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Moir RD, Merheb E, Chitu V, Richard Stanley E, Willis IM. Molecular basis of neurodegeneration in a mouse model of Polr3-related disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571310. [PMID: 38168294 PMCID: PMC10760057 DOI: 10.1101/2023.12.12.571310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pathogenic variants in subunits of RNA polymerase (Pol) III cause a spectrum of Polr3-related neurodegenerative diseases including 4H leukodystrophy. Disease onset occurs from infancy to early adulthood and is associated with a variable range and severity of neurological and non-neurological features. The molecular basis of Polr3-related disease pathogenesis is unknown. We developed a postnatal whole-body mouse model expressing pathogenic Polr3a mutations to examine the molecular mechanisms by which reduced Pol III transcription results primarily in central nervous system phenotypes. Polr3a mutant mice exhibit behavioral deficits, cerebral pathology and exocrine pancreatic atrophy. Transcriptome and immunohistochemistry analyses of cerebra during disease progression show a reduction in most Pol III transcripts, induction of innate immune and integrated stress responses and cell type-specific gene expression changes reflecting neuron and oligodendrocyte loss and microglial activation. Earlier in the disease when integrated stress and innate immune responses are minimally induced, mature tRNA sequencing revealed a global reduction in tRNA levels and an altered tRNA profile but no changes in other Pol III transcripts. Thus, changes in the size and/or composition of the tRNA pool have a causal role in disease initiation. Our findings reveal different tissue- and brain region-specific sensitivities to a defect in Pol III transcription.
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Affiliation(s)
- Robyn D. Moir
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - Emilio Merheb
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - Violeta Chitu
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - E. Richard Stanley
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
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2
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Shih HY, Raas Q, Bonkowsky JL. Progress in leukodystrophies with zebrafish. Dev Growth Differ 2024; 66:21-34. [PMID: 38239149 DOI: 10.1111/dgd.12907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024]
Abstract
Inherited leukodystrophies are genetic disorders characterized by abnormal white matter in the central nervous system. Although individually rare, there are more than 400 distinct types of leukodystrophies with a cumulative incidence of 1 in 4500 live births. The pathophysiology of most leukodystrophies is poorly understood, there are treatments for only a few, and there is significant morbidity and mortality, suggesting a critical need for improvements in this field. A variety of animal, cell, and induced pluripotent stem cell-derived models have been developed for leukodystrophies, but with significant limitations in all models. Many leukodystrophies lack animal models, and extant models often show no or mixed recapitulation of key phenotypes. Zebrafish (Danio rerio) have become increasingly used as disease models for studying leukodystrophies due to their early onset of disease phenotypes and conservation of molecular and neurobiological mechanisms. Here, we focus on reviewing new zebrafish disease models for leukodystrophy or models with recent progress. This includes discussion of leukodystrophy with vanishing white matter disease, X-linked adrenoleukodystrophy, Zellweger spectrum disorders and peroxisomal disorders, PSAP deficiency, metachromatic leukodystrophy, Krabbe disease, hypomyelinating leukodystrophy-8/4H leukodystrophy, Aicardi-Goutières syndrome, RNASET2-deficient cystic leukoencephalopathy, hereditary diffuse leukoencephalopathy with spheroids-1 (CSF1R-related leukoencephalopathy), and ultra-rare leukodystrophies. Zebrafish models offer important potentials for the leukodystrophy field, including testing of new variants in known genes; establishing causation of newly discovered genes; and early lead compound identification for therapies. There are also unrealized opportunities to use humanized zebrafish models which have been sparsely explored.
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Affiliation(s)
- Hung-Yu Shih
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Department of Biological Sciences, Utah Tech University, Saint George, Utah, USA
- Center for Precision & Functional Genomics, Utah Tech University, Saint George, Utah, USA
| | - Quentin Raas
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Laboratory of Translational Research for Neurological Disorders, Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France
| | - Joshua L Bonkowsky
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Center for Personalized Medicine, Primary Children's Hospital, Salt Lake City, Utah, USA
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3
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Michell-Robinson MA, Watt KEN, Grouza V, Macintosh J, Pinard M, Tuznik M, Chen X, Darbelli L, Wu CL, Perrier S, Chitsaz D, Uccelli NA, Liu H, Cox TC, Müller CW, Kennedy TE, Coulombe B, Rudko DA, Trainor PA, Bernard G. Hypomyelination, hypodontia and craniofacial abnormalities in a Polr3b mouse model of leukodystrophy. Brain 2023; 146:5070-5085. [PMID: 37635302 PMCID: PMC10690025 DOI: 10.1093/brain/awad249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023] Open
Abstract
RNA polymerase III (Pol III)-related hypomyelinating leukodystrophy (POLR3-HLD), also known as 4H leukodystrophy, is a severe neurodegenerative disease characterized by the cardinal features of hypomyelination, hypodontia and hypogonadotropic hypogonadism. POLR3-HLD is caused by biallelic pathogenic variants in genes encoding Pol III subunits. While approximately half of all patients carry mutations in POLR3B encoding the RNA polymerase III subunit B, there is no in vivo model of leukodystrophy based on mutation of this Pol III subunit. Here, we determined the impact of POLR3BΔ10 (Δ10) on Pol III in human cells and developed and characterized an inducible/conditional mouse model of leukodystrophy using the orthologous Δ10 mutation in mice. The molecular mechanism of Pol III dysfunction was determined in human cells by affinity purification-mass spectrometry and western blot. Postnatal induction with tamoxifen induced expression of the orthologous Δ10 hypomorph in triple transgenic Pdgfrα-Cre/ERT; R26-Stopfl-EYFP; Polr3bfl mice. CNS and non-CNS features were characterized using a variety of techniques including microCT, ex vivo MRI, immunofluorescence, immunohistochemistry, spectral confocal reflectance microscopy and western blot. Lineage tracing and time series analysis of oligodendrocyte subpopulation dynamics based on co-labelling with lineage-specific and/or proliferation markers were performed. Proteomics suggested that Δ10 causes a Pol III assembly defect, while western blots demonstrated reduced POLR3BΔ10 expression in the cytoplasm and nucleus in human cells. In mice, postnatal Pdgfrα-dependent expression of the orthologous murine mutant protein resulted in recessive phenotypes including severe hypomyelination leading to ataxia, tremor, seizures and limited survival, as well as hypodontia and craniofacial abnormalities. Hypomyelination was confirmed and characterized using classic methods to quantify myelin components such as myelin basic protein and lipids, results which agreed with those produced using modern methods to quantify myelin based on the physical properties of myelin membranes. Lineage tracing uncovered the underlying mechanism for the hypomyelinating phenotype: defective oligodendrocyte precursor proliferation and differentiation resulted in a failure to produce an adequate number of mature oligodendrocytes during postnatal myelinogenesis. In summary, we characterized the Polr3bΔ10 mutation and developed an animal model that recapitulates features of POLR3-HLD caused by POLR3B mutations, shedding light on disease pathogenesis, and opening the door to the development of therapeutic interventions.
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Affiliation(s)
- Mackenzie A Michell-Robinson
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Kristin E N Watt
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Vladimir Grouza
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
| | - Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Maxime Pinard
- Translational Proteomics Research Unit, Montreal Clinical Research Institute, Montréal, QC H2W 1R7, Canada
| | - Marius Tuznik
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
| | - Xiaoru Chen
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Lama Darbelli
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Chia-Lun Wu
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Stefanie Perrier
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Daryan Chitsaz
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
| | - Nonthué A Uccelli
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
| | - Hanwen Liu
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
| | - Timothy C Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry, and Pediatrics, School of Medicine, University of Missouri – Kansas City, Kansas City, MO 64108, USA
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Timothy E Kennedy
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
| | - Benoit Coulombe
- Translational Proteomics Research Unit, Montreal Clinical Research Institute, Montréal, QC H2W 1R7, Canada
- Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, QC H3C 3J7, Canada
| | - David A Rudko
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
- Department of Biomedical Engineering, McGill University, Montréal, QC H3A 2B4, Canada
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
- Department of Pediatrics, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Human Genetics, McGill University, Montréal, QC H4A 0C7, Canada
- Department of Specialized Medicine, Division of Medical Genetics, Montreal Children’s Hospital and McGill University Health Centre, Montréal, QC H4A 3J1, Canada
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Chen Q, Guo Y, Zhang J, Zheng N, Wang J, Liu Y, Lu J, Zhen S, Du X, Li L, Fu J, Wang G, Gu R, Wang J, Liu Y. RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize. Nucleic Acids Res 2023; 51:7832-7850. [PMID: 37403778 PMCID: PMC10450181 DOI: 10.1093/nar/gkad571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023] Open
Abstract
Maize (Zea mays) kernel size is an important factor determining grain yield; although numerous genes regulate kernel development, the roles of RNA polymerases in this process are largely unclear. Here, we characterized the defective kernel 701 (dek701) mutant that displays delayed endosperm development but normal vegetative growth and flowering transition, compared to its wild type. We cloned Dek701, which encoded ZmRPABC5b, a common subunit to RNA polymerases I, II and III. Loss-of-function mutation of Dek701 impaired the function of all three RNA polymerases and altered the transcription of genes related to RNA biosynthesis, phytohormone response and starch accumulation. Consistent with this observation, loss-of-function mutation of Dek701 affected cell proliferation and phytohormone homeostasis in maize endosperm. Dek701 was transcriptionally regulated in the endosperm by the transcription factor Opaque2 through binding to the GCN4 motif within the Dek701 promoter, which was subjected to strong artificial selection during maize domestication. Further investigation revealed that DEK701 interacts with the other common RNA polymerase subunit ZmRPABC2. The results of this study provide substantial insight into the Opaque2-ZmRPABC5b transcriptional regulatory network as a central hub for regulating endosperm development in maize.
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Affiliation(s)
- Quanquan Chen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingmei Guo
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Zhang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Nannan Zheng
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiawen Lu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Sihan Zhen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Li Li
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Macintosh J, Michell-Robinson M, Chen X, Bernard G. Decreased RNA polymerase III subunit expression leads to defects in oligodendrocyte development. Front Neurosci 2023; 17:1167047. [PMID: 37179550 PMCID: PMC10167296 DOI: 10.3389/fnins.2023.1167047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023] Open
Abstract
Introduction RNA polymerase III (Pol III) is a critical enzymatic complex tasked with the transcription of ubiquitous non-coding RNAs including 5S rRNA and all tRNA genes. Despite the constitutive nature of this enzyme, hypomorphic biallelic pathogenic variants in genes encoding subunits of Pol III lead to tissue-specific features and cause a hypomyelinating leukodystrophy, characterized by a severe and permanent deficit in myelin. The pathophysiological mechanisms in POLR3- related leukodystrophy and specifically, how reduced Pol III function impacts oligodendrocyte development to account for the devastating hypomyelination seen in the disease, remain poorly understood. Methods In this study, we characterize how reducing endogenous transcript levels of leukodystrophy-associated Pol III subunits affects oligodendrocyte maturation at the level of their migration, proliferation, differentiation, and myelination. Results Our results show that decreasing Pol III expression altered the proliferation rate of oligodendrocyte precursor cells but had no impact on migration. Additionally, reducing Pol III activity impaired the differentiation of these precursor cells into mature oligodendrocytes, evident at both the level of OL-lineage marker expression and on morphological assessment, with Pol III knockdown cells displaying a drastically more immature branching complexity. Myelination was hindered in the Pol III knockdown cells, as determined in both organotypic shiverer slice cultures and co-cultures with nanofibers. Analysis of Pol III transcriptional activity revealed a decrease in the expression of distinct tRNAs, which was significant in the siPolr3a condition. Discussion In turn, our findings provide insight into the role of Pol III in oligodendrocyte development and shed light on the pathophysiological mechanisms of hypomyelination in POLR3-related leukodystrophy.
