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Hu H, Huang Y, Hou R, Xu H, Liu Y, Liao X, Xu J, Jiang L, Wang D. Xp22.31 copy number variations in 87 fetuses: refined genotype-phenotype correlations by prenatal and postnatal follow-up. BMC Med Genomics 2023; 16:69. [PMID: 37013593 PMCID: PMC10069036 DOI: 10.1186/s12920-023-01493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Xp22.31 deletion and duplication have been described in various studies, but different laboratories interpret pathogenicity differently. OBJECTIVES Our study aimed to refine the genotype-phenotype associations between Xp22.31 copy number variants in fetuses, with the aim of providing data support to genetic counseling. METHODS We retrospectively analyzed karyotyping and single nucleotide polymorphism array results from 87 fetuses and their family members. Phenotypic data were obtained through follow-up visits. RESULTS The percentage of fetuses carrying the Xp22.31 deletions (9 females, 12 males) was 24.1% (n = 21), while duplications (38 females, 28 males) accounted for 75.9% (n = 66). Here, we noted that the typical region (from 6.4 to 8.1 Mb, hg19) was detected in the highest ratio, either in the fetuses with deletions (76.2%, 16 of 21) or duplications (69.7%, 46 of 66). In female deletion carriers, termination of pregnancy was chosen for two fetuses, and the remaining seven were born without distinct phenotypic abnormalities. In male deletion carriers, termination of pregnancy was chosen for four fetuses, and the remaining eight of them displayed ichthyosis without neurodevelopmental anomalies. In two of these cases, the chromosomal imbalance was inherited from the maternal grandfathers, who also only had ichthyosis phenotypes. Among the 66 duplication carriers, two cases were lost at follow-up, and pregnancy was terminated for eight cases. There were no other clinical findings in the rest of the 56 fetuses, including two with Xp22.31 tetrasomy, for either male or female carriers. CONCLUSION Our observations provide support for genetic counseling in male and female carriers of Xp22.31 copy number variants. Most of them are asymptomatic in male deletion carriers, except for skin findings. Our study is consistent with the view that the Xp22.31 duplication may be a benign variant in both sexes.
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Affiliation(s)
- Huamei Hu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yulin Huang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Renke Hou
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Huanhuan Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yalan Liu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xueqian Liao
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Juchun Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lupin Jiang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
| | - Dan Wang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
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Pavone P, Corsello G, Marino S, Ruggieri M, Falsaperla R. Microcephaly/Trigonocephaly, Intellectual Disability, Autism Spectrum Disorder, and Atypical Dysmorphic Features in a Boy with Xp22.31 Duplication. Mol Syndromol 2018; 9:253-258. [PMID: 30733660 DOI: 10.1159/000493174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 12/23/2022] Open
Abstract
The Xp22.31 segment of the short arm of the human X chromosome is a region of high instability with frequent rearrangement. The duplication of this region has been found in healthy people as well as in individuals with varying degrees of neurological impairment. The incidence has been reported in a range of 0.4-0.44% of the patients with neurological impairment. Moreover, there is evidence that Xp22.31 duplication may cause a common phenotype including developmental delay, intellectual disability, feeding difficulty, autistic spectrum disorders, hypotonia, seizures, and talipes. We report on a patient with microcephaly and trigonocephaly, moderate intellectual disability, speech and language delay, and poor social interaction in addition to minor but atypical dysmorphic features. This report provides further insight into the pathogenicity of the Xp22.31 duplication by extending knowledge of its clinical features. This case, in association with those reported in the literature, indicates that the Xp22.31 duplication may contribute to cause pathological phenotypes with minor facial dysmorphisms, microcephaly, and intellectual disability as main features.
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Affiliation(s)
- Piero Pavone
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
| | - Giovanni Corsello
- Department of Maternal and Child Health, University of Palermo, Palermo, Italy
| | - Silvia Marino
- University Hospital, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System, Section of Pediatrics and Child Neuropsychiatry, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
| | - Raffaele Falsaperla
- University Hospital, A.U.O. Policlinico-Vittorio Emanuele Catania, Catania, Italy
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Addis L, Sproviero W, Thomas SV, Caraballo RH, Newhouse SJ, Gomez K, Hughes E, Kinali M, McCormick D, Hannan S, Cossu S, Taylor J, Akman CI, Wolf SM, Mandelbaum DE, Gupta R, van der Spek RA, Pruna D, Pal DK. Identification of new risk factors for rolandic epilepsy: CNV at Xp22.31 and alterations at cholinergic synapses. J Med Genet 2018; 55:607-616. [PMID: 29789371 PMCID: PMC6119347 DOI: 10.1136/jmedgenet-2018-105319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/18/2018] [Accepted: 04/28/2018] [Indexed: 12/25/2022]
Abstract
Background Rolandic epilepsy (RE) is the most common genetic childhood epilepsy, consisting of focal, nocturnal seizures and frequent neurodevelopmental impairments in speech, language, literacy and attention. A complex genetic aetiology is presumed in most, with monogenic mutations in GRIN2A accounting for >5% of cases. Objective To identify rare, causal CNV in patients with RE. Methods We used high-density SNP arrays to analyse the presence of rare CNVs in 186 patients with RE from the UK, the USA, Sardinia, Argentina and Kerala, India. Results We identified 84 patients with one or more rare CNVs, and, within this group, 14 (7.5%) with recurrent risk factor CNVs and 15 (8.0%) with likely pathogenic CNVs. Nine patients carried recurrent hotspot CNVs including at 16p13.11 and 1p36, with the most striking finding that four individuals (three from Sardinia) carried a duplication, and one a deletion, at Xp22.31. Five patients with RE carried a rare CNV that disrupted genes associated with other epilepsies (KCTD7, ARHGEF15, CACNA2D1, GRIN2A and ARHGEF4), and 17 cases carried CNVs that disrupted genes associated with other neurological conditions or that are involved in neuronal signalling/development. Network analysis of disrupted genes with high brain expression identified significant enrichment in pathways of the cholinergic synapse, guanine-exchange factor activation and the mammalian target of rapamycin. Conclusion Our results provide a CNV profile of an ethnically diverse cohort of patients with RE, uncovering new areas of research focus, and emphasise the importance of studying non-western European populations in oligogenic disorders to uncover a full picture of risk variation.
