated by inversely correlated tDNA binding. The association of TFIIIC with tDNA was stronger under unfavorable respiratory conditions and in the presence of Maf1. Induction of tDNA transcription by glucose-activated protein kinase A (PKA) was correlated with the down-regulation of TFIIIC occupancy on tDNA. The conditions that activate the PKA signaling pathway promoted the binding of TFIIIB subunits, Brf1 and Bdp1, with tDNA, but decreased their interaction with TFIIIC. Association of Brf1 and Bdp1 with TFIIIC was much stronger under repressive conditions, potentially restricting TFIIIB recruitment to tDNA and preventing Pol III recruitment. Altogether, we propose a model in which, depending on growth conditions, TFIIIC promotes activation or repression of tDNA transcription.
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Affiliation(s)
- Malgorzata Ciesla
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Ewa Skowronek
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Magdalena Boguta
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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118
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Khoo SK, Wu CC, Lin YC, Chen HT. The TFIIE-related Rpc82 subunit of RNA polymerase III interacts with the TFIIB-related transcription factor Brf1 and the polymerase cleft for transcription initiation. Nucleic Acids Res 2019; 46:1157-1166. [PMID: 29177422 PMCID: PMC5814912 DOI: 10.1093/nar/gkx1179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
Rpc82 is a TFIIE-related subunit of the eukaryotic RNA polymerase III (pol III) complex. Rpc82 contains four winged-helix (WH) domains and a C-terminal coiled-coil domain. Structural resolution of the pol III complex indicated that Rpc82 anchors on the clamp domain of the pol III cleft to interact with the duplex DNA downstream of the transcription bubble. However, whether Rpc82 interacts with a transcription factor is still not known. Here, we report that a structurally disordered insertion in the third WH domain of Rpc82 is important for cell growth and in vitro transcription activity. Site-specific photo-crosslinking analysis indicated that the WH3 insertion interacts with the TFIIB-related transcription factor Brf1 within the pre-initiation complex (PIC). Moreover, crosslinking and hydroxyl radical probing analyses revealed Rpc82 interactions with the upstream DNA and the protrusion and wall domains of the pol III cleft. Our genetic and biochemical analyses thus provide new molecular insights into the function of Rpc82 in pol III transcription.
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Affiliation(s)
- Seok-Kooi Khoo
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2 Academia Rd., Taipei 115, Taiwan, R.O.C
| | - Chih-Chien Wu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2 Academia Rd., Taipei 115, Taiwan, R.O.C
| | - Yu-Chun Lin
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2 Academia Rd., Taipei 115, Taiwan, R.O.C
| | - Hung-Ta Chen
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2 Academia Rd., Taipei 115, Taiwan, R.O.C
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119
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Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
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120
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Liang X, Xie R, Su J, Ye B, Wei S, Liang Z, Bai R, Chen Z, Li Z, Gao X. Inhibition of RNA polymerase III transcription by Triptolide attenuates colorectal tumorigenesis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:217. [PMID: 31122284 PMCID: PMC6533717 DOI: 10.1186/s13046-019-1232-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/15/2019] [Indexed: 12/31/2022]
Abstract
Background Upregulation of RNA polymerase (Pol) III products, including tRNAs and 5S rRNA, in tumor cells leads to enhanced protein synthesis and tumor formation, making it a potential target for cancer treatment. In this study, we evaluated the inhibition of Pol III transcription by triptolide and the anti-cancer effect of this drug in colorectal tumorigenesis. Methods The effect of triptolide on colorectal cancer development was assessed in colorectal cancer mouse models, 3D organoids, and cultured cells. Colorectal cancer cells were treated with triptolide. Pol III transcription was measured by real-time quantitative polymerase chain reaction (PCR). The formation of TFIIIB, a multi-subunit transcription factor for Pol III, was determined by chromatin immunoprecipitation (ChIP), co-immunoprecipitation (Co-IP), and fluorescence resonance energy transfer (FRET). Results Triptolide reduced both tumor number and tumor size in adenomatous polyposis coli (Apc) mutated (ApcMin/+) mice as well as AOM/DSS-induced mice. Moreover, triptolide effectively inhibited colorectal cancer cell proliferation, colony formation, and organoid growth in vitro, which was associated with decreased Pol III target genes. Mechanistically, triptolide treatment blocked TBP/Brf1interaction, leading to the reduced formation of TFIIIB at the promoters of tRNAs and 5S rRNA. Conclusions Together, our data suggest that inhibition of Pol III transcription with existing drugs such as triptolide provides a new avenue for developing novel therapies for colorectal cancer. Electronic supplementary material The online version of this article (10.1186/s13046-019-1232-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xia Liang
- Medical Research Institute, & Guangdong Women and Children's Disease Precision Diagnosis and Treatment Engineering Technology Research Center, Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, 518102, China
| | - Renxiang Xie
- Department of Public Health, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jinfeng Su
- Medical Research Institute, & Guangdong Women and Children's Disease Precision Diagnosis and Treatment Engineering Technology Research Center, Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, 518102, China
| | - Bingqi Ye
- Department of Public Health, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Saisai Wei
- Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhibing Liang
- Medical Research Institute, & Guangdong Women and Children's Disease Precision Diagnosis and Treatment Engineering Technology Research Center, Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, 518102, China
| | - Rongpan Bai
- Department of Public Health, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhanghui Chen
- Affiliated Central People's Hospital of Zhanjiang, Guangdong Medical University, Zhanjiang, 524045, China
| | - Zhongxiang Li
- Medical Research Institute, & Guangdong Women and Children's Disease Precision Diagnosis and Treatment Engineering Technology Research Center, Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, 518102, China.
| | - Xiangwei Gao
- Department of Public Health, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Hardy MP, Audemard É, Migneault F, Feghaly A, Brochu S, Gendron P, Boilard É, Major F, Dieudé M, Hébert MJ, Perreault C. Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs. Sci Rep 2019; 9:7203. [PMID: 31076589 PMCID: PMC6510763 DOI: 10.1038/s41598-019-43591-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/26/2019] [Indexed: 02/07/2023] Open
Abstract
Endothelial cells have multifaceted interactions with the immune system, both as initiators and targets of immune responses. In vivo, apoptotic endothelial cells release two types of extracellular vesicles upon caspase-3 activation: apoptotic bodies and exosome-like nanovesicles (ApoExos). Only ApoExos are immunogenic: their injection causes inflammation and autoimmunity in mice. Based on deep sequencing of total RNA, we report that apoptotic bodies and ApoExos are loaded with divergent RNA cargos that are not released by healthy endothelial cells. Apoptotic bodies, like endothelial cells, contain mainly ribosomal RNA whereas ApoExos essentially contain non-ribosomal non-coding RNAs. Endogenous retroelements, bearing viral-like features, represented half of total ApoExos RNA content. ApoExos also contained several copies of unedited Alu repeats and large amounts of non-coding RNAs with a demonstrated role in autoimmunity such as U1 RNA and Y RNA. Moreover, ApoExos RNAs had a unique nucleotide composition and secondary structure characterized by strong enrichment in U-rich motifs and unstably folded RNAs. Globally, ApoExos were therefore loaded with RNAs that can stimulate a variety of RIG-I-like receptors and endosomal TLRs. Hence, apoptotic endothelial cells selectively sort in ApoExos a diversified repertoire of immunostimulatory "self RNAs" that are tailor-made for initiation of innate immune responses and autoimmunity.