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Affiliation(s)
- Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Mackenzie Michell-Robinson
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Xiaoru Chen
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
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6
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Watt KE, Macintosh J, Bernard G, Trainor PA. RNA Polymerases I and III in development and disease. Semin Cell Dev Biol 2023; 136:49-63. [PMID: 35422389 PMCID: PMC9550887 DOI: 10.1016/j.semcdb.2022.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/18/2022]
Abstract
Ribosomes are macromolecular machines that are globally required for the translation of all proteins in all cells. Ribosome biogenesis, which is essential for cell growth, proliferation and survival, commences with transcription of a variety of RNAs by RNA Polymerases I and III. RNA Polymerase I (Pol I) transcribes ribosomal RNA (rRNA), while RNA Polymerase III (Pol III) transcribes 5S ribosomal RNA and transfer RNAs (tRNA) in addition to a wide variety of small non-coding RNAs. Interestingly, despite their global importance, disruptions in Pol I and Pol III function result in tissue-specific developmental disorders, with craniofacial anomalies and leukodystrophy/neurodegenerative disease being among the most prevalent. Furthermore, pathogenic variants in genes encoding subunits shared between Pol I and Pol III give rise to distinct syndromes depending on whether Pol I or Pol III function is disrupted. In this review, we discuss the global roles of Pol I and III transcription, the consequences of disruptions in Pol I and III transcription, disorders arising from pathogenic variants in Pol I and Pol III subunits, and mechanisms underpinning their tissue-specific phenotypes.
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Affiliation(s)
- Kristin En Watt
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada; Departments of Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada; Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada.
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy & Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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7
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Yang F, Sun H, Yang Y, Wang Y, Dai S, Lin Z, Shen Y, Liu H. Identification of POLR3B biallelic mutations-associated hypomyelinating leukodystrophy-8 in two siblings. Clin Genet 2023; 103:596-602. [PMID: 36650939 DOI: 10.1111/cge.14300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
POLR3B gene encodes the 2nd largest catalytic subunit and affects the function of RNA polymerase III enzymes in transcription. Bi-allelic variants in POLR3B pathogenically cause hypomyelinating leukodystrophy-8 (HLD8). Herein, we recruited a family with two patients, who presented clinically with cerebellar atrophy, intellectual disability, hypogonadotropic hypogonadism, and visual problems. We identified the two affected siblings carrying the compound heterozygous variations (c.165_167del; c.1615G>T) in POLR3B by trio-whole-exome sequencing (trio-WES). The qPCR and western blot showed that both transcriptional and translational levels of the mutation (c.165_167del, p.I55_K56delinsM) were sharply attenuated. Following that, a thorough functional examination of a zebrafish line disrupted for human POLR3B validated the pathogenic effects of the two mutations. Our research broadens the spectrum of HLD8-related pathogenic POLR3B mutations and provides new molecular and animal evidence.
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Affiliation(s)
- Fan Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University, Chengdu, China.,Medical Genetics/Prenatal Diagnostic Department, Luoyang Maternal and Child Health Hospital, Henan University, Luoyang, China
| | - Huaqin Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University, Chengdu, China.,Department of Obstetrics/Gynecology, Joint Laboratory of Reproductive Medicine (SCU-CUHK), West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yanting Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University, Chengdu, China
| | - Yanan Wang
- Medical Genetics/Prenatal Diagnostic Department, Luoyang Maternal and Child Health Hospital, Henan University, Luoyang, China
| | - Siyu Dai
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University, Chengdu, China
| | - Ziyuan Lin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University, Chengdu, China.,Department of Obstetrics/Gynecology, Joint Laboratory of Reproductive Medicine (SCU-CUHK), West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ying Shen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University, Chengdu, China.,Department of Obstetrics/Gynecology, Joint Laboratory of Reproductive Medicine (SCU-CUHK), West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University, Chengdu, China
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8
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Kessler AC, Maraia RJ. The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance. Nucleic Acids Res 2021; 49:12017-12034. [PMID: 34850129 PMCID: PMC8643620 DOI: 10.1093/nar/gkab1145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022] Open
Abstract
A 1969 report that described biochemical and activity properties of the three eukaryotic RNA polymerases revealed Pol III as highly distinguishable, even before its transcripts were identified. Now known to be the most complex, Pol III contains several stably-associated subunits referred to as built-in transcription factors (BITFs) that enable highly efficient RNA synthesis by a unique termination-associated recycling process. In vertebrates, subunit RPC7(α/β) can be of two forms, encoded by POLR3G or POLR3GL, with differential activity. Here we review promoter-dependent transcription by Pol III as an evolutionary perspective of eukaryotic tRNA expression. Pol III also provides nonconventional functions reportedly by promoter-independent transcription, one of which is RNA synthesis from DNA 3'-ends during repair. Another is synthesis of 5'ppp-RNA signaling molecules from cytoplasmic viral DNA in a pathway of interferon activation that is dysfunctional in immunocompromised patients with mutations in Pol III subunits. These unconventional functions are also reviewed, including evidence that link them to the BITF subunits. We also review data on a fraction of the human Pol III transcriptome that evolved to include vault RNAs and snaRs with activities related to differentiation, and in innate immune and tumor surveillance. The Pol III of higher eukaryotes does considerably more than housekeeping.
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Affiliation(s)
- Alan C Kessler
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892 USA
| | - Richard J Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892 USA
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9
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Knockdown NRPC2, 3, 8, NRPABC1 and NRPABC2 Affects RNAPIII Activity and Disrupts Seed Development in Arabidopsis. Int J Mol Sci 2021; 22:ijms222111314. [PMID: 34768744 PMCID: PMC8583208 DOI: 10.3390/ijms222111314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
RNA polymerase III (RNAPIII) contains 17 subunits forming 4 functional domains that control the different stages of RNAPIII transcription and are dedicated to the synthesis of small RNAs such as 5S rRNA and tRNAs. Here, we identified 23 genes encoding these subunits in Arabidopsis (Arabidopsis thaliana) and further analyzed 5 subunits (NRPC2, NRPC3, NRPC8, NRPABC1, and NRPABC2) encoded by 6 genes with different expression patterns and belonging to different sub-complexes. The knockdown of these genes repressed the expression of 5S rRNA and tRNAs, causing seed developmental arrest at different stages. Among these knockdown mutants, RNA-seq analysis revealed 821 common differentially expressed genes (DEGs), significantly enriched in response to stress, abscisic acid, cytokinins, and the jasmonic acid signaling pathway. Weighted gene co-expression network analysis (WGCNA) revealed several hub genes involved in embryo development, carbohydrate metabolic and lipid metabolic processes. We identified numerous unique DEGs between the mutants belonging to pathways, including cell proliferation, ribosome biogenesis, cell death, and tRNA metabolic processes. Thus, NRPC2, NRPC3, NRPC8, NRPABC1, and NRPABC2 control seed development in Arabidopsis by influencing RNAPIII activity and, thus, hormone signaling. Reduced expression of these subunit genes causes an insufficient accumulation of the total RNAPIII, leading to the phenotypes observed following the genetic knockdown of these subunits.
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10
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Lata E, Choquet K, Sagliocco F, Brais B, Bernard G, Teichmann M. RNA Polymerase III Subunit Mutations in Genetic Diseases. Front Mol Biosci 2021; 8:696438. [PMID: 34395528 PMCID: PMC8362101 DOI: 10.3389/fmolb.2021.696438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. Surprisingly, it was discovered in the last decade that various inherited mutations in genes encoding nine distinct subunits of Pol III cause tissue-specific diseases rather than a general failure of all vital functions. Mutations in the POLR3A, POLR3C, POLR3E and POLR3F subunits are associated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. In addition, an ever-increasing number of distinct mutations in the POLR3A, POLR3B, POLR1C and POLR3K subunits cause a spectrum of neurodegenerative diseases, which includes most notably hypomyelinating leukodystrophy. Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. Although the causal relationship between these mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain enigmatic. Here, we review the current knowledge on the functional impact of specific mutations, possible Pol III-related disease-causing mechanisms, and animal models that may help to better understand the links between Pol III mutations and disease.
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Affiliation(s)
- Elisabeth Lata
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Karine Choquet
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Francis Sagliocco
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Martin Teichmann
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
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11
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Wu SW, Li L, Feng F, Wang L, Kong YY, Liu XW, Yin C. Whole-exome sequencing reveals POLR3B variants associated with progeria-related Wiedemann-Rautenstrauch syndrome. Ital J Pediatr 2021; 47:160. [PMID: 34289880 PMCID: PMC8296688 DOI: 10.1186/s13052-021-01112-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/04/2021] [Indexed: 11/10/2022] Open
Abstract
Background Wiedemann-Rautenstrauch syndrome (WRS) is a rare autosomal recessive neonatal progeroid disorder characterized by prenatal and postnatal growth retardation, short stature, a progeroid appearance, hypotonia, and mental impairment. Case presentation A 6-year-old patient, who initially presented with multiple postnatal abnormalities, facial dysplasia, micrognathia, skull appearance, hallux valgus, and congenital dislocation of the hip, was recruited in this study. The patient was initially diagnosed with progeria. The mother of the patient had abnormal fetal development during her second pregnancy check-up, and the clinical phenotype of the fetus was similar to that of the patient. Whole-exome sequencing (WES) of the patient was performed, and POLR3B compound heterozygous variants—c.2191G > C:p.E731Q and c.3046G > A:p.V1016M—were identified in the patient. Using Sanger sequencing, we found that the phenotypes and genotypes were segregated within the pedigree. These two variants are novel and not found in the gnomAD and 1000 Genomes databases. The two mutation sites are highly conserved between humans and zebrafish. Conclusions Our study not only identified a novel WRS-associated gene, POLR3B, but also broadened the mutational and phenotypic spectra of POLR3B. Furthermore, WES may be useful for identifying rare disease-related genetic variants. Supplementary Information The online version contains supplementary material available at 10.1186/s13052-021-01112-6.