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Affiliation(s)
- Laura Addis
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,Neuroscience Discovery Research, Eli Lilly and Company, Surrey, UK
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sanjeev V Thomas
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, Kerala, India
| | - Roberto H Caraballo
- Department of Neurology, Hospital de Pediatría Prof. Dr. J.P. Garrahan, Combate de los Pozos 1881, Buenos Aires, Argentina
| | - Stephen J Newhouse
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Beckenham, UK.,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
| | - Kumudini Gomez
- Department of Paediatrics, University Hospital Lewisham, Lewisham and Greenwich NHS Trust, London, UK
| | - Elaine Hughes
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, London, UK
| | - Maria Kinali
- Department of Paediatric Neurology, Chelsea and Westminster Hospital, London, UK
| | - David McCormick
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, London, UK
| | - Siobhan Hannan
- Department of Paediatric Neurology, Chelsea and Westminster Hospital, London, UK
| | - Silvia Cossu
- Neurosurgery Unit, Neuroscience and Neurorehabilitation Department, Bambino Gesù Children Hospital, Rome, Italy.,Neurology Unit, Pediatric Hospital A. Cao, Brotzu Hospital Trust, Cagliari, Italy
| | | | - Cigdem I Akman
- Division of Pediatric Neurology, College of Physicians and Surgeons of Columbia University, New York City, New York, USA
| | - Steven M Wolf
- Department of Neurology, Mount Sinai Health System, New York City, New York, USA
| | - David E Mandelbaum
- Departments of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Rajesh Gupta
- Department of Paediatrics, Tunbridge Wells Hospital, Pembury, UK
| | - Rick A van der Spek
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dario Pruna
- Neurology Unit, Pediatric Hospital A. Cao, Brotzu Hospital Trust, Cagliari, Italy
| | - Deb K Pal
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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Picard-Jean F, Brand C, Tremblay-Létourneau M, Allaire A, Beaudoin MC, Boudreault S, Duval C, Rainville-Sirois J, Robert F, Pelletier J, Geiss BJ, Bisaillon M. 2'-O-methylation of the mRNA cap protects RNAs from decapping and degradation by DXO. PLoS One 2018; 13:e0193804. [PMID: 29601584 PMCID: PMC5877831 DOI: 10.1371/journal.pone.0193804] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
The 5' RNA cap structure (m7GpppRNA) is a key feature of eukaryotic mRNAs with important roles in stability, splicing, polyadenylation, mRNA export, and translation. Higher eukaryotes can further modify this minimal cap structure with the addition of a methyl group on the ribose 2'-O position of the first transcribed nucleotide (m7GpppNmpRNA) and sometimes on the adjoining nucleotide (m7GpppNmpNmpRNA). In higher eukaryotes, the DXO protein was previously shown to be responsible for both decapping and degradation of RNA transcripts harboring aberrant 5’ ends such as pRNA, pppRNA, GpppRNA, and surprisingly, m7GpppRNA. It was proposed that the interaction of the cap binding complex with the methylated cap would prevent degradation of m7GpppRNAs by DXO. However, the critical role of the 2’-O-methylation found in higher eukaryotic cap structures was not previously addressed. In the present study, we demonstrate that DXO possesses both decapping and exoribonuclease activities toward incompletely capped RNAs, only sparing RNAs with a 2’-O-methylated cap structure. Fluorescence spectroscopy assays also revealed that the presence of the 2’-O-methylation on the cap structure drastically reduces the affinity of DXO for RNA. Moreover, immunofluorescence and structure-function assays also revealed that a nuclear localisation signal is located in the amino-terminus region of DXO. Overall, these results are consistent with a quality control mechanism in which DXO degrades incompletely capped RNAs.