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Affiliation(s)
- Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Canadian National Transplant Research Program, Edmonton, Alberta, T6G 2E1, Canada
| | - Éric Audemard
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Francis Migneault
- Canadian National Transplant Research Program, Edmonton, Alberta, T6G 2E1, Canada
- Research Centre, Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, H2X 0A9, Canada
| | - Albert Feghaly
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Canadian National Transplant Research Program, Edmonton, Alberta, T6G 2E1, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Éric Boilard
- Canadian National Transplant Research Program, Edmonton, Alberta, T6G 2E1, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Québec, Faculté de Médecine de l'Université Laval, Québec, Québec, Canada
| | - François Major
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Mélanie Dieudé
- Canadian National Transplant Research Program, Edmonton, Alberta, T6G 2E1, Canada
- Research Centre, Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, H2X 0A9, Canada
| | - Marie-Josée Hébert
- Canadian National Transplant Research Program, Edmonton, Alberta, T6G 2E1, Canada
- Research Centre, Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, H2X 0A9, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada.
- Canadian National Transplant Research Program, Edmonton, Alberta, T6G 2E1, Canada.
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada.
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tRNA Genes Affect Chromosome Structure and Function via Local Effects. Mol Cell Biol 2019; 39:MCB.00432-18. [PMID: 30718362 DOI: 10.1128/mcb.00432-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022] Open
Abstract
The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. In this study, we investigate the roles of tDNAs in genomic organization and chromosome function by editing a chromosome so that it lacked any tDNAs. Surprisingly our analyses of this tDNA-less chromosome show that loss of tDNAs does not grossly affect chromatin architecture or chromosome tethering and mobility. However, loss of tDNAs affects local nucleosome positioning and the binding of SMC proteins at these loci. The absence of tDNAs also leads to changes in centromere clustering and a reduction in the frequency of long-range HML-HMR heterochromatin clustering with concomitant effects on gene silencing. We propose that the tDNAs primarily affect local chromatin structure, which results in effects on long-range chromosome architecture.
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Román-Carraro FC, Florencio-Martínez LE, Romero-Meza G, Nepomuceno-Mejía T, Carrero JC, Arroyo R, Ortega-López J, Manning-Cela RG, Martínez-Calvillo S. TFIIIB Subunit Bdp1 Participates in RNA Polymerase III Transcription in the Protozoan Parasite Leishmania major. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1425281. [PMID: 31058184 PMCID: PMC6463643 DOI: 10.1155/2019/1425281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/13/2019] [Indexed: 01/03/2023]
Abstract
Leishmania major, a protozoan parasite that diverged early from the main eukaryotic lineage, exhibits unusual mechanisms of gene expression. Little is known in this organism about the transcription factors involved in the synthesis of tRNA, 5S rRNA, and snRNAs, transcribed by RNA Polymerase III (Pol III). Here we identify and characterize the TFIIIB subunit Bdp1 in L. major (LmBdp1). Bdp1 plays key roles in Pol III transcription initiation in other organisms, as it participates in Pol III recruitment and promoter opening. In silico analysis showed that LmBdp1 contains the typical extended SANT domain as well as other Bdp1 conserved regions. Nevertheless, LmBdp1 also displays distinctive features, including the presence of only one aromatic residue in the N-linker region. We were not able to produce null mutants of LmBdp1 by homologous recombination, as the obtained double replacement cell line contained an extra copy of LmBdp1, indicating that LmBdp1 is essential for the viability of L. major promastigotes. Notably, the mutant cell line showed reduced levels of the LmBdp1 protein, and its growth was significantly decreased in relation to wild-type cells. Nuclear run-on assays demonstrated that Pol III transcription was affected in the mutant cell line, and ChIP experiments showed that LmBdp1 binds to 5S rRNA, tRNA, and snRNA genes. Thus, our results indicate that LmBdp1 is an essential protein required for Pol III transcription in L. major.
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Affiliation(s)
- Fiordaliso C. Román-Carraro
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, Mexico
| | - Luis E. Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, Mexico
| | - Gabriela Romero-Meza
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, Mexico
| | - Tomás Nepomuceno-Mejía
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, Mexico
| | - Julio C. Carrero
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CP 04510, Mexico
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, Ciudad de México, CP 07360, Mexico
| | - Jaime Ortega-López
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, Ciudad de México, CP 07360, Mexico
| | - Rebeca G. Manning-Cela
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, Ciudad de México, CP 07360, Mexico
| | - Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de Los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, Mexico
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Bahin M, Noël BF, Murigneux V, Bernard C, Bastianelli L, Le Hir H, Lebreton A, Genovesio A. ALFA: annotation landscape for aligned reads. BMC Genomics 2019; 20:250. [PMID: 30922228 PMCID: PMC6440077 DOI: 10.1186/s12864-019-5624-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 03/20/2019] [Indexed: 01/14/2023] Open
Abstract
Background The last 10 years have seen the rise of countless functional genomics studies based on Next-Generation Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two first steps of data analysis consist of a quality control of the raw reads followed by a mapping of those reads to a reference genome/transcriptome. Subsequent steps then depend on the type of study that is being made. While some tools have been proposed for investigating data quality after the mapping step, there is no commonly adopted framework that would be easy to use and broadly applicable to any NGS data type. Results We present ALFA, a simple but universal tool that can be used after the mapping step on any kind of NGS experiment data for any organism with available genomic annotations. In a single command line, ALFA can compute and display distribution of reads by categories (exon, intron, UTR, etc.) and biotypes (protein coding, miRNA, etc.) for a given aligned dataset with nucleotide precision. We present applications of ALFA to Ribo-Seq and RNA-Seq on Homo sapiens, CLIP-Seq on Mus musculus, RNA-Seq on Saccharomyces cerevisiae, Bisulfite sequencing on Arabidopsis thaliana and ChIP-Seq on Caenorhabditis elegans. Conclusions We show that ALFA provides a powerful and broadly applicable approach for post mapping quality control and to produce a global overview using common or dedicated annotations. It is made available to the community as an easy to install command line tool and from the Galaxy Tool Shed.