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Affiliation(s)
- Shao-Wen Wu
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, Chaoyang, China.,Beijing Maternal and Child Health Care Hospital, Beijing, 100026, Chaoyang, China
| | - Lin Li
- Beijing Maternal and Child Health Care Hospital, Beijing, 100026, Chaoyang, China.,Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, Chaoyang, China
| | - Fan Feng
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Haidian, Beijing, 100084, China
| | - Li Wang
- Beijing Maternal and Child Health Care Hospital, Beijing, 100026, Chaoyang, China.,Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, Chaoyang, China
| | - Yuan-Yuan Kong
- Beijing Maternal and Child Health Care Hospital, Beijing, 100026, Chaoyang, China.,Department of Newborn Screening, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, Chaoyang, China
| | - Xiao-Wei Liu
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, Chaoyang, China. .,Beijing Maternal and Child Health Care Hospital, Beijing, 100026, Chaoyang, China.
| | - Chenghong Yin
- Beijing Maternal and Child Health Care Hospital, Beijing, 100026, Chaoyang, China. .,Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, Chaoyang, China.
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12
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Templehof H, Moshe N, Avraham-Davidi I, Yaniv K. Zebrafish mutants provide insights into Apolipoprotein B functions during embryonic development and pathological conditions. JCI Insight 2021; 6:e130399. [PMID: 34236046 PMCID: PMC8410079 DOI: 10.1172/jci.insight.130399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/02/2021] [Indexed: 01/01/2023] Open
Abstract
Apolipoprotein B (ApoB) is the primary protein of chylomicrons, VLDLs, and LDLs and is essential for their production. Defects in ApoB synthesis and secretion result in several human diseases, including abetalipoproteinemia and familial hypobetalipoproteinemia (FHBL1). In addition, ApoB-related dyslipidemia is linked to nonalcoholic fatty liver disease (NAFLD), a silent pandemic affecting billions globally. Due to the crucial role of APOB in supplying nutrients to the developing embryo, ApoB deletion in mammals is embryonic lethal. Thus, a clear understanding of the roles of this protein during development is lacking. Here, we established zebrafish mutants for 2 apoB genes: apoBa and apoBb.1. Double-mutant embryos displayed hepatic steatosis, a common hallmark of FHBL1 and NAFLD, as well as abnormal liver laterality, decreased numbers of goblet cells in the gut, and impaired angiogenesis. We further used these mutants to identify the domains within ApoB responsible for its functions. By assessing the ability of different truncated forms of human APOB to rescue the mutant phenotypes, we demonstrate the benefits of this model for prospective therapeutic screens. Overall, these zebrafish models uncover what are likely previously undescribed functions of ApoB in organ development and morphogenesis and shed light on the mechanisms underlying hypolipidemia-related diseases.
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13
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Zhao H, Qin Y, Xiao Z, Li Q, Yang N, Pan Z, Gong D, Sun Q, Yang F, Zhang Z, Wu Y, Xu C, Qiu F. Loss of Function of an RNA Polymerase III Subunit Leads to Impaired Maize Kernel Development. PLANT PHYSIOLOGY 2020; 184:359-373. [PMID: 32591429 PMCID: PMC7479876 DOI: 10.1104/pp.20.00502] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 05/03/2023]
Abstract
Kernel size is an important factor determining grain yield. Although a number of genes affecting kernel development in maize (Zea mays) have been identified by analyzing kernel mutants, most of the corresponding mutants cannot be used in maize breeding programs due to low germination or incomplete seed development. Here, we characterized small kernel7, a recessive small-kernel mutant with a mutation in the gene encoding the second-largest subunit of RNA polymerase III (RNAPΙΙΙ; NRPC2). A frame shift in ZmNRPC2 leads to a premature stop codon, resulting in significantly reduced levels of transfer RNAs and 5S ribosomal RNA, which are transcribed by RNAPΙΙΙ. Loss-of-function nrpc2 mutants created by CRISPR/CAS9 showed significantly reduced kernel size due to altered endosperm cell size and number. ZmNRPC2 affects RNAPIII activity and the expression of genes involved in cell proliferation and endoreduplication to control kernel development via physically interacting with RNAPIII subunits RPC53 and AC40, transcription factor class C1 and Floury3. Notably, unlike the semidominant negative mutant floury3, which has defects in starchy endosperm, small kernel7 only affects kernel size but not the composition of kernel storage proteins. Our findings provide novel insights into the molecular network underlying maize kernel size, which could facilitate the genetic improvement of maize in the future.
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Affiliation(s)
- Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Ziyi Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Li
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ning Yang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenyuan Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cao Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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14
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Tuo Y, Chu W, Zhang J, Cheng J, Chen L, Bao L, Xiao T. Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing. Front Genet 2020; 11:714. [PMID: 32793279 PMCID: PMC7393255 DOI: 10.3389/fgene.2020.00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 06/11/2020] [Indexed: 12/03/2022] Open
Abstract
Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.
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Affiliation(s)
- Yun Tuo
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China.,College of Life Science and Resources Environment, Yichun University, Yichun, China
| | - Wuying Chu
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jianshe Zhang
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jia Cheng
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lin Chen
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lingsheng Bao
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Tiaoyi Xiao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China
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15
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Yamaguchi A, Uchida M, Ishibashi H, Hirano M, Ichikawa N, Arizono K, Koyama J, Tominaga N. Potential mechanisms underlying embryonic developmental toxicity caused by benzo[a]pyrene in Japanese medaka (Oryzias latipes). CHEMOSPHERE 2020; 242:125243. [PMID: 31704526 DOI: 10.1016/j.chemosphere.2019.125243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), such as benzo[a]pyrene (BaP), are widely distributed in air, water, and sediments; however, limited data are available regarding their potential adverse effects on the early life stages of fish. In this study, we evaluated the embryonic teratogenicity and developmental toxicity of BaP in Japanese medaka (Oryzias latipes) using a nanosecond pulsed electric field (nsPEF) technique and predicted their molecular mechanisms via transcriptome analysis. The gas chromatography/mass spectrometry analyses revealed that the BaP was efficiently incorporated into the embryos by nsPEF treatment. The embryos incorporating BaP presented typical teratogenic and developmental effects, such as cardiovascular abnormalities, developmental abnormalities, and curvature of backbone. DNA microarray analysis revealed several unique upregulated genes, such as those involved in cardiovascular diseases, various cellular processes, and neural development. Furthermore, the gene set enrichment and network analyses found several genes and hub proteins involved in the developmental effects of BaP on the embryos. These findings suggest a potential mechanism of teratogenicity and developmental toxicity caused by exposure to BaP. The nsPEF and transcriptome analyses in combination can be effective for evaluating the potential effects of chemical substances on medaka embryos.
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Affiliation(s)
- Akemi Yamaguchi
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan
| | - Masaya Uchida
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan
| | - Hiroshi Ishibashi
- Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, 790-8566, Japan
| | - Masashi Hirano
- Department of Biological and Chemical Systems Engineering, National Institute of Technology, Kumamoto College, 2627 Hirayama-shinmachi, Yatsushiro, Kumamoto, 866-8501, Japan
| | - Nobuhiro Ichikawa
- College of Pharmaceutical Sciences, Department of Pharmacy, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Koji Arizono
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, 3-1-100 Higashi-ku, Tsukide, Kumamoto, 862-8502, Japan
| | - Jiro Koyama
- Faculty of Fisheries, Kagoshima University, 4-50-20 Shimoarata, Kagoshima, 890-0056, Japan
| | - Nobuaki Tominaga
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan.
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16
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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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17
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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: 26] [Impact Index Per Article: 5.2] [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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18
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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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19
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Chen CY, Lanz RB, Walkey CJ, Chang WH, Lu W, Johnson DL. Maf1 and Repression of RNA Polymerase III-Mediated Transcription Drive Adipocyte Differentiation. Cell Rep 2018; 24:1852-1864. [PMID: 30110641 PMCID: PMC6138453 DOI: 10.1016/j.celrep.2018.07.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/05/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase (pol) III transcribes a variety of small untranslated RNAs involved in transcription, RNA processing, and translation. RNA pol III and its components are altered in various human developmental disorders, yet their roles in cell fate determination and development are poorly understood. Here we demonstrate that Maf1, a transcriptional repressor, promotes induction of mouse embryonic stem cells (mESCs) into mesoderm. Reduced Maf1 expression in mESCs and preadipocytes impairs adipogenesis, while ectopic Maf1 expression in Maf1-deficient cells enhances differentiation. RNA pol III repression by chemical inhibition or knockdown of Brf1 promotes adipogenesis. Altered RNA pol III-dependent transcription produces select changes in mRNAs with a significant enrichment of adipogenic gene signatures. Furthermore, RNA pol III-mediated transcription positively regulates long non-coding RNA H19 and Wnt6 expression, established adipogenesis inhibitors. Together, these studies reveal an important and unexpected function for RNA pol III-mediated transcription and Maf1 in mesoderm induction and adipocyte differentiation.
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Affiliation(s)
- Chun-Yuan Chen
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA; Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher J Walkey
- Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wen-Hsuan Chang
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Wange Lu
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Deborah L Johnson
- Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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20
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Fiore APZP, Spencer VA, Mori H, Carvalho HF, Bissell MJ, Bruni-Cardoso A. Laminin-111 and the Level of Nuclear Actin Regulate Epithelial Quiescence via Exportin-6. Cell Rep 2018; 19:2102-2115. [PMID: 28591581 DOI: 10.1016/j.celrep.2017.05.050] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 03/19/2017] [Accepted: 05/12/2017] [Indexed: 02/08/2023] Open
Abstract
Nuclear actin (N-actin) is known to participate in the regulation of gene expression. We showed previously that N-actin levels mediate the growth and quiescence of mouse epithelial cells in response to laminin-111 (LN1), a component of the mammary basement membrane (BM). We know that BM is defective in malignant cells, and we show here that it is the LN1/N-actin pathway that is aberrant in human breast cancer cells, leading to continuous growth. Photobleaching assays revealed that N-actin exit in nonmalignant cells begins as early as 30 min after LN1 treatment. LN1 attenuates the PI3K pathway leading to upregulation of exportin-6 (XPO6) activity and shuttles actin out of the nucleus. Silencing XPO6 prevents quiescence. Malignant cells are impervious to LN1 signaling. These results shed light on the crucial role of LN1 in quiescence and differentiation and how defects in the LN1/PI3K/XPO6/N-actin axis explain the loss of tissue homeostasis and growth control that contributes to malignant progression.
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Affiliation(s)
- Ana Paula Zen Petisco Fiore
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | | | - Hidetoshi Mori
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Comparative Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Hernandes F Carvalho
- INFABiC - National Institute of Science and Technology on Photonics Applied to Cell Biology, Campinas, SP 13083-862, Brazil; Structural and Functional Biology Department, Institute of Biology, State University of Campinas, Campinas, SP 13083-865, Brazil
| | - Mina J Bissell
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Alexandre Bruni-Cardoso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; INFABiC - National Institute of Science and Technology on Photonics Applied to Cell Biology, Campinas, SP 13083-862, Brazil.