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Affiliation(s)
- Frédéric Picard-Jean
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Carolin Brand
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Maude Tremblay-Létourneau
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Andréa Allaire
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Maxime C. Beaudoin
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon Boudreault
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Cyntia Duval
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Julien Rainville-Sirois
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Martin Bisaillon
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
- * E-mail:
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5
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Deng H, Zeng J, Zhang T, Gong L, Zhang H, Cheung E, Jones C, Li G. Histone H3.3K27M Mobilizes Multiple Cancer/Testis (CT) Antigens in Pediatric Glioma. Mol Cancer Res 2018; 16:623-633. [DOI: 10.1158/1541-7786.mcr-17-0460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/07/2017] [Accepted: 01/16/2018] [Indexed: 11/16/2022]
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Polo-Antúnez A, Arroyo-Carrera I. Severe Neurological Phenotype in a Girl with Xp22.31 Triplication. Mol Syndromol 2017; 8:219-223. [PMID: 28690489 DOI: 10.1159/000475795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2017] [Indexed: 11/19/2022] Open
Abstract
The Xp22.31 duplication is a copy number variant which is challenging to categorize as pathogenic or benign. There is an increasing number of patients with the duplication and a neurobehavioral phenotype, but the duplication is almost always inherited from a parent, who in some cases is phenotypically normal. Also, the duplication is detected in the general population, though in a smaller percentage than in clinically ascertained populations. The Xp22.31 triplication has only been identified in 3 individuals of a large cohort of developmental delay cases but never in the control cohorts or general population. We report a severely affected female with an Xp22.31 tetrasomy, inherited from duplications identified in both phenotypically normal parents. Although our study has limitations, it suggests that the Xp22.31 triplication seems to be more penetrant than the duplication and is associated with a neurological phenotype.
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Affiliation(s)
| | - Ignacio Arroyo-Carrera
- Neonatology Unit, San Pedro de Alcántara Hospital, Cáceres, Spain.,CIBER de Enfermedades Raras (CIBERER) (U724), Instituto de Salud Carlos III, Madrid, Spain
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7
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Enhanced Neuroplasticity by the Metabolic Enhancer Piracetam Associated with Improved Mitochondrial Dynamics and Altered Permeability Transition Pore Function. Neural Plast 2016; 2016:8075903. [PMID: 27747106 PMCID: PMC5056292 DOI: 10.1155/2016/8075903] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/01/2016] [Indexed: 02/07/2023] Open
Abstract
The mitochondrial cascade hypothesis of dementia assumes mitochondrial dysfunction leading to reduced energy supply, impaired neuroplasticity, and finally cell death as one major pathomechanism underlying the continuum from brain aging over mild cognitive impairment to initial and advanced late onset Alzheimer's disease. Accordingly, improving mitochondrial function has become an important strategy to treat the early stages of this continuum. The metabolic enhancer piracetam has been proposed as possible prototype for those compounds by increasing impaired mitochondrial function and related aspects like mechanisms of neuroplasticity. We here report that piracetam at therapeutically relevant concentrations improves neuritogenesis in the human cell line SH-SY5Y over conditions mirroring the whole spectrum of age-associated cognitive decline. These effects go parallel with improvement of impaired mitochondrial dynamics shifting back fission and fusion balance to the energetically more favorable fusion site. Impaired fission and fusion balance can also be induced by a reduction of the mitochondrial permeability transition pore (mPTP) function as atractyloside which indicates the mPTP has similar effects on mitochondrial dynamics. These changes are also reduced by piracetam. These findings suggest the mPTP as an important target for the beneficial effects of piracetam on mitochondrial function.
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Ahmed I, Buchert R, Zhou M, Jiao X, Mittal K, Sheikh TI, Scheller U, Vasli N, Rafiq MA, Brohi MQ, Mikhailov A, Ayaz M, Bhatti A, Sticht H, Nasr T, Carter MT, Uebe S, Reis A, Ayub M, John P, Kiledjian M, Vincent JB, Jamra RA. Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment. Hum Mol Genet 2015; 24:3172-80. [PMID: 25701870 DOI: 10.1093/hmg/ddv069] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/16/2015] [Indexed: 01/09/2023] Open
Abstract
There are two known mRNA degradation pathways, 3' to 5' and 5' to 3'. We identified likely pathogenic variants in two genes involved in these two pathways in individuals with intellectual disability. In a large family with multiple branches, we identified biallelic variants in DCPS in three affected individuals; a splice site variant (c.636+1G>A) that results in an in-frame insertion of 45 nucleotides and a missense variant (c.947C>T; p.Thr316Met). DCPS decaps the cap structure generated by 3' to 5' exonucleolytic degradation of mRNA. In vitro decapping assays showed an ablation of decapping function for both variants in DCPS. In another family, we identified a homozygous mutation (c.161T>C; p.Phe54Ser) in EDC3 in two affected children. EDC3 stimulates DCP2, which decaps mRNAs at the beginning of the 5' to 3' degradation pathway. In vitro decapping assays showed that altered EDC3 is unable to enhance DCP2 decapping at low concentrations and even inhibits DCP2 decapping at high concentration. We show that individuals with biallelic mutations in these genes of seemingly central functions are viable and that these possibly lead to impairment of neurological functions linking mRNA decapping to normal cognition. Our results further affirm an emerging theme linking aberrant mRNA metabolism to neurological defects.