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Affiliation(s)
- Mathieu Bahin
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Benoit F Noël
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Bacterial Infection & RNA Destiny group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Valentine Murigneux
- Expression of eukaryotic messenger RNAs group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Charles Bernard
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Leila Bastianelli
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Expression of eukaryotic messenger RNAs group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Hervé Le Hir
- Expression of eukaryotic messenger RNAs group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Alice Lebreton
- Bacterial Infection & RNA Destiny group, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France. .,INRA, IBENS, 75005, Paris, France.
| | - Auguste Genovesio
- Computational Biology and Bioinformatics group,, Institut de biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.
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125
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Choquet K, Forget D, Meloche E, Dicaire MJ, Bernard G, Vanderver A, Schiffmann R, Fabian MR, Teichmann M, Coulombe B, Brais B, Kleinman CL. Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200. J Biol Chem 2019; 294:7445-7459. [PMID: 30898877 PMCID: PMC6509492 DOI: 10.1074/jbc.ra118.006271] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small noncoding RNAs, a number of which are involved in mRNA translation. Recessive mutations in POLR3A, encoding the largest subunit of Pol III, cause POLR3-related hypomyelinating leukodystrophy (POLR3–HLD), characterized by deficient central nervous system myelination. Identification of the downstream effectors of pathogenic POLR3A mutations has so far been elusive. Here, we used CRISPR-Cas9 to introduce the POLR3A mutation c.2554A→G (p.M852V) into human cell lines and assessed its impact on Pol III biogenesis, nuclear import, DNA occupancy, transcription, and protein levels. Transcriptomic profiling uncovered a subset of transcripts vulnerable to Pol III hypofunction, including a global reduction in tRNA levels. The brain cytoplasmic BC200 RNA (BCYRN1), involved in translation regulation, was consistently affected in all our cellular models, including patient-derived fibroblasts. Genomic BC200 deletion in an oligodendroglial cell line led to major transcriptomic and proteomic changes, having a larger impact than those of POLR3A mutations. Upon differentiation, mRNA levels of the MBP gene, encoding myelin basic protein, were significantly decreased in POLR3A-mutant cells. Our findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3–HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease.
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Affiliation(s)
- Karine Choquet
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Diane Forget
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Elisabeth Meloche
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Marie-Josée Dicaire
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Geneviève Bernard
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,Pediatrics, McGill University, Montréal, Québec H3A 0G4, Canada.,the Department of Internal Medicine, Division of Medical Genetics, Montréal Children's Hospital, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Child Health and Human Development Program, and.,MyeliNeuroGene Laboratory, Research Institute, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Departments of Neurology and Neurosurgery and
| | - Adeline Vanderver
- the Division of Neurology, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania 19104
| | - Raphael Schiffmann
- the Institute of Metabolic Disease, Baylor Research Institute, Dallas, Texas 75204
| | - Marc R Fabian
- the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Martin Teichmann
- INSERM U1212-CNRS UMR5320, Université de Bordeaux, Bordeaux, France, and
| | - Benoit Coulombe
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada.,the Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Bernard Brais
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada.,the Departments of Neurology and Neurosurgery and
| | - Claudia L Kleinman
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada, .,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
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Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1530. [PMID: 30843375 PMCID: PMC6619189 DOI: 10.1002/wrna.1530] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/06/2023]
Abstract
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Vincent Boivin
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurence Faucher-Giguère
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Michelle Scott
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sherif Abou-Elela
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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127
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Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine. Sci Rep 2019; 9:3552. [PMID: 30837504 PMCID: PMC6401051 DOI: 10.1038/s41598-019-38989-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes–i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like ‘photosynthesis’ and ‘oxidative phosphorylation’. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.
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128
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Karlik E, Ari S, Gozukirmizi N. LncRNAs: genetic and epigenetic effects in plants. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1581085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Elif Karlik
- Department of Biotechnology Institute of Graduate Studies in Science and Engineering, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
| | - Sule Ari
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
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129
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Long Non-Coding RNA and Acute Leukemia. Int J Mol Sci 2019; 20:ijms20030735. [PMID: 30744139 PMCID: PMC6387068 DOI: 10.3390/ijms20030735] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022] Open
Abstract
Acute leukemia (AL) is the main type of cancer in children worldwide. Mortality by this disease is high in developing countries and its etiology remains unanswered. Evidences showing the role of the long non-coding RNAs (lncRNAs) in the pathophysiology of hematological malignancies have increased drastically in the last decade. In addition to the contribution of these lncRNAs in leukemogenesis, recent studies have suggested that lncRNAs could be used as biomarkers in the diagnosis, prognosis, and therapeutic response in leukemia patients. The focus of this review is to describe the functional classification, biogenesis, and the role of lncRNAs in leukemogenesis, to summarize the evidence about the lncRNAs which are playing a role in AL, and how these genes could be useful as potential therapeutic targets.
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130
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Ahn CS, Lee DH, Pai HS. Characterization of Maf1 in Arabidopsis: function under stress conditions and regulation by the TOR signaling pathway. PLANTA 2019; 249:527-542. [PMID: 30293201 DOI: 10.1007/s00425-018-3024-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
Maf1 repressor activity is critical for plant survival during environmental stresses, and is regulated by its phosphorylation/dephosphorylation through the activity of TOR and PP4/PP2A phosphatases. Maf1 is a global repressor of RNA polymerase III (Pol III), and is conserved in eukaryotes. Pol III synthesizes small RNAs, 5S rRNA, and tRNAs that are essential for protein translation and cell growth. Maf1 is a phosphoprotein and dephosphorylation of Maf1 promotes its repressor activity in yeast and mammals. Plant Maf1 was identified in citrus plants as a canker elicitor-binding protein, and citrus Maf1 represses cell growth associated with canker development. However, functions of plant Maf1 under diverse stress conditions and its regulation by the target of rapamycin (TOR) signaling components are poorly understood. In this study, the Arabidopsis maf1 mutants were more susceptible to diverse stresses and treatment with the TOR inhibitor Torin-1 than wild-type plants. The maf1 mutants expressed higher levels of Maf1 target RNAs, including 5S rRNA and pre-tRNAs in leaf cells, supporting Pol III repressor activity of Arabidopsis Maf1. Cellular stresses and Torin-1 treatment induced dephosphorylation of Maf1, suggesting Maf1 activation under diverse stress conditions. TOR silencing also stimulated Maf1 dephosphorylation, while silencing of catalytic subunit genes of PP4 and PP2A repressed it. Thus, TOR kinase and PP4/PP2A phosphatases appeared to oppositely modulate the Maf1 phosphorylation status. TOR silencing decreased the abundance of the target RNAs, while silencing of the PP4 and PP2A subunit genes increased it, supporting the positive correlation between Maf1 dephosphorylation and its repressor activity. Taken together, these results suggest that repressor activity of Maf1, regulated by the TOR signaling pathway, is critical for plant cell survival during environmental stresses.