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21
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Minnerop M, Kurzwelly D, Wagner H, Soehn AS, Reichbauer J, Tao F, Rattay TW, Peitz M, Rehbach K, Giorgetti A, Pyle A, Thiele H, Altmüller J, Timmann D, Karaca I, Lennarz M, Baets J, Hengel H, Synofzik M, Atasu B, Feely S, Kennerson M, Stendel C, Lindig T, Gonzalez MA, Stirnberg R, Sturm M, Roeske S, Jung J, Bauer P, Lohmann E, Herms S, Heilmann-Heimbach S, Nicholson G, Mahanjah M, Sharkia R, Carloni P, Brüstle O, Klopstock T, Mathews KD, Shy ME, de Jonghe P, Chinnery PF, Horvath R, Kohlhase J, Schmitt I, Wolf M, Greschus S, Amunts K, Maier W, Schöls L, Nürnberg P, Zuchner S, Klockgether T, Ramirez A, Schüle R. Hypomorphic mutations in POLR3A are a frequent cause of sporadic and recessive spastic ataxia. Brain 2017; 140:1561-1578. [PMID: 28459997 PMCID: PMC6402316 DOI: 10.1093/brain/awx095] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 02/08/2017] [Accepted: 02/26/2017] [Indexed: 11/12/2022] Open
Abstract
Despite extensive efforts, half of patients with rare movement disorders such as hereditary spastic paraplegias and cerebellar ataxias remain genetically unexplained, implicating novel genes and unrecognized mutations in known genes. Non-coding DNA variants are suspected to account for a substantial part of undiscovered causes of rare diseases. Here we identified mutations located deep in introns of POLR3A to be a frequent cause of hereditary spastic paraplegia and cerebellar ataxia. First, whole-exome sequencing findings in a recessive spastic ataxia family turned our attention to intronic variants in POLR3A, a gene previously associated with hypomyelinating leukodystrophy type 7. Next, we screened a cohort of hereditary spastic paraplegia and cerebellar ataxia cases (n = 618) for mutations in POLR3A and identified compound heterozygous POLR3A mutations in ∼3.1% of index cases. Interestingly, >80% of POLR3A mutation carriers presented the same deep-intronic mutation (c.1909+22G>A), which activates a cryptic splice site in a tissue and stage of development-specific manner and leads to a novel distinct and uniform phenotype. The phenotype is characterized by adolescent-onset progressive spastic ataxia with frequent occurrence of tremor, involvement of the central sensory tracts and dental problems (hypodontia, early onset of severe and aggressive periodontal disease). Instead of the typical hypomyelination magnetic resonance imaging pattern associated with classical POLR3A mutations, cases carrying c.1909+22G>A demonstrated hyperintensities along the superior cerebellar peduncles. These hyperintensities may represent the structural correlate to the cerebellar symptoms observed in these patients. The associated c.1909+22G>A variant was significantly enriched in 1139 cases with spastic ataxia-related phenotypes as compared to unrelated neurological and non-neurological phenotypes and healthy controls (P = 1.3 × 10-4). In this study we demonstrate that (i) autosomal-recessive mutations in POLR3A are a frequent cause of hereditary spastic ataxias, accounting for about 3% of hitherto genetically unclassified autosomal recessive and sporadic cases; and (ii) hypomyelination is frequently absent in POLR3A-related syndromes, especially when intronic mutations are present, and thus can no longer be considered as the unifying feature of POLR3A disease. Furthermore, our results demonstrate that substantial progress in revealing the causes of Mendelian diseases can be made by exploring the non-coding sequences of the human genome.
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Affiliation(s)
- Martina Minnerop
- Institute of Neuroscience and Medicine (INM-1), Research Centre Juelich,
52425 Jülich, Germany
- Department of Neurology, University of Bonn, 53127 Bonn, Germany
| | - Delia Kurzwelly
- Department of Neurology, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
| | - Holger Wagner
- Department of Psychiatry and Psychotherapy, University of Bonn, 53127
Bonn, Germany
| | - Anne S Soehn
- Institute of Medical Genetics and Applied Genomics, University of
Tübingen, 72076 Tübingen, Germany
| | - Jennifer Reichbauer
- Center for Neurology and Hertie Institute for Clinical Brain Research,
University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
| | - Feifei Tao
- Dr. John T. Macdonald Foundation Department of Human Genetics and John
P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine,
Miami, Florida 33136, USA
| | - Tim W Rattay
- Center for Neurology and Hertie Institute for Clinical Brain Research,
University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
| | - Michael Peitz
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
- Institute of Reconstructive Neurobiology, Life and Brain Center, 53127
Bonn, Germany
| | - Kristina Rehbach
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
- Institute of Reconstructive Neurobiology, Life and Brain Center, 53127
Bonn, Germany
| | - Alejandro Giorgetti
- Computational Biophysics, German Research School for Simulation
Sciences, and Computational Biomedicine, Institute for Advanced Simulation (IAS-5) and
Institute of Neuroscience and Medicine (INM-9), Research Centre Juelich, 52425 Jülich,
Germany
- Department of Biotechnology, University of Verona, 37134 Verona,
Italy
| | - Angela Pyle
- Institute of Genetic Medicine, Newcastle University, Newcastle upon
Tyne NE1 3BZ, UK
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, 50931
Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, 50931
Cologne, Germany
- Institute of Human Genetics, University Hospital of Cologne, 50931
Cologne, Germany
| | - Dagmar Timmann
- Department of Neurology, University of Duisburg-Essen, 45147 Essen,
Germany
| | - Ilker Karaca
- Department of Psychiatry and Psychotherapy, University of Bonn, 53127
Bonn, Germany
| | - Martina Lennarz
- Department of Psychiatry and Psychotherapy, University of Bonn, 53127
Bonn, Germany
| | - Jonathan Baets
- Neurogenetics Group, VIB-Department of Molecular Genetics, VIB, 2610
Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, 2650 Antwerp,
Belgium
- Institute Born-Bunge, University of Antwerp, 2610 Antwerp,
Belgium
| | - Holger Hengel
- Center for Neurology and Hertie Institute for Clinical Brain Research,
University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
| | - Matthis Synofzik
- Center for Neurology and Hertie Institute for Clinical Brain Research,
University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
| | - Burcu Atasu
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical
Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Shawna Feely
- Department of Neurology, University of Iowa, 52242 Iowa, USA
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord
NSW 2139, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord NSW 2139,
Australia
- Sydney Medical School, University of Sydney, Sydney NSW 2006,
Australia
| | - Claudia Stendel
- Department of Neurology, Friedrich-Baur-Institute,
Ludwig-Maximilians-Universität, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 81337 Munich,
Germany
| | - Tobias Lindig
- Department of Diagnostic and Interventional Neuroradiology, University
Hospital Tübingen, 72076 Tübingen, Germany
| | - Michael A Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics and John
P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine,
Miami, Florida 33136, USA
| | - Rüdiger Stirnberg
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of
Tübingen, 72076 Tübingen, Germany
| | - Sandra Roeske
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
| | - Johanna Jung
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of
Tübingen, 72076 Tübingen, Germany
| | - Ebba Lohmann
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
- Department of Neurology, Antwerp University Hospital, 2650 Antwerp,
Belgium
- Behavioural Neurology and Movement Disorders Unit, Department of
Neurology, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, 53127 Bonn,
Germany
- Department of Genomics, Life and Brain Center, University of Bonn,
53127, Bonn, Germany
- Division of Medical Genetics, University Hospital and Department of
Biomedicine, University of Basel, CH-4058, Basel, Switzerland
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, 53127 Bonn,
Germany
- Department of Genomics, Life and Brain Center, University of Bonn,
53127, Bonn, Germany
| | - Garth Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord
NSW 2139, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord NSW 2139,
Australia
- Sydney Medical School, University of Sydney, Sydney NSW 2006,
Australia
| | - Muhammad Mahanjah
- Child Neurology and Development Center, Hillel-Yaffe Medical Center,
38100 Hadera, Israel
- Bruce and Ruth Rappaport Faculty of Medicine, Technion, 31096 Haifa,
Israel
| | - Rajech Sharkia
- The Triangle Regional Research and Development Center, P. O. Box-2167,
Kfar Qari’ 30075, Israel
- Beit-Berl Academic College, Beit-Berl 44905, Israel
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation
Sciences, and Computational Biomedicine, Institute for Advanced Simulation (IAS-5) and
Institute of Neuroscience and Medicine (INM-9), Research Centre Juelich, 52425 Jülich,
Germany
| | - Oliver Brüstle
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
- Institute of Reconstructive Neurobiology, Life and Brain Center, 53127
Bonn, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute,
Ludwig-Maximilians-Universität, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 81337 Munich,
Germany
- Munich Cluster of Systems Neurology (SyNergy), 80336 Munich,
Germany
| | - Katherine D Mathews
- Department of Pediatrics, Carver College of Medicine, University of
Iowa, 52242 Iowa, USA
| | - Michael E Shy
- Department of Neurology, University of Iowa, 52242 Iowa, USA
| | - Peter de Jonghe
- Neurogenetics Group, VIB-Department of Molecular Genetics, VIB, 2610
Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, 2650 Antwerp,
Belgium
- Institute Born-Bunge, University of Antwerp, 2610 Antwerp,
Belgium
| | - Patrick F Chinnery
- Institute of Genetic Medicine, Newcastle University, Newcastle upon
Tyne NE1 3BZ, UK
- Department of Clinical Neurosciences, Cambridge Biomedical Campus,
University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rita Horvath
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic
Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | | | - Ina Schmitt
- Department of Neurology, University of Bonn, 53127 Bonn, Germany
| | - Michael Wolf
- Departement of Orthodontics, University of Bonn, 53111 Bonn,
Germany
| | - Susanne Greschus
- Department of Radiology, University of Bonn, 53127 Bonn, Germany
| | - Katrin Amunts
- Institute of Neuroscience and Medicine (INM-1), Research Centre Juelich,
52425 Jülich, Germany
- C. & O. Vogt-Institute of Brain Research, University of Düsseldorf,
40212 Düsseldorf, Germany
| | - Wolfgang Maier
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
- Department of Psychiatry and Psychotherapy, University of Bonn, 53127
Bonn, Germany
| | - Ludger Schöls
- Center for Neurology and Hertie Institute for Clinical Brain Research,
University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
| | - Peter Nürnberg
- Institute of Neuroscience and Medicine (INM-1), Research Centre Juelich,
52425 Jülich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne,
50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in
Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John
P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine,
Miami, Florida 33136, USA
| | - Thomas Klockgether
- Department of Neurology, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn,
Germany
| | - Alfredo Ramirez
- Department of Psychiatry and Psychotherapy, University of Bonn, 53127
Bonn, Germany
- Institute of Human Genetics, University of Bonn, 53127 Bonn,
Germany
- Department of Psychiatry and Psychotherapy, University of Cologne,
50937 Cologne, Germany
| | - Rebecca Schüle
- Center for Neurology and Hertie Institute for Clinical Brain Research,
University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen,
Germany
- Dr. John T. Macdonald Foundation Department of Human Genetics and John
P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine,
Miami, Florida 33136, USA
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22
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Choquet K, Yang S, Moir RD, Forget D, Larivière R, Bouchard A, Poitras C, Sgarioto N, Dicaire MJ, Noohi F, Kennedy TE, Rochford J, Bernard G, Teichmann M, Coulombe B, Willis IM, Kleinman CL, Brais B. Absence of neurological abnormalities in mice homozygous for the Polr3a G672E hypomyelinating leukodystrophy mutation. Mol Brain 2017; 10:13. [PMID: 28407788 PMCID: PMC5391615 DOI: 10.1186/s13041-017-0294-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/04/2017] [Indexed: 01/08/2023] Open
Abstract
Recessive mutations in the ubiquitously expressed POLR3A gene cause one of the most frequent forms of childhood-onset hypomyelinating leukodystrophy (HLD): POLR3-HLD. POLR3A encodes the largest subunit of RNA Polymerase III (Pol III), which is responsible for the transcription of transfer RNAs (tRNAs) and a large array of other small non-coding RNAs. In order to study the central nervous system pathophysiology of the disease, we introduced the French Canadian founder Polr3a mutation c.2015G > A (p.G672E) in mice, generating homozygous knock-in (KI/KI) as well as compound heterozygous mice for one Polr3a KI and one null allele (KI/KO). Both KI/KI and KI/KO mice are viable and are able to reproduce. To establish if they manifest a motor phenotype, WT, KI/KI and KI/KO mice were submitted to a battery of behavioral tests over one year. The KI/KI and KI/KO mice have overall normal balance, muscle strength and general locomotion. Cerebral and cerebellar Luxol Fast Blue staining and measurement of levels of myelin proteins showed no significant differences between the three groups, suggesting that myelination is not overtly impaired in Polr3a KI/KI and KI/KO mice. Finally, expression levels of several Pol III transcripts in the brain showed no statistically significant differences. We conclude that the first transgenic mice with a leukodystrophy-causing Polr3a mutation do not recapitulate the childhood-onset HLD observed in the majority of human patients with POLR3A mutations, and provide essential information to guide selection of Polr3a mutations for developing future mouse models of the disease.