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Affiliation(s)
- Iltaf Ahmed
- Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8 Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | | | - Mi Zhou
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Kirti Mittal
- Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8
| | - Taimoor I Sheikh
- Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8
| | | | - Nasim Vasli
- Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8
| | - Muhammad Arshad Rafiq
- Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8
| | - M Qasim Brohi
- Sir Cowasji Jehangir Institute of Psychiatry, Hyderabad, Sindh 71000, Pakistan
| | - Anna Mikhailov
- Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8
| | - Muhammad Ayaz
- Lahore Institute of Research and Development, Lahore 51000, Pakistan
| | - Attya Bhatti
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Heinrich Sticht
- Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Tanveer Nasr
- Department of Psychiatry, Mayo Hospital, Lahore 54000, Pakistan Department of Psychiatry, Chaudhary Hospital, Gujranwala 52250, Pakistan
| | - Melissa T Carter
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada M5G1X8
| | | | | | - Muhammad Ayub
- Lahore Institute of Research and Development, Lahore 51000, Pakistan Division of Developmental Disabilities, Department of Psychiatry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Peter John
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - John B Vincent
- Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8 Department of Psychiatry and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada M5S 2J7
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9
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Park HA, Licznerski P, Alavian KN, Shanabrough M, Jonas EA. Bcl-xL is necessary for neurite outgrowth in hippocampal neurons. Antioxid Redox Signal 2015; 22:93-108. [PMID: 24787232 PMCID: PMC4281845 DOI: 10.1089/ars.2013.5570] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AIMS B-cell lymphoma-extra large (Bcl-xL) protects survival in dividing cells and developing neurons, but was not known to regulate growth. Growth and synapse formation are indispensable for neuronal survival in development, inextricably linking these processes. We have previously shown that, during synaptic plasticity, Bcl-xL produces changes in synapse number, size, activity, and mitochondrial metabolism. In this study, we determine whether Bcl-xL is required for healthy neurite outgrowth and whether neurite outgrowth is necessary for survival in developing neurons in the presence or absence of stress. RESULTS Depletion of endogenous Bcl-xL impairs neurite outgrowth in hippocampal neurons followed by delayed cell death which is dependent on upregulation of death receptor 6 (DR6), a molecule that regulates axonal pruning. Under hypoxic conditions, Bcl-xL-depleted neurons demonstrate increased vulnerability to neuronal process loss and to death compared with hypoxic controls. Endogenous DR6 expression and upregulation during hypoxia are associated with worsened neurite damage; depletion of DR6 partially rescues neuronal process loss, placing DR6 downstream of the effects of Bcl-xL on neuronal process outgrowth and protection. In vivo ischemia produces early increases in DR6, suggesting a role for DR6 in brain injury. INNOVATION We suggest that DR6 levels are usually suppressed by Bcl-xL; Bcl-xL depletion leads to upregulation of DR6, failure of neuronal outgrowth in nonstressed cells, and exacerbation of hypoxia-induced neuronal injury. CONCLUSION Bcl-xL regulates neuronal outgrowth during development and protects neurites from hypoxic insult, as opposed by DR6. Factors that enhance neurite formation may protect neurons against hypoxic injury or neurodegenerative stimuli.
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Affiliation(s)
- Han-A Park
- Section of Endocrinology, Department of Internal Medicine, Yale University , New Haven, Connecticut
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10
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Szelinger S, Malenica I, Corneveaux JJ, Siniard AL, Kurdoglu AA, Ramsey KM, Schrauwen I, Trent JM, Narayanan V, Huentelman MJ, Craig DW. Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing. PLoS One 2014; 9:e113036. [PMID: 25503791 PMCID: PMC4264736 DOI: 10.1371/journal.pone.0113036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/23/2014] [Indexed: 12/30/2022] Open
Abstract
In females, X chromosome inactivation (XCI) is an epigenetic, gene dosage compensatory mechanism by inactivation of one copy of X in cells. Random XCI of one of the parental chromosomes results in an approximately equal proportion of cells expressing alleles from either the maternally or paternally inherited active X, and is defined by the XCI ratio. Skewed XCI ratio is suggestive of non-random inactivation, which can play an important role in X-linked genetic conditions. Current methods rely on indirect, semi-quantitative DNA methylation-based assay to estimate XCI ratio. Here we report a direct approach to estimate XCI ratio by integrated, family-trio based whole-exome and mRNA sequencing using phase-by-transmission of alleles coupled with allele-specific expression analysis. We applied this method to in silico data and to a clinical patient with mild cognitive impairment but no clear diagnosis or understanding molecular mechanism underlying the phenotype. Simulation showed that phased and unphased heterozygous allele expression can be used to estimate XCI ratio. Segregation analysis of the patient's exome uncovered a de novo, interstitial, 1.7 Mb deletion on Xp22.31 that originated on the paternally inherited X and previously been associated with heterogeneous, neurological phenotype. Phased, allelic expression data suggested an 83∶20 moderately skewed XCI that favored the expression of the maternally inherited, cytogenetically normal X and suggested that the deleterious affect of the de novo event on the paternal copy may be offset by skewed XCI that favors expression of the wild-type X. This study shows the utility of integrated sequencing approach in XCI ratio estimation.