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Affiliation(s)
- Chang Sook Ahn
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Future Technology Research Center, Corporate R&D, LG Chem/LG Science Park, Seoul, 07796, Korea
| | - Du-Hwa Lee
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea.
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131
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Wang P. The Opening of Pandora's Box: An Emerging Role of Long Noncoding RNA in Viral Infections. Front Immunol 2019; 9:3138. [PMID: 30740112 PMCID: PMC6355698 DOI: 10.3389/fimmu.2018.03138] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence has proved that long noncoding RNAs (lncRNAs) participate in various physiological and pathological processes. Recent evidence has demonstrated that lncRNAs are crucial regulators of virus infections and antiviral immune responses. Upon viral infections, significant changes take place at the transcriptional level and the majority of the expression modifications occur in lncRNAs from both the host and viral genomes with dynamic regulatory courses. These lncRNAs exert diverse effects. Some are antiviral either through directly inhibiting viral infections or through stimulating antiviral immune responses, while others are pro-viral through directly promoting virus replication or through influencing cellular status, such as suppressing antiviral mechanisms. Consequently, these dynamic regulations lead to disparate pathophysiological outcomes and clinical manifestations. This review will focus on the roles of lncRNAs in viral infection and antiviral responses, summarize expression patterns of both host- and virally derived lncRNAs, describe their acting stages and modes of action, discuss challenges and novel concepts, and propose solutions and perspectives. Research into lncRNA will help identify novel viral infection-related regulators and design preventative and therapeutic strategies against virus-related diseases and immune disorders.
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Affiliation(s)
- Pin Wang
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
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132
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Mohanta TK, Khan AL, Hashem A, Allah EFA, Yadav D, Al-Harrasi A. Genomic and evolutionary aspects of chloroplast tRNA in monocot plants. BMC PLANT BIOLOGY 2019; 19:39. [PMID: 30669974 PMCID: PMC6341768 DOI: 10.1186/s12870-018-1625-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/28/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Chloroplasts are one of the most indispensable organelles that make life forms on the earth possible by their capacity to photosynthesize. These organelles possess a circular genome with a number of coding genes responsible for self-regulation. tRNAs are an important evolutionary-conserved gene family that are responsible for protein translation. However, within the chloroplast genome, tRNA machinery are poorly understood. RESULTS In the present study, the chloroplast genome of six monocot plants, Oryza nivara (NC_005973), Oryza sativa (NC_001320), Sachharum officinarum (NC_006084), Sorghum bicolor (NC_008602), Triticum aestivum (NC_002762), and Zea mays (NC_001666) were downloaded and analyzed to identify tRNA sequences. Further analysis of the tRNA sequences in the chloroplast genomes of the monocot plants resulted in the identification of several novel features. The length of tRNAs in the chloroplast genome of the monocot plants ranged from 59 to 155 nucleotides. Pair-wise sequence alignment revealed the presence of a conserved A-C-x-U-A-x-U-A-x-U-x5-U-A-A nucleotide consensus sequence. In addition, the tRNAs in chloroplast genomes of the monocot plants also contain 21-28 anti-codons against 61 sense codons in the genome. They also contain a group I intron and a C-A-U anti-codon for tRNAIle, which is a common anti-codon of tRNAMet. Evolutionary analysis indicates that tRNAs in the chloroplast genome have evolved from multiple common ancestors, and tRNAMet appears to be the ancestral tRNA that underwent duplication and diversification to give rise to other tRNAs. CONCLUSION The results obtained from the study of chloroplast tRNA will greatly help to increase our understanding of tRNA biology at a new level. Functional studies of the reported novel aspects of the chloroplast tRNA of the monocot plants will greatly help to decipher their roles in diverse cellular processes.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, 11451 Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, Egypt
| | - Elsayed Fathi Abd_ Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, Riyadh, 11451 Saudi Arabia
| | - Dhananjay Yadav
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541 Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
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133
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Huang C, Zhang Y, Zhong S. Alcohol Intake and Abnormal Expression of Brf1 in Breast Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:4818106. [PMID: 31781337 PMCID: PMC6874981 DOI: 10.1155/2019/4818106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/28/2019] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most common malignant disease of females. Overall, one woman in every nine will get breast cancer at some time in her life. Epidemiological studies have indicated that alcohol consumption has most consistently been associated with breast cancer risk. However, the mechanism of alcohol-associated breast cancer remains to be addressed. Little is known about the effects of alcohol consumption on Brf1 (TFIIIB-related factor 1) expression and RNA Pol III gene (RNA polymerase III-dependent gene) transcription, which are responsible for protein synthesis and tightly linked to cell proliferation, cell transformation, and tumor development. Emerging evidences have indicated that alcohol induces deregulation of Brf1 and Pol III genes to cause the alterations of cell phenotypes and tumor formation. In this paper, we summarize the progresses regarding alcohol-caused increase in the expression of Brf1 and Pol III genes and analysis of its molecular mechanism of breast cancer. As the earlier and accurate diagnosis approach of breast cancer is not available yet, exploring the molecular mechanism and identifying the biomarker of alcohol-associated breast cancer are especially important. Recent studies have demonstrated that Brf1 is overexpressed in most ER+ (estrogen receptor positive) cases of breast cancer and the change in cellular levels of Brf1 reflects the therapeutic efficacy and prognosis of this disease. It suggests that Brf1 may be a potential diagnosis biomarker and a therapeutic target of alcohol-associated breast cancer.