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Affiliation(s)
- Karine Choquet
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada.,Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Sharon Yang
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Robyn D Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Diane Forget
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Roxanne Larivière
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Annie Bouchard
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Christian Poitras
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Nicolas Sgarioto
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Marie-Josée Dicaire
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | - Forough Noohi
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada.,Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Timothy E Kennedy
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada
| | | | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, and Pediatrics, McGill University, Montreal, Canada.,Department of Medical Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Martin Teichmann
- INSERM U1212 - CNRS UMR5320, Université de Bordeaux, Bordeaux, France
| | - Benoit Coulombe
- Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec, Canada.,Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec, Canada
| | - Ian M Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, 3801 University Street, room 622, Montréal, Québec, H3A 2B4, Canada. .,Department of Human Genetics, McGill University, Montréal, Québec, Canada.
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23
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Abstract
Although the zebrafish was initially developed as a model system to study embryonic development, it has gained increasing attention as an advantageous system to investigate human diseases, including intestinal disorders. Zebrafish embryos develop rapidly, and their digestive system is fully functional and visible by 5days post fertilization. There is a large degree of homology between the intestine of zebrafish and higher vertebrate organisms in terms of its cellular composition and function as both a digestive and immune organ. Furthermore, molecular pathways regulating injury and immune responses are highly conserved. In this chapter, we provide an overview of studies addressing developmental and physiological processes relevant to human intestinal disease. These studies include those related to congenital disorders, host-microbiota interactions, inflammatory diseases, motility disorders, and intestinal cancer. We also highlight the utility of zebrafish to functionally validate candidate genes identified through mutational analyses and genome-wide association studies, and discuss methodologies to investigate the intestinal biology that are unique to zebrafish.
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Affiliation(s)
- X Zhao
- University of Pennsylvania, Philadelphia, PA, United States
| | - M Pack
- University of Pennsylvania, Philadelphia, PA, United States
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24
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Natural Selection, Crypt Fitness, and Pol III Dependency in the Intestine. Cell Mol Gastroenterol Hepatol 2016; 2:714-715. [PMID: 28174745 PMCID: PMC5247341 DOI: 10.1016/j.jcmgh.2016.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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25
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Kieckhaefer JE, Lukovac S, Ye DZ, Lee D, Beetler DJ, Pack M, Kaestner KH. The RNA polymerase III subunit Polr3b is required for the maintenance of small intestinal crypts in mice. Cell Mol Gastroenterol Hepatol 2016; 2:783-795. [PMID: 28090567 PMCID: PMC5235342 DOI: 10.1016/j.jcmgh.2016.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND & AIMS The continuously self-renewing mammalian intestinal epithelium, with high cellular turnover, depends on adequate protein synthesis for its proliferative capacity. RNA polymerase III activity is closely related to cellular growth and proliferation. Here, we studied the role of Polr3b, a large RNA polymerase III subunit, in the mammalian intestinal epithelium. METHODS We derived mice with an intestinal epithelium-specific hypomorphic mutation of the Polr3b gene, using VillinCre-mediated gene ablation. Phenotypic consequences of the Polr3b mutation on the intestinal epithelium in mice were assessed using histological and molecular methodologies, including genetic lineage tracing. RESULTS The Polr3b mutation severely reduced survival and growth in mice during the first postnatal week, the period when the expansion of the intestinal epithelium, and thus the requirement for protein synthesis, are highest. The neonatal intestinal epithelium of Polr3bloxP/loxP;VillinCre mice was characterized by areas with reduced proliferation, abnormal epithelial architecture, loss of Wnt signaling and a dramatic increase in apoptotic cells in crypts. Genetic lineage tracing using Polr3bLoxP/LoxP;Rosa26-lox-stop-lox-YFP;VillinCre mice demonstrated that in surviving mutant mice, Polr3b-deficient dying crypts were progressively replaced by 'Cre-escaper' cells that had retained wild type Polr3b function. In addition, enteroids cultured from Polr3bloxP/loxP;VillinCre mice show reduced proliferative activity and increased apoptosis. CONCLUSIONS We provide evidence for an essential role of the Pol III subunit Polr3b in orchestrating the maintenance of the intestinal crypt during early postnatal development in mice.
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Affiliation(s)
- Julia E. Kieckhaefer
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sabina Lukovac
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Diana Z. Ye
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Dolim Lee
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Danielle J. Beetler
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Michael Pack
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Michael Pack, MD, University of Pennsylvania, Perelman School of Medicine, 1212 Biomedical Research Building II/III, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104. fax: (215) 898-9871.University of PennsylvaniaPerelman School of Medicine1212 Biomedical Research Building II/III421 Curie BoulevardPhiladelphiaPennsylvania 19104
| | - Klaus H. Kaestner
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Correspondence Address correspondence to: Klaus H. Kaestner, PhD, 12-126 Smilow Center for Translational Research, University of Pennsylvania, Perelman School of Medicine, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104. fax: (215) 573-5892.12-126 Smilow Center for Translational ResearchUniversity of PennsylvaniaPerelman School of Medicine3400 Civic Center BoulevardPhiladelphiaPennsylvania 19104
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26
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Rijal K, Maraia RJ. Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo. PLoS Genet 2016; 12:e1006253. [PMID: 27518095 PMCID: PMC4982682 DOI: 10.1371/journal.pgen.1006253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/21/2016] [Indexed: 01/18/2023] Open
Abstract
The ability of RNA polymerase (RNAP) III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC); they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT) mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease.
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Affiliation(s)
- Keshab Rijal
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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27
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RNA Polymerase III Advances: Structural and tRNA Functional Views. Trends Biochem Sci 2016; 41:546-559. [PMID: 27068803 DOI: 10.1016/j.tibs.2016.03.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 12/25/2022]
Abstract
RNA synthesis in eukaryotes is divided among three RNA polymerases (RNAPs). RNAP III transcribes hundreds of tRNA genes and fewer additional short RNA genes. We survey recent work on transcription by RNAP III including an atomic structure, mechanisms of action, interactions with chromatin and retroposons, and a conserved link between its activity and a tRNA modification that enhances mRNA decoding. Other new work suggests important mechanistic connections to oxidative stress, autoimmunity and cancer, embryonic stem cell pluripotency, and tissue-specific developmental effects. We consider that, for some of its complex functions, variation in RNAP III activity levels lead to nonuniform changes in tRNAs that can shift the translation profiles of key codon-biased mRNAs with resultant phenotypes or disease states.
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28
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Wei Y, Xu J, Zhang W, Wen Z, Liu F. RNA polymerase III component Rpc9 regulates hematopoietic stem and progenitor cell maintenance in zebrafish. Development 2016; 143:2103-10. [DOI: 10.1242/dev.126797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 04/25/2016] [Indexed: 12/18/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are capable of self-renewal and replenishing all lineages of blood cells throughout the lifetime and thus critical for tissue homeostasis. However, the mechanism regulating HSPC development is still incompletely understood. Here, we isolate a zebrafish mutant with defective T lymphopoiesis and positional cloning identifies that Rpc9, a component of DNA-directed RNA polymerase III (Pol III) complex, is responsible for the mutant phenotype. Further analysis shows that rpc9-deficiency leads to the impairment of HSPCs and their derivatives in zebrafish embryos. Excessive apoptosis is observed in the caudal hematopoietic tissue (CHT, the equivalent of fetal liver in mammals) of rpc9−/− embryos and the hematopoietic defects in rpc9−/− embryos can be fully rescued by suppression of p53. Thus, our work illustrate that Rpc9, a component of Pol III, plays an important tissue-specific role in HSPC maintenance during zebrafish embryogenesis and that it might be conserved across vertebrates including mammals.
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Affiliation(s)
- Yonglong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Xu
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Wenqing Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, China
| | - Zilong Wen
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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29
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Lobert VH, Mouradov D, Heath JK. Focusing the Spotlight on the Zebrafish Intestine to Illuminate Mechanisms of Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:411-37. [PMID: 27165364 DOI: 10.1007/978-3-319-30654-4_18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colorectal cancer, encompassing colon and rectal cancer, arises from the epithelial lining of the large bowel. It is most prevalent in Westernised societies and is increasing in frequency as the world becomes more industrialised. Unfortunately, metastatic colorectal cancer is not cured by chemotherapy and the annual number of deaths caused by colorectal cancer, currently 700,000, is expected to rise. Our understanding of the contribution that genetic mutations make to colorectal cancer, although incomplete, is reasonably well advanced. However, it has only recently become widely appreciated that in addition to the ongoing accumulation of genetic mutations, chronic inflammation also plays a critical role in the initiation and progression of this disease. While a robust and tractable genetic model of colorectal cancer in zebrafish, suitable for pre-clinical studies, is not yet available, the identification of genes required for the rapid proliferation of zebrafish intestinal epithelial cells during development has highlighted a number of essential genes that could be targeted to disable colorectal cancer cells. Moreover, appreciation of the utility of zebrafish to study intestinal inflammation is on the rise. In particular, zebrafish provide unique opportunities to investigate the impact of genetic and environmental factors on the integrity of intestinal epithelial barrier function. With currently available tools, the interplay between epigenetic regulators, intestinal injury, microbiota composition and innate immune cell mobilisation can be analysed in exquisite detail. This provides excellent opportunities to define critical events that could potentially be targeted therapeutically. Further into the future, the use of zebrafish larvae as hosts for xenografts of human colorectal cancer tissue, while still in its infancy, holds great promise that zebrafish could one day provide a practical, preclinical personalized medicine platform for the rapid assessment of the metastatic potential and drug-sensitivity of patient-derived cancers.