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Affiliation(s)
- Szabolcs Szelinger
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Molecular and Cellular Biology Interdisciplinary Graduate Program, College of Liberal Arts and Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Ivana Malenica
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Jason J. Corneveaux
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ashley L. Siniard
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ahmet A. Kurdoglu
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Keri M. Ramsey
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jeffrey M. Trent
- Genetic Basis of Human Disease Division, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- Neurology Research, Barrow Neurological Institute, Phoenix, Arizona, United States of America
| | - Matthew J. Huentelman
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - David W. Craig
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
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11
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Mahboubi H, Stochaj U. Nucleoli and Stress Granules: Connecting Distant Relatives. Traffic 2014; 15:1179-93. [DOI: 10.1111/tra.12191] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Hicham Mahboubi
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
| | - Ursula Stochaj
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
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12
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Esplin ED, Li B, Slavotinek A, Novelli A, Battaglia A, Clark R, Curry C, Hudgins L. Nine patients with Xp22.31 microduplication, cognitive deficits, seizures, and talipes anomalies. Am J Med Genet A 2014; 164A:2097-103. [DOI: 10.1002/ajmg.a.36598] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 04/13/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Edward D. Esplin
- Division of Medical Genetics, Department of Pediatrics; Stanford University School of Medicine; Stanford California
| | - Ben Li
- Division of Medical Genetics, Department of Pediatrics; University of California San Francisco; San Francisco California
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics; University of California San Francisco; San Francisco California
| | - Antonio Novelli
- Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza Hospital; San Giovanni Rotondo (FG) Italy
| | - Agatino Battaglia
- The Stella Maris Clinical Research Institute for Child and Adolescent Neurology and Psychiatry; Calambrone (Pisa) Italy
| | - Robin Clark
- Division of Medical Genetics, Department of Pediatrics; Loma Linda University; Loma Linda California
| | - Cynthia Curry
- Division of Medical Genetics, Department of Pediatrics; UCSF Fresno; Fresno California
| | - Louanne Hudgins
- Division of Medical Genetics, Department of Pediatrics; Stanford University School of Medicine; Stanford California
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13
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Harrison BJ, Flight RM, Gomes C, Venkat G, Ellis SR, Sankar U, Twiss JL, Rouchka EC, Petruska JC. IB4-binding sensory neurons in the adult rat express a novel 3' UTR-extended isoform of CaMK4 that is associated with its localization to axons. J Comp Neurol 2014; 522:308-36. [PMID: 23817991 PMCID: PMC3855891 DOI: 10.1002/cne.23398] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 06/13/2013] [Accepted: 06/19/2013] [Indexed: 01/22/2023]
Abstract
Calcium/calmodulin-dependent protein kinase 4 (gene and transcript: CaMK4; protein: CaMKIV) is the nuclear effector of the Ca(2+) /calmodulin kinase (CaMK) pathway where it coordinates transcriptional responses. However, CaMKIV is present in the cytoplasm and axons of subpopulations of neurons, including some sensory neurons of the dorsal root ganglia (DRG), suggesting an extranuclear role for this protein. We observed that CaMKIV was expressed strongly in the cytoplasm and axons of a subpopulation of small-diameter DRG neurons, most likely cutaneous nociceptors by virtue of their binding the isolectin IB4. In IB4+ spinal nerve axons, 20% of CaMKIV was colocalized with the endocytic marker Rab7 in axons that highly expressed CAM-kinase-kinase (CAMKK), an upstream activator of CaMKIV, suggesting a role for CaMKIV in signaling though signaling endosomes. Using fluorescent in situ hybridization (FISH) with riboprobes, we also observed that small-diameter neurons expressed high levels of a novel 3' untranslated region (UTR) variant of CaMK4 mRNA. Using rapid amplification of cDNA ends (RACE), reverse-transcription polymerase chain reaction (RT-PCR) with gene-specific primers, and cDNA sequencing analyses we determined that the novel transcript contains an additional 10 kb beyond the annotated gene terminus to a highly conserved alternate polyadenylation site. Quantitative PCR (qPCR) analyses of fluorescent-activated cell sorted (FACS) DRG neurons confirmed that this 3'-UTR-extended variant was preferentially expressed in IB4-binding neurons. Computational analyses of the 3'-UTR sequence predict that UTR-extension introduces consensus sites for RNA-binding proteins (RBPs) including the embryonic lethal abnormal vision (ELAV)/Hu family proteins. We consider the possible implications of axonal CaMKIV in the context of the unique properties of IB4-binding DRG neurons.