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Affiliation(s)
- Chenghao Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, China
| | - Yanmei Zhang
- Department of Pharmacology of Shantou University Medical College, China
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shuping Zhong
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Bhalla P, Vernekar DV, Gilquin B, Couté Y, Bhargava P. Interactome of the yeast RNA polymerase III transcription machinery constitutes several chromatin modifiers and regulators of the genes transcribed by RNA polymerase II. Gene 2018; 702:205-214. [PMID: 30593915 DOI: 10.1016/j.gene.2018.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023]
Abstract
Eukaryotic transcription is a highly regulated fundamental life process. A large number of regulatory proteins and complexes, many of them with sequence-specific DNA-binding activity are known to influence transcription by RNA polymerase (pol) II with a fine precision. In comparison, only a few regulatory proteins are known for pol III, which transcribes genes encoding small, stable, non-translated RNAs. The pol III transcription is precisely regulated under various stress conditions. We used pol III transcription complex (TC) components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits and mass spectrometry to identify their potential interactors in vivo. A large interactome constituting chromatin modifiers, regulators and factors of transcription by pol I and pol II supports the possibility of a crosstalk between the three transcription machineries. The association of proteins and complexes involved in various basic life processes like ribogenesis, RNA processing, protein folding and degradation, DNA damage response, replication and transcription underscores the possibility of the pol III TC serving as a signaling hub for communication between the transcription and other cellular physiological activities under normal growth conditions. We also found an equally large number of proteins and complexes interacting with the TC under nutrient starvation condition, of which at least 25% were non-identical under the two conditions. The data reveal the possibility of a large number of signaling cues for pol III transcription against adverse conditions, necessary for an efficient co-ordination of various cellular functions.
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Affiliation(s)
- Pratibha Bhalla
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad, India
| | - Dipti Vinayak Vernekar
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad, India
| | - Benoit Gilquin
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad, India.
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Dorboz I, Dumay-Odelot H, Boussaid K, Bouyacoub Y, Barreau P, Samaan S, Jmel H, Eymard-Pierre E, Cances C, Bar C, Poulat AL, Rousselle C, Renaldo F, Elmaleh-Bergès M, Teichmann M, Boespflug-Tanguy O. Mutation in POLR3K causes hypomyelinating leukodystrophy and abnormal ribosomal RNA regulation. NEUROLOGY-GENETICS 2018; 4:e289. [PMID: 30584594 PMCID: PMC6283457 DOI: 10.1212/nxg.0000000000000289] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/05/2018] [Indexed: 11/17/2022]
Abstract
Objective To identify the genetic cause of hypomyelinating leukodystrophy in 2 consanguineous families. Methods Homozygosity mapping combined with whole-exome sequencing of consanguineous families was performed. Mutation consequences were determined by studying the structural change of the protein and by the RNA analysis of patients' fibroblasts. Results We identified a biallelic mutation in a gene coding for a Pol III–specific subunit, POLR3K (c.121C>T/p.Arg41Trp), that cosegregates with the disease in 2 unrelated patients. Patients expressed neurologic and extraneurologic signs found in POLR3A- and POLR3B-related leukodystrophies with a peculiar severe digestive dysfunction. The mutation impaired the POLR3K-POLR3B interactions resulting in zebrafish in abnormal gut development. Functional studies in the 2 patients' fibroblasts revealed a severe decrease (60%–80%) in the expression of 5S and 7S ribosomal RNAs in comparison with control. Conclusions These analyses underlined the key role of ribosomal RNA regulation in the development and maintenance of the white matter and the cerebellum as already reported for diseases related to genes involved in transfer RNA or translation initiation factors.
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Affiliation(s)
- Imen Dorboz
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Hélene Dumay-Odelot
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Karima Boussaid
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Yosra Bouyacoub
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Pauline Barreau
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Simon Samaan
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Haifa Jmel
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Eleonore Eymard-Pierre
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Claude Cances
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Céline Bar
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Anne-Lise Poulat
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Christophe Rousselle
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Florence Renaldo
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Monique Elmaleh-Bergès
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Martin Teichmann
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
| | - Odile Boespflug-Tanguy
- INSERM UMR 1141 PROTECT (I.D., P.B., S.S., O.B.-T.), Université Paris Diderot- Sorbonne Paris Cité; INSERM U1212-CNRS UMR 5320 (H.D.-O., M.T.), Université de Bordeaux; Neurologie Pédiatrique et Maladies Métaboliques (K.B., F.R., O.B-.T.), Centre de référence des leucodystrophies et leucoencéphalopathies de cause rare (LEUKOFRANCE), CHU APHP Robert-Debré, Paris, France; LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory (H.J., Y.B.), Institut Pasteur de Tunis; Department of Medical Genetics, UF Molecular Genetics (S.S.), CHU APHP Robert-Debré Paris; Service de Cytogénétique Médicale (E.E.P.), CHU Clermont-Ferrand; Neurologie Pédiatrique (C.C.), Endocrinologie Pédiatrique (C.B.), CHU Hôpital des Enfants, Toulouse; Hôpital Femme Mère Enfant, Neurologie Pédiatrique (A.L.P., C.R.), Hospices Civils de Lyon, Bron; Department of Pediatric Radiology (M.E.-B.), CHU APHP Robert-Debré, Paris, France
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Bin X, Hongjian Y, Xiping Z, Bo C, Shifeng Y, Binbin T. Research progresses in roles of LncRNA and its relationships with breast cancer. Cancer Cell Int 2018; 18:179. [PMID: 30459529 PMCID: PMC6233376 DOI: 10.1186/s12935-018-0674-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/01/2018] [Indexed: 12/21/2022] Open
Abstract
Some progresses have been made in research of long non-coding RNA (hereunder referred to as LncRNA) related to breast cancer. Lots of data about LncRNA transcription concerning breast cancer have been obtained from large-scale omics research (e.g. transcriptomes and chips). Some LncRNAs would become indices for detecting breast cancer and judging its development and prognosis. LncRNAs may affect genesis and development of breast cancer in multiple ways. Perhaps they could develop into potential targets for treating breast cancer if they are carcinogenic. Like those from other studies of breast cancer, many data gained from omics research remain to be validated by much experimental work. For instance, it is still necessary to demonstrate reliability of LncRNAs as indices for diagnosing breast cancer and judging its prognosis (particularly for various subtypes of breast cancer), effectiveness and feasibility of these genes for treating breast cancer as targets. In this paper, recent years’ literatures about LncRNAs which are related to breast cancer are summarized and sorted out to review the research progresses in relationships between LncRNAs and breast cancer.