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Affiliation(s)
- Viola H Lobert
- Development and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379, Oslo, Norway
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Joan K Heath
- Development and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification. PLoS Genet 2015; 11:e1005671. [PMID: 26720005 PMCID: PMC4697793 DOI: 10.1371/journal.pgen.1005671] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/26/2015] [Indexed: 11/19/2022] Open
Abstract
Control of the differential abundance or activity of tRNAs can be important determinants of gene regulation. RNA polymerase (RNAP) III synthesizes all tRNAs in eukaryotes and it derepression is associated with cancer. Maf1 is a conserved general repressor of RNAP III under the control of the target of rapamycin (TOR) that acts to integrate transcriptional output and protein synthetic demand toward metabolic economy. Studies in budding yeast have indicated that the global tRNA gene activation that occurs with derepression of RNAP III via maf1-deletion is accompanied by a paradoxical loss of tRNA-mediated nonsense suppressor activity, manifested as an antisuppression phenotype, by an unknown mechanism. We show that maf1-antisuppression also occurs in the fission yeast S. pombe amidst general activation of RNAP III. We used tRNA-HydroSeq to document that little changes occurred in the relative levels of different tRNAs in maf1Δ cells. By contrast, the efficiency of N2,N2-dimethyl G26 (m(2)2G26) modification on certain tRNAs was decreased in response to maf1-deletion and associated with antisuppression, and was validated by other methods. Over-expression of Trm1, which produces m(2)2G26, reversed maf1-antisuppression. A model that emerges is that competition by increased tRNA levels in maf1Δ cells leads to m(2)2G26 hypomodification due to limiting Trm1, reducing the activity of suppressor-tRNASerUCA and accounting for antisuppression. Consistent with this, we show that RNAP III mutations associated with hypomyelinating leukodystrophy decrease tRNA transcription, increase m(2)2G26 efficiency and reverse antisuppression. Extending this more broadly, we show that a decrease in tRNA synthesis by treatment with rapamycin leads to increased m(2)2G26 modification and that this response is conserved among highly divergent yeasts and human cells.
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Arimbasseri AG, Rijal K, Maraia RJ. Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation. Transcription 2015; 5:e27639. [PMID: 25764110 DOI: 10.4161/trns.27369] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, RNA polymerase (RNAP) III transcribes hundreds of genes for tRNAs and 5S rRNA, among others, which share similar promoters and stable transcription initiation complexes (TIC), which support rapid RNAP III recycling. In contrast, RNAP II transcribes a large number of genes with highly variable promoters and interacting factors, which exert fine regulatory control over TIC lability and modifications of RNAP II at different transitional points in the transcription cycle. We review data that illustrate a relatively smooth continuity of RNAP III initiation-elongation-termination and reinitiation toward its function to produce high levels of tRNAs and other RNAs that support growth and development.
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Affiliation(s)
- Aneeshkumar G Arimbasseri
- a Intramural Research Program; Eunice Kennedy Shriver National Institute of Child Health and Human Development; National Institutes of Health; Bethesda, MD USA
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Grewal SS. Why should cancer biologists care about tRNAs? tRNA synthesis, mRNA translation and the control of growth. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:898-907. [PMID: 25497380 DOI: 10.1016/j.bbagrm.2014.12.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
Transfer RNAs (tRNAs) are essential for mRNA translation. They are transcribed in the nucleus by RNA polymerase III and undergo many modifications before contributing to cytoplasmic protein synthesis. In this review I highlight our understanding of how tRNA biology may be linked to the regulation of mRNA translation, growth and tumorigenesis. First, I review how oncogenes and tumour suppressor signalling pathways, such as the PI3 kinase/TORC1, Ras/ERK, Myc, p53 and Rb pathways, regulate Pol III and tRNA synthesis. In several cases, this regulation contributes to cell, tissue and body growth, and has implications for our understanding of tumorigenesis. Second, I highlight some recent work, particularly in model organisms such as yeast and Drosophila, that shows how alterations in tRNA synthesis may be not only necessary, but also sufficient to drive changes in mRNA translation and growth. These effects may arise due to both absolute increases in total tRNA levels, but also changes in the relative levels of tRNAs in the overall pool. Finally, I review some recent studies that have revealed how tRNA modifications (amino acid acylation, base modifications, subcellular shuttling, and cleavage) can be regulated by growth and stress cues to selectively influence mRNA translation. Together these studies emphasize the importance of the regulation of tRNA synthesis and modification as critical control points in protein synthesis and growth. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Savraj S Grewal
- Department of Biochemistry and Molecular Biology, Clark H. Smith Brain Tumour Centre, Southern Alberta Cancer Research Institute, University of Calgary, HRIC, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada.
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Rijal K, Maraia RJ, Arimbasseri AG. A methods review on use of nonsense suppression to study 3' end formation and other aspects of tRNA biogenesis. Gene 2014; 556:35-50. [PMID: 25447915 DOI: 10.1016/j.gene.2014.11.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 12/26/2022]
Abstract
Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to Schizosaccharomyces pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5' and 3' processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3' oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3' oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a 'technical approaches' section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses.
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Affiliation(s)
- Keshab Rijal
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Aneeshkumar G Arimbasseri
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Qin W, Chen Z, Zhang Y, Yan R, Yan G, Li S, Zhong H, Lin S. Nom1 mediates pancreas development by regulating ribosome biogenesis in zebrafish. PLoS One 2014; 9:e100796. [PMID: 24967912 PMCID: PMC4072693 DOI: 10.1371/journal.pone.0100796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022] Open
Abstract
Ribosome biogenesis is an important biological process for proper cellular function and development. Defects leading to improper ribosome biogenesis can cause diseases such as Diamond-Blackfan anemia and Shwachman-Bodian-Diamond syndrome. Nucleolar proteins are a large family of proteins and are involved in many cellular processes, including the regulation of ribosome biogenesis. Through a forward genetic screen and positional cloning, we identified and characterized a zebrafish line carrying mutation in nucleolar protein with MIF4G domain 1 (nom1), which encodes a conserved nulceolar protein with a role in pre-rRNA processing. Zebrafish nom1 mutants exhibit major defects in endoderm development, especially in exocrine pancreas. Further studies revealed that impaired proliferation of ptf1a-expressing pancreatic progenitor cells mainly contributed to the phenotype. RNA-seq and molecular analysis showed that ribosome biogenesis and pre-mRNA splicing were both affected in the mutant embryos. Several defects of ribosome assembly have been shown to have a p53-dependent mechanism. In the nom1 mutant, loss of p53 did not rescue the pancreatic defect, suggesting a p53-independent role. Further studies indicate that protein phosphatase 1 alpha, an interacting protein to Nom1, could partially rescue the pancreatic defect in nom1 morphants if a human nucleolar localization signal sequence was artificially added. This suggests that targeting Pp1α into the nucleolus by Nom1 is important for pancreatic proliferation. Altogether, our studies revealed a new mechanism involving Nom1 in controlling vertebrate exocrine pancreas formation.
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Affiliation(s)
- Wei Qin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zelin Chen
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yihan Zhang
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Guanrong Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Song Li
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Hanbing Zhong
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
| | - Shuo Lin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Shimojima K, Shimada S, Tamasaki A, Akaboshi S, Komoike Y, Saito A, Furukawa T, Yamamoto T. Novel compound heterozygous mutations of POLR3A revealed by whole-exome sequencing in a patient with hypomyelination. Brain Dev 2014; 36:315-21. [PMID: 23694757 DOI: 10.1016/j.braindev.2013.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 04/16/2013] [Accepted: 04/23/2013] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Congenital white matter disorders are a heterogeneous group of hypomyelination disorders affecting the white matter of the brain. Recently, mutations in the genes encoding the subunits of RNA polymerase III (Pol III), POLR3A and POLR3B, have been identified as new genetic causes for hypomyelinating disorders. METHOD Whole-exome sequencing was applied to identify responsible gene mutations in a 29-year-old female patient showing hypomyelination of unknown cause. To investigate the pathological mechanism underlying the hypomyelination in this patient, the expression level of 7SL RNA, a transcriptional target of Pol III, was analyzed in cultured skin fibroblasts derived from the patient with POLR3A mutations. RESULTS Novel compound heterozygous mutations of POLR3A were identified in the patient, who started to show cerebellar signs at 3 years, lost ambulation at 7 years, and became bedridden at 18 years. Brain magnetic resonance imaging showed severe volume loss in the brainstem, the cerebellum, and the white matter associated with hypomyelination. In addition to hypodontia and hypogonadism, she showed many pituitary hormone-related deficiencies. The expression level of 7SL RNA in cultured skin fibroblasts derived from this patient showed no significant abnormality. CONCLUSION The many pituitary hormone-related deficiencies identified in this patient may be an essential finding for the Pol III-related leukodystrophies spectrum. Further investigation is needed for a better understanding of the disease mechanism.
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Affiliation(s)
- Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo 162-8666, Japan
| | - Shino Shimada
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo 162-8666, Japan; Department of Pediatrics, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Akiko Tamasaki
- Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Shinjiro Akaboshi
- Department of Pediatrics, National Hospital Organization Tottori Medical Center, Tottori 689-0203, Japan
| | - Yuta Komoike
- Department of Hygiene and Public Health, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | | | - Toru Furukawa
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo 162-8666, Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo 162-8666, Japan.
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Yee NS, Kazi AA, Yee RK. Translating discovery in zebrafish pancreatic development to human pancreatic cancer: biomarkers, targets, pathogenesis, and therapeutics. Zebrafish 2013; 10:132-46. [PMID: 23682805 DOI: 10.1089/zeb.2012.0817] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Abstract Experimental studies in the zebrafish have greatly facilitated understanding of genetic regulation of the early developmental events in the pancreas. Various approaches using forward and reverse genetics, chemical genetics, and transgenesis in zebrafish have demonstrated generally conserved regulatory roles of mammalian genes and discovered novel genetic pathways in exocrine pancreatic development. Accumulating evidence has supported the use of zebrafish as a model of human malignant diseases, including pancreatic cancer. Studies have shown that the genetic regulators of exocrine pancreatic development in zebrafish can be translated into potential clinical biomarkers and therapeutic targets in human pancreatic adenocarcinoma. Transgenic zebrafish expressing oncogenic K-ras and zebrafish tumor xenograft model have emerged as valuable tools for dissecting the pathogenetic mechanisms of pancreatic cancer and for drug discovery and toxicology. Future analysis of the pancreas in zebrafish will continue to advance understanding of the genetic regulation and biological mechanisms during organogenesis. Results of those studies are expected to provide new insights into how aberrant developmental pathways contribute to formation and growth of pancreatic neoplasia, and hopefully generate valid biomarkers and targets as well as effective and safe therapeutics in pancreatic cancer.
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Affiliation(s)
- Nelson S Yee
- Division of Hematology-Oncology, Program of Experimental Therapeutics, Department of Medicine, Penn State Milton S. Hershey Medical Center, Penn State College of Medicine, Penn State Hershey Cancer Institute, Pennsylvania State University , Hershey, PA 17033-0850, USA.