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Affiliation(s)
- Benjamin J. Harrison
- Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, 40202, USA
- Kentucky Spinal Cord Injury Research Center (KSCIRC), University of Louisville, Louisville, Kentucky, 40292, USA
| | - Robert M. Flight
- Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, 40202, USA
| | - Cynthia Gomes
- Department of Biochemistry and Molecular Bi ology, University of Louisville School of Medicine, Kentucky, 40202, USA
| | - Gayathri Venkat
- Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, 40202, USA
- Kentucky Spinal Cord Injury Research Center (KSCIRC), University of Louisville, Louisville, Kentucky, 40292, USA
| | - Steven R Ellis
- Department of Biochemistry and Molecular Bi ology, University of Louisville School of Medicine, Kentucky, 40202, USA
| | - Uma Sankar
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40292, USA
- Owensboro Cancer Research Program, University of Louisville, Owensboro, KY 42303, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Jeffery L. Twiss
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, 19104, USA
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Jeffrey C. Petruska
- Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, 40202, USA
- Kentucky Spinal Cord Injury Research Center (KSCIRC), University of Louisville, Louisville, Kentucky, 40292, USA
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, 40202, USA
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14
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Song MG, Bail S, Kiledjian M. Multiple Nudix family proteins possess mRNA decapping activity. RNA (NEW YORK, N.Y.) 2013; 19:390-9. [PMID: 23353937 PMCID: PMC3677249 DOI: 10.1261/rna.037309.112] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/20/2012] [Indexed: 05/23/2023]
Abstract
RNA decapping is an important contributor to gene expression and is a critical determinant of mRNA decay. The recent demonstration that mammalian cells harbor at least two distinct decapping enzymes that preferentially modulate a subset of mRNAs raises the intriguing possibility of whether additional decapping enzymes exist. Because both known decapping proteins, Dcp2 and Nudt16, are members of the Nudix hydrolase family, we set out to determine whether other members of this family of proteins also contain intrinsic RNA decapping activity. Here we demonstrate that six additional mouse Nudix proteins--Nudt2, Nudt3, Nudt12, Nudt15, Nudt17, and Nudt19--have varying degrees of decapping activity in vitro on both monomethylated and unmethylated capped RNAs. The decapping products from Nudt17 and Nudt19 were analogous to Dcp2 and predominantly generated m⁷GDP, while cleavage by Nudt2, Nudt3, Nudt12, and Nudt15 was more pleiotropic and generated both m⁷GMP and m⁷GDP. Interestingly, all six Nudix proteins as well as both Dcp2 and Nudt16 could hydrolyze the cap of an unmethylated capped RNA, indicating that decapping enzymes may be less constrained for the presence of the methyl moiety. Investigation of Saccharomyces cerevisiae Nudix proteins revealed that the yeast homolog of Nudt3, Ddp1p, also possesses decapping activity in vitro. Moreover, the bacterial Nudix pyrophosphohydrolase RppH displayed RNA decapping activity and released m⁷GDP product comparable to Dcp2, indicating that decapping is an evolutionarily conserved activity that preceded mammalian cap formation. These findings demonstrate that multiple Nudix family hydrolases may function in mRNA decapping and mRNA stability.
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Affiliation(s)
| | | | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854-8082, USA
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15
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Bardoni B, Abekhoukh S, Zongaro S, Melko M. Intellectual disabilities, neuronal posttranscriptional RNA metabolism, and RNA-binding proteins: three actors for a complex scenario. PROGRESS IN BRAIN RESEARCH 2012; 197:29-51. [PMID: 22541287 DOI: 10.1016/b978-0-444-54299-1.00003-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intellectual disability (ID) is the most frequent cause of serious handicap in children and young adults and interests 2-3% of worldwide population, representing a serious problem from the medical, social, and economic points of view. The causes are very heterogeneous. Genes involved in ID have various functions altering different pathways important in neuronal function. Regulation of mRNA metabolism is particularly important in neurons for synaptic structure and function. Here, we review ID due to alteration of mRNA metabolism. Functional absence of some RNA-binding proteins--namely, FMRP, FMR2P, PQBP1, UFP3B, VCX-A--causes different forms of ID. These proteins are involved in different steps of RNA metabolism and, even if a detailed analysis of their RNA targets has been performed so far only for FMRP, it appears clear that they modulate some aspects (translation, stability, transport, and sublocalization) of a subset of RNAs coding for proteins, whose function must be relevant for neurons. Two other proteins, DYRK1A and CDKL5, involved in Down syndrome and Rett syndrome, respectively, have been shown to have an impact on splicing efficiency of specific mRNAs. Both proteins are kinases and their effect is indirect. Interestingly, both are localized in nuclear speckles, the nuclear domains where splicing factors are assembled, stocked, and recycled and influence their biogenesis and/or their organization.
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Affiliation(s)
- Barbara Bardoni
- Institute of Molecular and Cellular Pharmacology, CNRS-UMR6097, Université de Nice Sophia-Antipolis,Valbonne, France.
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16
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Faletra F, D'Adamo AP, Santa Rocca M, Carrozzi M, Perrone MD, Pecile V, Gasparini P. Does the 1.5 Mb microduplication in chromosome band Xp22.31 have a pathogenetic role? New contribution and a review of the literature. Am J Med Genet A 2011; 158A:461-4. [PMID: 22140086 DOI: 10.1002/ajmg.a.34398] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 10/31/2011] [Indexed: 02/05/2023]
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17
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Izumi K, Mikesell H, Daber R, Chao G, Hutchinson AL, Spinner NB, Parikh AS. 8p21 microdeletion in a patient with intellectual disability and behavioral abnormalities. Am J Med Genet A 2011; 155A:3148-52. [PMID: 22065607 DOI: 10.1002/ajmg.a.34317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 08/24/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Kosuke Izumi
- Center for Human Genetics, University Hospitals Case Medical Center, Cleveland, Ohio, USA.