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Affiliation(s)
- Xu Bin
- Department of Surgery, Zhejiang Rehabilitation Medical Center, Hangzhou, 310053 Zhejiang, China
| | - Yang Hongjian
- 2Department of Breast Surgery, Zhejiang Cancer Hospital, Banshanqiao, No. 38 Guangji Road, Hangzhou, 310022 Zhejiang China
| | - Zhang Xiping
- 2Department of Breast Surgery, Zhejiang Cancer Hospital, Banshanqiao, No. 38 Guangji Road, Hangzhou, 310022 Zhejiang China
| | - Chen Bo
- 3Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, 310022 Zhejiang, China
| | - Yang Shifeng
- 3Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, 310022 Zhejiang, China
| | - Tang Binbin
- 4Second Outpatient Department of Traditional Chinese Internal Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, 310012 Zhejiang, China
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Warkocki Z, Liudkovska V, Gewartowska O, Mroczek S, Dziembowski A. Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0162. [PMID: 30397099 PMCID: PMC6232586 DOI: 10.1098/rstb.2018.0162] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
In eukaryotes, almost all RNA species are processed at their 3′ ends and most mRNAs are polyadenylated in the nucleus by canonical poly(A) polymerases. In recent years, several terminal nucleotidyl transferases (TENTs) including non-canonical poly(A) polymerases (ncPAPs) and terminal uridyl transferases (TUTases) have been discovered. In contrast to canonical polymerases, TENTs' functions are more diverse; some, especially TUTases, induce RNA decay while others, such as cytoplasmic ncPAPs, activate translationally dormant deadenylated mRNAs. The mammalian genome encodes 11 different TENTs. This review summarizes the current knowledge about the functions and mechanisms of action of these enzymes. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Zbigniew Warkocki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, Poland
| | - Vladyslava Liudkovska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Olga Gewartowska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland .,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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138
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Aubert M, O'Donohue MF, Lebaron S, Gleizes PE. Pre-Ribosomal RNA Processing in Human Cells: From Mechanisms to Congenital Diseases. Biomolecules 2018; 8:biom8040123. [PMID: 30356013 PMCID: PMC6315592 DOI: 10.3390/biom8040123] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomal RNAs, the most abundant cellular RNA species, have evolved as the structural scaffold and the catalytic center of protein synthesis in every living organism. In eukaryotes, they are produced from a long primary transcript through an intricate sequence of processing steps that include RNA cleavage and folding and nucleotide modification. The mechanisms underlying this process in human cells have long been investigated, but technological advances have accelerated their study in the past decade. In addition, the association of congenital diseases to defects in ribosome synthesis has highlighted the central place of ribosomal RNA maturation in cell physiology regulation and broadened the interest in these mechanisms. Here, we give an overview of the current knowledge of pre-ribosomal RNA processing in human cells in light of recent progress and discuss how dysfunction of this pathway may contribute to the physiopathology of congenital diseases.
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Affiliation(s)
- Maxime Aubert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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139
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Carter-Timofte ME, Paludan SR, Mogensen TH. RNA Polymerase III as a Gatekeeper to Prevent Severe VZV Infections. Trends Mol Med 2018; 24:904-915. [PMID: 30115567 DOI: 10.1016/j.molmed.2018.07.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/07/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022]
Abstract
In most individuals, varicella zoster virus (VZV) causes varicella upon primary infection and zoster during reactivation. However, in a subset of individuals, VZV may cause severe disease, including encephalitis. Host genetics is believed to be the main determinant of exacerbated disease manifestations. Recent studies have demonstrated that defects in the DNA sensor RNA polymerase III (POL III) confer selective increased susceptibility to VZV infection, thus providing fundamental new insight into VZV immunity. Here we describe the roles of POL III in housekeeping and immune surveillance during VZV infection. We present the latest knowledge on the role of POL III in VZV infection and discuss outstanding questions related to the role of POL III in VZV immunity, and how this insight can be translated into clinical medicine.
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MESH Headings
- Adult
- Chickenpox/genetics
- Chickenpox/immunology
- Chickenpox/pathology
- Chickenpox/virology
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DNA, Viral/genetics
- DNA, Viral/immunology
- Encephalitis, Varicella Zoster/genetics
- Encephalitis, Varicella Zoster/immunology
- Encephalitis, Varicella Zoster/pathology
- Encephalitis, Varicella Zoster/virology
- Gene Expression Regulation
- Genetic Predisposition to Disease
- Herpes Zoster/genetics
- Herpes Zoster/immunology
- Herpes Zoster/pathology
- Herpes Zoster/virology
- Herpesvirus 3, Human/genetics
- Herpesvirus 3, Human/immunology
- Host-Pathogen Interactions
- Humans
- Immunity, Innate
- Immunologic Surveillance
- Interferons/genetics
- Interferons/immunology
- Protein Subunits/genetics
- Protein Subunits/immunology
- RNA Polymerase III/genetics
- RNA Polymerase III/immunology
- Receptors, Immunologic
- Virus Activation
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Affiliation(s)
- Madalina E Carter-Timofte
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark; Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark; Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark; Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark; Department of Clinical Medicine, Aarhus University, Palle Juul Jensens Boulevard 82, 8200 Aarhus N, Denmark.
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140
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Wang Y, Song X, Li Z, Liu B. Long non-coding RNAs in coronary atherosclerosis. Life Sci 2018; 211:189-197. [PMID: 30195033 DOI: 10.1016/j.lfs.2018.08.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 12/26/2022]
Abstract
Coronary atherosclerosis (CAS), a leading cause of cardiovascular disease, is a major cause of death worldwide. CAS is a chronic disease in the aorta that can be caused by dyslipidemia, abnormal glucose metabolism, endothelial cell dysfunction, vascular smooth muscle cell (VSMC) or fibrous connective tissue hyperplasia, immune inflammatory reactions, and many other factors. The pathogenesis of CAS is not fully understood, as it is a complex lesion complicated by multiple factors. Damage-response theories have put forward endothelial cell (EC) injury as the initiating factor for CAS; the addition of lipid metabolism disorders may enhance monocyte adhesion, increase the proliferation and migration of fibroblasts and VSMCs, and accelerate the development of CAS. Furthermore, inflammatory and immune responses can create a vicious cycle of endothelial injury, which also plays key roles in the formation of CAS. Therefore, in order to elucidate the mechanisms controlling CAS, it is important to study the etiology of vascular cell dysfunction, abnormal energy and metabolism disorders, and immune and inflammatory reactions. Non-coding RNAs play regulatory roles in the pathogenesis of CAS, especially long non-coding RNAs (lncRNAs); lncRNAs have recently become a major focus for cardiovascular disease mechanisms, as they play numerous roles in the progression of CAS. Therefore, in this review, we discuss the role of lncRNAs in the pathogenesis of coronary CAS, and their role in the prevention and treatment of coronary CAS.