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Arimbasseri AG, Rijal K, Maraia RJ. Transcription termination by the eukaryotic RNA polymerase III. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:318-30. [PMID: 23099421 PMCID: PMC3568203 DOI: 10.1016/j.bbagrm.2012.10.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/15/2012] [Accepted: 10/16/2012] [Indexed: 01/22/2023]
Abstract
RNA polymerase (pol) III transcribes a multitude of tRNA and 5S rRNA genes as well as other small RNA genes distributed through the genome. By being sequence-specific, precise and efficient, transcription termination by pol III not only defines the 3' end of the nascent RNA which directs subsequent association with the stabilizing La protein, it also prevents transcription into downstream DNA and promotes efficient recycling. Each of the RNA polymerases appears to have evolved unique mechanisms to initiate the process of termination in response to different types of termination signals. However, in eukaryotes much less is known about the final stage of termination, destabilization of the elongation complex with release of the RNA and DNA from the polymerase active center. By comparison to pols I and II, pol III exhibits the most direct coupling of the initial and final stages of termination, both of which occur at a short oligo(dT) tract on the non-template strand (dA on the template) of the DNA. While pol III termination is autonomous involving the core subunits C2 and probably C1, it also involves subunits C11, C37 and C53, which act on the pol III catalytic center and exhibit homology to the pol II elongation factor TFIIS and TFIIFα/β respectively. Here we compile knowledge of pol III termination and associate mutations that affect this process with structural elements of the polymerase that illustrate the importance of C53/37 both at its docking site on the pol III lobe and in the active center. The models suggest that some of these features may apply to the other eukaryotic pols. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Yee NS. Toward the goal of personalized therapy in pancreatic cancer by targeting the molecular phenotype. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 779:91-143. [PMID: 23288637 DOI: 10.1007/978-1-4614-6176-0_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The purpose of this article is to provide a critical review of the molecular alterations in pancreatic cancer that are clinically investigated as therapeutic targets and their potential impact on clinical outcomes. Adenocarcinoma of exocrine pancreas is generally associated with poor prognosis and the conventional therapies are marginally effective. Advances in understanding the genetic regulation of normal and neoplastic development of pancreas have led to development and clinical evaluation of new therapeutic strategies that target the signaling pathways and molecular alterations in pancreatic cancer. Applications have begun to utilize the genetic targets as biomarkers for prediction of therapeutic responses and selection of treatment options. The goal of accomplishing personalized tumor-specific therapy with tolerable side effects for patients with pancreatic cancer is hopefully within reach in the foreseeable future.
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Affiliation(s)
- Nelson S Yee
- Division of Hematology-Oncology, Department of Medicine, Penn State College of Medicine, Penn State Hershey Cancer Institute, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, PA 17033-0850, USA.
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Yunlei Z, Zhe C, Yan L, Pengcheng W, Yanbo Z, Le S, Qianjin L. INMAP, a novel truncated version of POLR3B, represses AP-1 and p53 transcriptional activity. Mol Cell Biochem 2012; 374:81-9. [PMID: 23124897 DOI: 10.1007/s11010-012-1507-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 10/25/2012] [Indexed: 12/17/2022]
Abstract
INMAP was first identified as an interphase nucleus and mitotic apparatus-associated protein that plays essential roles in the formation of the spindle and cell-cycle progression. Here, we report that INMAP might be conserved from prokaryotes to humans, is a truncated version of the RNA polymerase III subunit B POLR3B, and is up-regulated in several human cancer cell lines including HeLa, Bel-7402, HepG2 and BGC-823. Deletion analysis revealed that the 209-290 amino-acid region is necessary for the punctate distribution of INMAP in the nucleus. Furthermore, over-expression of INMAP inhibited the transcriptional activities of p53 and AP-1 in a dose-dependent manner. These results suggest that INMAP may function through the p53 and AP-1 pathways, thus providing a possible link of its activity with tumourigenesis. Integrating our data and those in previous studies, it can be concluded that INMAP plays dual functional roles in the coordination of mitotic kinetics with gene expression as well as in cell-fate determination and proliferation.
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Affiliation(s)
- Zhou Yunlei
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, 100875, People's Republic of China
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Yee NS, Chan AS, Yee JD, Yee RK. TRPM7 and TRPM8 Ion Channels in Pancreatic Adenocarcinoma: Potential Roles as Cancer Biomarkers and Targets. SCIENTIFICA 2012; 2012:415158. [PMID: 24278689 PMCID: PMC3820452 DOI: 10.6064/2012/415158] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/08/2012] [Indexed: 06/01/2023]
Abstract
Transient receptor potential (TRP) ion channels are essential for normal functions and health by acting as molecular sensors and transducing various stimuli into cellular and physiological responses. Growing evidence has revealed that TRP ion channels play important roles in a wide range of human diseases, including malignancies. In light of recent discoveries, it has been found that TRP melastatin-subfamily members, TRPM7 and TRPM8, are required for normal and cancerous development of exocrine pancreas. We are currently investigating the mechanisms which mediate the functional roles of TRPM7 and TRPM8 and attempting to develop these ion channels as clinical biomarkers and therapeutic targets for achieving the goal of personalized therapy in pancreatic cancer.
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Affiliation(s)
- Nelson S. Yee
- Division of Hematology-Oncology, Department of Medicine, Penn State College of Medicine, Penn State Hershey Cancer Institute, Penn State Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, PA 17033-0850, USA
| | - Ada S. Chan
- Division of Hematology-Oncology, Department of Medicine, Penn State College of Medicine, Penn State Hershey Cancer Institute, Penn State Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, PA 17033-0850, USA
| | - Julian D. Yee
- Division of Hematology-Oncology, Department of Medicine, Penn State College of Medicine, Penn State Hershey Cancer Institute, Penn State Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, PA 17033-0850, USA
| | - Rosemary K. Yee
- Penn State Harrisburg School of Humanities, Pennsylvania State University, Middletown, PA 17057, USA
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Hozumi S, Hirabayashi R, Yoshizawa A, Ogata M, Ishitani T, Tsutsumi M, Kuroiwa A, Itoh M, Kikuchi Y. DEAD-box protein Ddx46 is required for the development of the digestive organs and brain in zebrafish. PLoS One 2012; 7:e33675. [PMID: 22442707 PMCID: PMC3307747 DOI: 10.1371/journal.pone.0033675] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 02/14/2012] [Indexed: 01/12/2023] Open
Abstract
Spatially and temporally controlled gene expression, including transcription, several mRNA processing steps, and the export of mature mRNA to the cytoplasm, is essential for developmental processes. It is well known that RNA helicases of the DExD/H-box protein family are involved in these gene expression processes, including transcription, pre-mRNA splicing, and rRNA biogenesis. Although one DExD/H-box protein, Prp5, a homologue of vertebrate Ddx46, has been shown to play important roles in pre-mRNA splicing in yeast, the in vivo function of Ddx46 remains to be fully elucidated in metazoans. In this study, we isolated zebrafish morendo (mor), a mutant that shows developmental defects in the digestive organs and brain, and found that it encodes Ddx46. The Ddx46 transcript is maternally supplied, and as development proceeds in zebrafish larvae, its ubiquitous expression gradually becomes restricted to those organs. The results of whole-mount in situ hybridization showed that the expression of various molecular markers in these organs is considerably reduced in the Ddx46 mutant. Furthermore, splicing status analysis with RT-PCR revealed unspliced forms of mRNAs in the digestive organ and brain tissues of the Ddx46 mutant, suggesting that Ddx46 may be required for pre-mRNA splicing during zebrafish development. Therefore, our results suggest a model in which zebrafish Ddx46 is required for the development of the digestive organs and brain, possibly through the control of pre-mRNA splicing.
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Affiliation(s)
- Shunya Hozumi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Ryo Hirabayashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akio Yoshizawa
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Mitsuko Ogata
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Tohru Ishitani
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Makiko Tsutsumi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Motoyuki Itoh
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
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Yee NS, Zhou W, Chun SG, Liang IC, Yee RK. Targeting developmental regulators of zebrafish exocrine pancreas as a therapeutic approach in human pancreatic cancer. Biol Open 2012; 1:295-307. [PMID: 23213420 PMCID: PMC3509454 DOI: 10.1242/bio.2012539] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Histone deacetylases (HDACs) and RNA polymerase III (POLR3) play vital roles in fundamental cellular processes, and deregulation of these enzymes has been implicated in malignant transformation. Hdacs and Polr3 are required for exocrine pancreatic epithelial proliferation during morphogenesis in zebrafish. We aim to test the hypothesis that Hdacs and Polr3 cooperatively control exocrine pancreatic growth, and combined inhibition of HDACs and POLR3 produces enhanced growth suppression in pancreatic cancer. In zebrafish larvae, combination of a Hdac inhibitor (Trichostatin A) and an inhibitor of Polr3 (ML-60218) synergistically prohibited the expansion of exocrine pancreas. In human pancreatic adenocarcinoma cells, combination of the HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) and ML-60218 produced augmented suppression of colony formation and proliferation, and induction of cell cycle arrest and apoptotic cell death. The enhanced cytotoxicity was associated with supra-additive upregulation of the pro-apoptotic regulator BAX and the cyclin-dependent kinase inhibitor p21CDKN1A. tRNAs have been shown to have pro-proliferative and anti-apoptotic roles, and SAHA-stimulated expression of tRNAs was reversed by ML-60218. These findings demonstrate that chemically targeting developmental regulators of exocrine pancreas can be translated into an approach with potential impact on therapeutic response in pancreatic cancer, and suggest that counteracting the pro-malignant side effect of HDAC inhibitors can enhance their anti-tumor activity.
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Affiliation(s)
- Nelson S Yee
- Division of Hematology-Oncology, Department of Medicine, Penn State College of Medicine; Penn State Hershey Cancer Institute; Penn State Milton S. Hershey Medical Center; The Pennsylvania State University, Hershey, PA 17033 , USA
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Wong RCB, Pollan S, Fong H, Ibrahim A, Smith EL, Ho M, Laslett AL, Donovan PJ. A novel role for an RNA polymerase III subunit POLR3G in regulating pluripotency in human embryonic stem cells. Stem Cells 2012; 29:1517-27. [PMID: 21898682 DOI: 10.1002/stem.714] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The pluripotency of human embryonic stem cells (hESC) could have great potential for the development of cell replacement therapies. Previous studies have converged on the finding that OCT4, SOX2, and NANOG serve as key regulators in the maintenance of hESC. However, other signals that regulate hESC maintenance remain poorly studied. Here we describe a novel role of an RNA polymerase III (Pol III) subunit, POLR3G, in the maintenance of pluripotency in hESC. We demonstrate the presence of POLR3G in undifferentiated hESC, human induced pluripotent stem cells (hiPSC), and early mouse blastocysts. Downregulation of POLR3G is observed on differentiation of hESC and hiPSC, suggesting that POLR3G can be used as a molecular marker to readily identify undifferentiated pluripotent stem cells from their differentiated derivatives. Using an inducible shRNA lentiviral system, we found evidence that decreased levels of POLR3G result in loss of pluripotency and promote differentiation of hESC to all three germ layers but have no effect on cell apoptosis. On the other hand, overexpression of POLR3G has no effect on pluripotency and apoptosis in undifferentiated hESC. Interestingly, hESC expressing elevated levels of POLR3G are more resistant to differentiation. Furthermore, our experimental results show that POLR3G is a downstream target of OCT4 and NANOG, and our pharmacological study indicated that POLR3G expression can be readily regulated by the Erk1/2 signaling pathway. This study is the first to show an important role of POLR3G in the maintenance of hESC, suggesting a potential role of Pol III transcription in regulating hESC pluripotency.