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18
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Kunde SA, Musante L, Grimme A, Fischer U, Muller E, Wanker EE, Kalscheuer VM. The X-chromosome-linked intellectual disability protein PQBP1 is a component of neuronal RNA granules and regulates the appearance of stress granules. Hum Mol Genet 2011; 20:4916-31. [DOI: 10.1093/hmg/ddr430] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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19
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Liu P, Erez A, Nagamani SCS, Bi W, Carvalho CMB, Simmons AD, Wiszniewska J, Fang P, Eng PA, Cooper ML, Sutton VR, Roeder ER, Bodensteiner JB, Delgado MR, Prakash SK, Belmont JW, Stankiewicz P, Berg JS, Shinawi M, Patel A, Cheung SW, Lupski JR. Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications. Hum Mol Genet 2011; 20:1975-88. [PMID: 21355048 DOI: 10.1093/hmg/ddr078] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genomic instability is a feature of the human Xp22.31 region wherein deletions are associated with X-linked ichthyosis, mental retardation and attention deficit hyperactivity disorder. A putative homologous recombination hotspot motif is enriched in low copy repeats that mediate recurrent deletion at this locus. To date, few efforts have focused on copy number gain at Xp22.31. However, clinical testing revealed a high incidence of duplication of Xp22.31 in subjects ascertained and referred with neurobehavioral phenotypes. We systematically studied 61 unrelated subjects with rearrangements revealing gain in copy number, using multiple molecular assays. We detected not only the anticipated recurrent and simple nonrecurrent duplications, but also unexpectedly identified recurrent triplications and other complex rearrangements. Breakpoint analyses enabled us to surmise the mechanisms for many of these rearrangements. The clinical significance of the recurrent duplications and triplications were assessed using different approaches. We cannot find any evidence to support pathogenicity of the Xp22.31 duplication. However, our data suggest that the Xp22.31 duplication may serve as a risk factor for abnormal phenotypes. Our findings highlight the need for more robust Xp22.31 triplication detection in that such further gain may be more penetrant than the duplications. Our findings reveal the distribution of different mechanisms for genomic duplication rearrangements at a given locus, and provide insights into aspects of strand exchange events between paralogous sequences in the human genome.
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Affiliation(s)
- Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030, USA
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20
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Song MG, Li Y, Kiledjian M. Multiple mRNA decapping enzymes in mammalian cells. Mol Cell 2010; 40:423-32. [PMID: 21070968 DOI: 10.1016/j.molcel.2010.10.010] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 07/10/2010] [Accepted: 08/25/2010] [Indexed: 01/18/2023]
Abstract
Regulation of RNA degradation plays an important role in the control of gene expression. One mechanism of eukaryotic mRNA decay proceeds through an initial deadenylation followed by 5' end decapping and exonucleolytic decay. Dcp2 is currently believed to be the only cytoplasmic decapping enzyme responsible for decapping of all mRNAs. Here we report that Dcp2 protein modestly contributes to bulk mRNA decay and surprisingly is not detectable in a subset of mouse and human tissues. Consistent with these findings, a hypomorphic knockout of Dcp2 had no adverse consequences in mice. In contrast, the previously reported Xenopus nucleolar decapping enzyme, Nudt16, is an ubiquitous cytoplasmic decapping enzyme in mammalian cells. Like Dcp2, Nudt16 also regulates the stability of a subset of mRNAs including a member of the motin family of proteins involved in angiogenesis, Angiomotin-like 2. These data demonstrate mammalian cells possess multiple mRNA decapping enzymes, including Nudt16 to regulate mRNA turnover.
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Affiliation(s)
- Man-Gen Song
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
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21
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Wang Y, Lacroix G, Haines J, Doukhanine E, Almazan G, Richard S. The QKI-6 RNA binding protein localizes with the MBP mRNAs in stress granules of glial cells. PLoS One 2010; 5. [PMID: 20862255 PMCID: PMC2941464 DOI: 10.1371/journal.pone.0012824] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Accepted: 08/12/2010] [Indexed: 12/23/2022] Open
Abstract
Background The quaking viable (qkv) mouse has several developmental defects that result in rapid tremors in the hind limbs. The qkI gene expresses three major alternatively spliced mRNAs (5, 6 and 7 kb) that encode the QKI-5, QKI-6 and QKI-7 RNA binding proteins that differ in their C-terminal 30 amino acids. The QKI isoforms are known to regulate RNA metabolism within oligodendrocytes, however, little is known about their roles during cellular stress. Methodology/Principal Findings In this study, we report an interaction between the QKI-6 isoform and a component of the RNA induced silencing complex (RISC), argonaute 2 (Ago2). We show in glial cells that QKI-6 co-localizes with Ago2 and the myelin basic protein mRNA in cytoplasmic stress granules. Conclusions Our findings define the QKI isoforms as Ago2-interacting proteins. We also identify the QKI-6 isoform as a new component of stress granules in glial cells.
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Affiliation(s)
- Yunling Wang
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
| | - Geneviève Lacroix
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
| | - Jeffery Haines
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Evgueni Doukhanine
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
| | - Guillermina Almazan
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, Bloomfield Center for Research on Aging, McGill University, Montréal, Québec, Canada
- * E-mail:
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22
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Ling SHM, Qamra R, Song H. Structural and functional insights into eukaryotic mRNA decapping. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:193-208. [PMID: 21957006 DOI: 10.1002/wrna.44] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The control of messenger RNA (mRNA) translation and degradation is important in regulation of eukaryotic gene expression. In the general and specialized mRNA decay pathways which involve 5(') →3(') decay, decapping is the central step because it is the controlling gate preceding the actual degradation of mRNA and is a site of numerous control inputs. Removal of the cap structure is catalyzed by a decapping holoenzyme composed of the catalytic Dcp2 subunit and the coactivator Dcp1. Decapping is regulated by decapping activators and inhibitors. Recent structural and kinetics studies indicated that Dcp1 and the substrate RNA promote the closed form of the enzyme and the catalytic step of decapping is rate limiting and accelerated by Dcp1. The conformational change between the open and closed decapping enzyme is important for controlling decapping, and regulation of this transition has been proposed to be a checkpoint for determining the fate of mRNAs. Here we summarize the past and recent advances on the structural and functional studies of protein factors involved in regulating mRNA decapping.