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Affiliation(s)
- Yiran Wang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xianjing Song
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zhibo Li
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China.
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141
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Samson J, Cronin S, Dean K. BC200 (BCYRN1) - The shortest, long, non-coding RNA associated with cancer. Noncoding RNA Res 2018; 3:131-143. [PMID: 30175286 PMCID: PMC6114260 DOI: 10.1016/j.ncrna.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022] Open
Abstract
With the discovery that the level of RNA synthesis in human cells far exceeds what is required to express protein-coding genes, there has been a concerted scientific effort to identify, catalogue and uncover the biological functions of the non-coding transcriptome. Long, non-coding RNAs (lncRNAs) are a diverse group of RNAs with equally wide-ranging biological roles in the cell. An increasing number of studies have reported alterations in the expression of lncRNAs in various cancers, although unravelling how they contribute specifically to the disease is a bigger challenge. Originally described as a brain-specific, non-coding RNA, BC200 (BCYRN1) is a 200-nucleotide, predominantly cytoplasmic lncRNA that has been linked to neurodegenerative disease and several types of cancer. Here we summarise what is known about BC200, primarily from studies in neuronal systems, before turning to a review of recent work that aims to understand how this lncRNA contributes to cancer initiation, progression and metastasis, along with its possible clinical utility as a biomarker or therapeutic target.
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Affiliation(s)
| | | | - K. Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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142
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Zhang L, Peng D, Sood AK, Dang CV, Zhong X. Shedding Light on the Dark Cancer Genomes: Long Noncoding RNAs as Novel Biomarkers and Potential Therapeutic Targets for Cancer. Mol Cancer Ther 2018; 17:1816-1823. [PMID: 30181330 PMCID: PMC6127856 DOI: 10.1158/1535-7163.mct-18-0124] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/09/2018] [Accepted: 07/05/2018] [Indexed: 12/19/2022]
Abstract
Recently there have been explosive discoveries of new long noncoding RNAs (lncRNA) obtained by progress in the technology of second-generation sequencing. Genome scale analysis of transcriptome, in conjunction with studies on chromatin modifications at the epigenetic level, identified lncRNAs as a novel type of noncoding transcripts whose length is longer than 200 nucleotides. These transcripts are later found as major participants in various physiologic processes and diseases, especially in human cancers. LncRNAs have been found to function as novel types of oncogenes and tumor suppressors during cancer progression through various mechanisms, which endow them with the potential of serving as reliable biomarkers and novel therapeutic targets for cancers. Mol Cancer Ther; 17(9); 1816-23. ©2018 AACR.
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Affiliation(s)
- Lin Zhang
- Center for Research on Reproduction and Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dan Peng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Anil K Sood
- Center for RNA Interference and Non-coding RNA, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chi V Dang
- Wistar Institute, Philadelphia, Pennsylvania
- Ludwig Institute for Cancer Research, New York City, New York
| | - Xiaomin Zhong
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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143
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Siira SJ, Rossetti G, Richman TR, Perks K, Ermer JA, Kuznetsova I, Hughes L, Shearwood AMJ, Viola HM, Hool LC, Rackham O, Filipovska A. Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z. EMBO Rep 2018; 19:embr.201846198. [PMID: 30126926 DOI: 10.15252/embr.201846198] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/26/2018] [Accepted: 07/03/2018] [Indexed: 11/09/2022] Open
Abstract
The molecular roles of the dually targeted ElaC domain protein 2 (ELAC2) during nuclear and mitochondrial RNA processing in vivo have not been distinguished. We generated conditional knockout mice of ELAC2 to identify that it is essential for life and its activity is non-redundant. Heart and skeletal muscle-specific loss of ELAC2 causes dilated cardiomyopathy and premature death at 4 weeks. Transcriptome-wide analyses of total RNAs, small RNAs, mitochondrial RNAs, and miRNAs identified the molecular targets of ELAC2 in vivo We show that ELAC2 is required for processing of tRNAs and for the balanced maintenance of C/D box snoRNAs, miRNAs, and a new class of tRNA fragments. We identify that correct biogenesis of regulatory non-coding RNAs is essential for both cytoplasmic and mitochondrial protein synthesis and the assembly of mitochondrial ribosomes and cytoplasmic polysomes. We show that nuclear tRNA processing is required for the balanced production of snoRNAs and miRNAs for gene expression and that 3' tRNA processing is an essential step in the production of all mature mitochondrial RNAs and the majority of nuclear tRNAs.
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Affiliation(s)
- Stefan J Siira
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Tara R Richman
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Kara Perks
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Laetitia Hughes
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Anne-Marie J Shearwood
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia
| | - Helena M Viola
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Livia C Hool
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,School of Human Sciences (Physiology), The University of Western Australia, Crawley, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and Centre for Medical Research, Nedlands, WA, Australia .,School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
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144
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Structural visualization of RNA polymerase III transcription machineries. Cell Discov 2018; 4:40. [PMID: 30083386 PMCID: PMC6066478 DOI: 10.1038/s41421-018-0044-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III-TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft. The architecture of Pol III PIC more resembles that of the Pol II PIC than the Pol I PIC. In addition, we also obtain a 3D reconstruction of Pol III in complex with TFIIIB using the elongation complex (EC) scaffold, shedding light on the mechanism of facilitated recycling of Pol III prior to transcription re-initiation.
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145
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Policarpi C, Crepaldi L, Brookes E, Nitarska J, French SM, Coatti A, Riccio A. Enhancer SINEs Link Pol III to Pol II Transcription in Neurons. Cell Rep 2018; 21:2879-2894. [PMID: 29212033 PMCID: PMC5732322 DOI: 10.1016/j.celrep.2017.11.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 06/30/2017] [Accepted: 11/02/2017] [Indexed: 12/25/2022] Open
Abstract
Spatiotemporal regulation of gene expression depends on the cooperation of multiple mechanisms, including the functional interaction of promoters with distally located enhancers. Here, we show that, in cortical neurons, a subset of short interspersed nuclear elements (SINEs) located in the proximity of activity-regulated genes bears features of enhancers. Enhancer SINEs (eSINEs) recruit the Pol III cofactor complex TFIIIC in a stimulus-dependent manner and are transcribed by Pol III in response to neuronal depolarization. Characterization of an eSINE located in proximity to the Fos gene (FosRSINE1) indicated that the FosRSINE1-encoded transcript interacts with Pol II at the Fos promoter and mediates Fos relocation to Pol II factories, providing an unprecedented molecular link between Pol III and Pol II transcription. Strikingly, knockdown of the FosRSINE1 transcript induces defects of both cortical radial migration in vivo and activity-dependent dendritogenesis in vitro, demonstrating that FosRSINE1 acts as a strong enhancer of Fos expression in diverse physiological contexts.