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Affiliation(s)
- Raymond Ching-Bong Wong
- Department of Biological Chemistry, University of California Irvine, Irvine, California, USA
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Saitsu H, Osaka H, Sasaki M, Takanashi JI, Hamada K, Yamashita A, Shibayama H, Shiina M, Kondo Y, Nishiyama K, Tsurusaki Y, Miyake N, Doi H, Ogata K, Inoue K, Matsumoto N. Mutations in POLR3A and POLR3B encoding RNA Polymerase III subunits cause an autosomal-recessive hypomyelinating leukoencephalopathy. Am J Hum Genet 2011; 89:644-51. [PMID: 22036171 DOI: 10.1016/j.ajhg.2011.10.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/05/2011] [Accepted: 10/10/2011] [Indexed: 11/30/2022] Open
Abstract
Congenital hypomyelinating disorders are a heterogeneous group of inherited leukoencephalopathies characterized by abnormal myelin formation. We have recently reported a hypomyelinating syndrome characterized by diffuse cerebral hypomyelination with cerebellar atrophy and hypoplasia of the corpus callosum (HCAHC). We performed whole-exome sequencing of three unrelated individuals with HCAHC and identified compound heterozygous mutations in POLR3B in two individuals. The mutations include a nonsense mutation, a splice-site mutation, and two missense mutations at evolutionally conserved amino acids. Using reverse transcription-PCR and sequencing, we demonstrated that the splice-site mutation caused deletion of exon 18 from POLR3B mRNA and that the transcript harboring the nonsense mutation underwent nonsense-mediated mRNA decay. We also identified compound heterozygous missense mutations in POLR3A in the remaining individual. POLR3A and POLR3B encode the largest and second largest subunits of RNA Polymerase III (Pol III), RPC1 and RPC2, respectively. RPC1 and RPC2 together form the active center of the polymerase and contribute to the catalytic activity of the polymerase. Pol III is involved in the transcription of small noncoding RNAs, such as 5S ribosomal RNA and all transfer RNAs (tRNA). We hypothesize that perturbation of Pol III target transcription, especially of tRNAs, could be a common pathological mechanism underlying POLR3A and POLR3B mutations.
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Affiliation(s)
- Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan.
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Abstract
The enteric nervous system (ENS) is composed of neurons and glia that modulate many aspects of intestinal function. The ability to use both forward and reverse genetic approaches and to visualize development in living embryos and larvae has made zebrafish an attractive model in which to study mechanisms underlying ENS development. In this chapter, we review the recent work describing the development and organization of the zebrafish ENS and how this relates to intestinal motility. We also discuss the cellular, molecular, and genetic mechanisms that have been revealed by these studies and how they are providing new insights into human ENS diseases.
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Affiliation(s)
- Iain Shepherd
- Department of Biology, Emory University Rollins Research Building, Atlanta, Georgia, USA
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Spencer VA, Costes S, Inman JL, Xu R, Chen J, Hendzel MJ, Bissell MJ. Depletion of nuclear actin is a key mediator of quiescence in epithelial cells. J Cell Sci 2011; 124:123-32. [PMID: 21172822 DOI: 10.1242/jcs.073197] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Functional differentiation is orchestrated by precise growth-regulatory controls conveyed by the tissue microenvironment. Cues from laminin 111 (LN1) lower transcription and suppress mammary epithelial cell growth in culture, but how LN1 induces quiescence is unknown. Recent literature points to involvement of nuclear β-actin in transcriptional regulation. Here, we show that quiescence induced by growth factor withdrawal, or LN1 addition, rapidly decreases nuclear β-actin. LN1, but not other extracellular matrix (ECM) molecules, decreases the levels of nuclear β-actin and destabilizes RNA polymerase (RNA Pol) II and III binding to transcription sites, leading to a dramatic drop in transcription and DNA synthesis. Constitutive overexpression of globular β-actin in the nucleus reverses the effect of LN1 on transcription and RNA Pol II association and prevents the cells from becoming quiescent in the presence of LN1. The physiological relevance of our findings was verified by identifying a clear spatial separation of LN1 and β-actin in developing mammary end buds. These data indicate a novel role for nuclear β-actin in growth arrest of epithelial cells and underscore the importance of the integrity of the basement membrane in homeostasis.
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Affiliation(s)
- Virginia A Spencer
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 977R225A, Berkeley, CA 94720, USA.
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Zhou W, Liang IC, Yee NS. Histone deacetylase 1 is required for exocrine pancreatic epithelial proliferation in development and cancer. Cancer Biol Ther 2011; 11:659-70. [PMID: 21301206 DOI: 10.4161/cbt.11.7.14720] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in the epigenetic control of development, and aberrant expression of HDACs has been implicated in human diseases including cancer. Among the mammalian HDACs, HDAC1 has been extensively studied, but its role in exocrine pancreatic morphogenesis and cancer is still poorly understood. The goal of this study is to determine the functional role of HDAC1 in normal development of exocrine pancreas using zebrafish as the model organism as well as in human pancreatic adenocarcinoma. The zebrafish germline loss-of-function mutation hdac1(hi1618) caused impaired cell cycle progression in pancreatic epithelia, resulting in growth arrest and dysmorphogenesis of exocrine pancreas. In human pancreatic adenocarcinoma tissues and cell lines, HDAC1 was expressed at variably elevated levels. RNA interference-induced silencing of HDAC1 diminished proliferation of the cancer cells and cell cycle progression. The proliferative arrest in the developing exocrine pancreas and pancreatic cancer cells was associated with up-regulated expression of the cyclin-dependent kinase inhibitors and the sonic hedgehog signaling components. This study indicates that HDAC1 is required for pancreatic epithelial proliferation in development and cancer. We hypothesize that aberrant expression of HDAC1 modulates the developmental and signaling pathways in exocrine pancreatic epithelia and consequently the genes required for cellular proliferation during development and progression of pancreatic neoplasia.
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Affiliation(s)
- Weiqiang Zhou
- Division of Hematology, Oncology and Blood & Marrow Transplantation, Department of Internal Medicine, Carver College of Medicine, Program of Cancer Signaling and Experimental Therapeutics, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, USA
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Iben JR, Mazeika JK, Hasson S, Rijal K, Arimbasseri AG, Russo AN, Maraia RJ. Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III. Nucleic Acids Res 2011; 39:6100-13. [PMID: 21450810 PMCID: PMC3152337 DOI: 10.1093/nar/gkr182] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl regions of C11 are homologous to domains of the pol II subunit Rpb9p, and the pol II elongation and RNA cleavage factor, TFIIS, respectively. We isolated C11 mutants from Schizosaccharomyces pombe that cause pol III to readthrough terminators in vivo. Mutant RNA confirmed the presence of terminator readthrough transcripts. A predominant mutation site, F32, resides in the C11 Rpb9-like domain. Another mutagenic approach confirmed the F32 mutation and also isolated I34 and Y30 mutants. Modeling Y30, F32 and I34 of C11 in available cryoEM pol III structures predicts a hydrophobic patch that may interface with C53/37. Another termination mutant, Rpc2-T455I, appears to reside internally, near the RNA-DNA hybrid. We show that the Rpb9 and TFIIS homologous mutants of C11 reflect distinct activities, that differentially affect terminator recognition and RNA 3' cleavage. We propose that these C11 domains integrate action at the upper jaw and center of pol III during termination.
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Affiliation(s)
- James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Commissioned Corps, US Public Health Service, Bethesda, MD, USA. 20892
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Marshall KE, Tomasini AJ, Makky K, N Kumar S, Mayer AN. Dynamic Lkb1-TORC1 signaling as a possible mechanism for regulating the endoderm-intestine transition. Dev Dyn 2011; 239:3000-12. [PMID: 20925120 DOI: 10.1002/dvdy.22437] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The intestinal epithelium arises from undifferentiated endoderm via a developmental program known as the endoderm-intestine transition (EIT). Previously we found that the target of rapamycin complex 1 (TORC1) regulates intestinal growth and differentiation during the EIT in zebrafish. Here we address a possible role for the tumor-suppressor kinase Lkb1 in regulating TORC1 in this context. We find that TORC1 activity is transiently upregulated during the EIT in both zebrafish and mouse. Concomitantly, Lkb1 becomes transiently localized to the nucleus, suggesting that these two phenomena may be linked. Morpholino-mediated knockdown of lkb1 stimulated intestinal growth via upregulation of TORC1, and also induced precocious intestine-specific gene expression in the zebrafish gut epithelium. Knockdown of tsc2, which acts downstream of lkb1, likewise induced early expression of intestine-specific genes. These data suggest that programmed localization of Lkb1 could represent a novel mechanism for regulating the EIT during intestinal development in vertebrates.
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Affiliation(s)
- Kathryn E Marshall
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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Yee NS, Zhou W, Liang IC. Transient receptor potential ion channel Trpm7 regulates exocrine pancreatic epithelial proliferation by Mg2+-sensitive Socs3a signaling in development and cancer. Dis Model Mech 2010; 4:240-54. [PMID: 21183474 PMCID: PMC3046099 DOI: 10.1242/dmm.004564] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic analysis of pancreatic development has provided new insights into the mechanisms underlying the formation of exocrine pancreatic neoplasia. Zebrafish sweetbread (swd) mutants develop hypoplastic acini and dysmorphic ducts in the exocrine pancreas, with impeded progression of cell division cycle and of epithelial growth. Positional cloning and allelic complementation have revealed that the swd mutations affect the transient receptor potential melastatin-subfamily member 7 (trpm7) gene, which encodes a divalent cation-permeable channel with kinase activity. Supplementary Mg(2+) partially rescued the exocrine pancreatic defects of the trpm7 mutants by improving cell-cycle progression and growth and repressing the suppressor of cytokine signaling 3a (socs3a) gene. The role of Socs3a in Trpm7-mediated signaling is supported by the findings that socs3a mRNA level is elevated in the trpm7 mutants, and antisense inhibition of socs3a expression improved their exocrine pancreatic growth. TRPM7 is generally overexpressed in human pancreatic adenocarcinoma. TRPM7-deficient cells are impaired in proliferation and arrested in the G0-G1 phases of the cell division cycle. Supplementary Mg(2+) rescued the proliferative defect of the TRPM7-deficient cells. Results of this study indicate that Trpm7 regulates exocrine pancreatic development via the Mg(2+)-sensitive Socs3a pathway, and suggest that aberrant TRPM7-mediated signaling contributes to pancreatic carcinogenesis.
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Affiliation(s)
- Nelson S Yee
- Division of Hematology, Oncology, and Blood & Marrow Transplantation, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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