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Affiliation(s)
- Sharon H M Ling
- Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673
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Jiao X, Xiang S, Oh C, Martin CE, Tong L, Kiledjian M. Identification of a quality-control mechanism for mRNA 5'-end capping. Nature 2010; 467:608-11. [PMID: 20802481 PMCID: PMC2948066 DOI: 10.1038/nature09338] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 07/06/2010] [Indexed: 11/11/2022]
Abstract
The 7-methylguanosine cap structure at the 5′-end of eukaryotic mRNAs is a critical determinant of their stability and translational efficiency1–3. It is generally believed that 5’-end capping is a constitutive process that occurs during mRNA maturation and lacks the need for a quality control mechanism to ensure its fidelity. We recently reported that the yeast Rai1 protein has pyrophosphohydrolase activity towards mRNAs lacking a 5’-end cap4. Here we show that, in vitro as well as in yeast cells, Rai1 possess a novel decapping endonuclease activity that can also remove the entire cap structure dinucleotide from an mRNA. Interestingly this activity is targeted preferentially towards mRNAs with unmethylated caps in contrast to the canonical decapping enzyme, Dcp2, that targets mRNAs with a methylated cap. Capped but unmethylated mRNAs generated in yeast cells with a defect in the methyltransferase gene are more stable in a rai1 gene disrupted background. Moreover, rai1Δ yeast cells with wild-type capping enzymes show significant accumulation of mRNAs with 5’-end capping defects under nutritional stress conditions of glucose or amino acid starvation. These findings provide evidence that 5’-end capping is not a constitutive process that necessarily always proceeds to completion and demonstrates that Rai1 plays an essential role in clearing mRNAs with aberrant 5’-end caps. We propose Rai1 is involved in a hitherto-uncharacterized quality control process that ensures mRNA 5’-end integrity by an aberrant-cap mediated mRNA decay mechanism.
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Affiliation(s)
- Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA
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24
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Melko M, Bardoni B. The role of G-quadruplex in RNA metabolism: involvement of FMRP and FMR2P. Biochimie 2010; 92:919-26. [PMID: 20570707 DOI: 10.1016/j.biochi.2010.05.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 05/28/2010] [Indexed: 12/20/2022]
Abstract
Regulation of post-transcriptional gene expression is a cellular process that is accomplished through the activity of multiple mRNP (messenger RiboNucleoProtein) complexes which are composed of mRNA-binding proteins and RNA molecules interacting with those proteins. The specificity of these interactions is mediated by the ability of the RNA-binding proteins to precisely recognize and bind RNA sequences or structures. Alterations of their function may have some dramatic consequences, resulting in different pathologies. An increasing body of data is emerging showing the impact of a G-quadruplex forming structure in the maturation and expression of some RNA molecules. We review here the role of the G-quadruplex RNA structure in the regulation of translation and splicing, when it interacts with two RNA-binding proteins: FMRP (Fragile X Mental Retardation Protein) and FMR2P (Fragile X Mental Retardation 2 protein). Impaired expression of these proteins causes two forms of intellectual disability: the Fragile X Mental Retardation syndrome (FXS) and the FRAXE-associated mental retardation (FRAXE), respectively. FMRP is involved in different steps of RNA metabolism and, in particular, in translational regulation. FMR2P has been initially described as a transcription factor and we recently showed also its role in regulation of alternative splicing. By the study of the functional significance of the interaction of both FMRP and FMR2P with a G-quadruplex forming RNA we were able to show an impact of this structure in translational regulation and also in splicing, behaving as an Exonic Splicing Enhancer.
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Affiliation(s)
- Mireille Melko
- CNRS UMR 6097, Institute of Molecular and Cellular Pharmacology, University of Nice-Sophia Antipolis, 06560 Valbonne Sophia-Antipolis, France
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25
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Li Y, Kiledjian M. Regulation of mRNA decapping. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:253-65. [PMID: 21935889 DOI: 10.1002/wrna.15] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Decapping is a critical step in the control of mRNA stability and the regulation of gene expression. Two major decapping enzymes involved in mRNA turnover have been identified, each functioning in one of the two exonucleolytic mRNA decay pathways in eukaryotic cells. The Dcp2 protein cleaves capped mRNA and initiates 5' to 3' degradation; the scavenger decapping enzyme, DcpS, hydrolyzes the cap structure generated by the 3' to 5' decay pathway. Consistent with the important role of decapping in gene expression, cap hydrolysis is exquisitely controlled by multiple regulators that influence association with the cap and the catalytic step. In this review, we will discuss the functions of the two different decapping enzymes, their regulation by cis-elements and trans-factors, and the potential role of the decapping enzymes in human neurological disorders.
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Affiliation(s)
- You Li
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854-8082, USA
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