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Affiliation(s)
- Cristina Policarpi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Luca Crepaldi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Emily Brookes
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Justyna Nitarska
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Sarah M French
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Alessandro Coatti
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Antonella Riccio
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
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146
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Ulitsky I. Interactions between short and long noncoding RNAs. FEBS Lett 2018; 592:2874-2883. [PMID: 29749606 DOI: 10.1002/1873-3468.13085] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 04/26/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022]
Abstract
It is now evident that noncoding RNAs play key roles in regulatory networks determining cell fate and behavior, in a myriad of different conditions, and across all species. Among these noncoding RNAs are short RNAs, such as MicroRNAs, snoRNAs, and Piwi-interacting RNAs, and the functions of those are relatively well understood. Other noncoding RNAs are longer, and their modes of action and functions are also increasingly explored and deciphered. Short RNAs and long noncoding RNAs (lncRNAs) interact with each other with reciprocal consequences for their fates and functions. LncRNAs serve as precursors for many types of small RNAs and, therefore, the pathways for small RNA biogenesis can impinge upon the fate of lncRNAs. In addition, lncRNA expression can be repressed by small RNAs, and lncRNAs can affect small RNA activity and abundance through competition for binding or by triggering small RNA degradation. Here, I review the known types of interactions between small and long RNAs, discuss their outcomes, and bring representative examples from studies in mammals.
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Affiliation(s)
- Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
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147
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Engel C, Neyer S, Cramer P. Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II. Annu Rev Biophys 2018; 47:425-446. [DOI: 10.1146/annurev-biophys-070317-033058] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated. Comparison with the well-studied Pol II initiation system reveals a distinct architecture of the initiation complex and visualizes promoter- and gene-class-specific aspects of transcription initiation. On the basis of new structural studies, we derive a model of the Pol I transcription cycle and provide a molecular movie of Pol I transcription that can be used for teaching.
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Affiliation(s)
- Christoph Engel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Current affiliation: Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Simon Neyer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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148
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Li M, Wang Y, Cheng L, Niu W, Zhao G, Raju JK, Huo J, Wu B, Yin B, Song Y, Bu R. Long non-coding RNAs in renal cell carcinoma: A systematic review and clinical implications. Oncotarget 2018; 8:48424-48435. [PMID: 28467794 PMCID: PMC5564659 DOI: 10.18632/oncotarget.17053] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/20/2017] [Indexed: 12/27/2022] Open
Abstract
Renal cell carcinoma is one of the most common malignancy in adults, its prognosis is poor in an advanced stage and early detection is difficult due to the lack of molecular biomarkers. The identification of novel biomarkers for RCC is an urgent and meaningful project. Long non-coding RNA (lncRNA) is transcribed from genomic regions with a minimum length of 200 bases and limited protein-coding potential. Recently, lncRNAs have been greatly studied in a variety of cancer types. They participate in a wide variety of biological processes including cancer biology. In this review, we provide a new insight of the profiling of lncRNAs in RCC and their roles in renal carcinogenesis, with an emphasize on their potential in diagnosis, prognosis and potential roles in RCC therapy.
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Affiliation(s)
- Ming Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Ying Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wanting Niu
- Department of Orthopedics, Brigham and Women's Hospital, VA Boston Healthcare System, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Guoan Zhao
- School of Network Education, Beijing University of Posts and Telecommunications, Hebei, Beijing 100088, P.R. China
| | - Jithin K Raju
- Department of Clinical Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Jun Huo
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Bin Wu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Bo Yin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yongsheng Song
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Renge Bu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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149
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Liu SS, Liu N, Liu MY, Sun L, Xia WY, Lu HM, Fu YJ, Yang GL, Bo JJ, Liu XX, Feng H, Wu H, Li LF, Gao JX. An unusual intragenic promoter of PIWIL2 contributes to aberrant activation of oncogenic PL2L60. Oncotarget 2018; 8:46104-46120. [PMID: 28545024 PMCID: PMC5542253 DOI: 10.18632/oncotarget.17553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 03/28/2017] [Indexed: 12/24/2022] Open
Abstract
PIWIL2-like (PL2L) protein 60 (PL2L60), a product of aberrantly activated PIWIL2 gene, is widely expressed in various types of tumors and may promote tumorigenesis. However, the mechanisms underlying the activation of expression of PL2L60 remain unknown. In this study, an intragenic promoter responsible for the activation of PL2L60 within the human PIWIL2 gene has been identified, cloned and characterized. The promoter of PL2L60 is located in the intron 10 of the host gene PIWIL2. Bioinformatic and mutagenic analysis reveals that this intragenic promoter within the sequence of 50 nucleotides contains two closely arranged cis-acting elements specific for the hepatic leukemia factor (HLF) in the positive strand and signal transducer and activator of transcription 3 (STAT3) in the negative strand. Chromatin immunoprecipitation analysis demonstrates that both the HLF and polymerase II (Pol II), a hallmark of active promoters, directly bind to the sequence, although STAT3 does not. Knockdown of HLF and STAT3 alone or both by RNA interference significantly reduced both promoter activity and the PL2L60 protein expression, although there is no additive effect. The expression of PL2L60 proteins was enhanced when host gene Piwil2 was genetically disrupted in a murine cell model. Taken together, we have identified a PL2L60-specific intragenic promoter in the host gene of PIWIL2, which is interdependently activated by HLF and STAT3 through steric interaction. This activation is dependent on cellular milieu rather than the integrity of host gene PIWIL2, highlighting a novel, important mechanism for a cancer-causing gene to be activated during tumorigenesis.
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Affiliation(s)
- Shan-Shan Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Yao Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Sun
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wu-Yan Xia
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-Min Lu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu-Jie Fu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Liang Yang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Juan-Jie Bo
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Xing Liu
- Department of Radiotherapy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haizhong Feng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hailong Wu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin-Feng Li
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Xin Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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150
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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