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Giacomini T, Scala M, Nobile G, Severino M, Tortora D, Nobili L, Accogli A, Torella A, Capra V, Mancardi MM, Nigro V. De novo POLR2A p.(Ile457Thr) variant associated with early-onset encephalopathy and cerebellar atrophy: expanding the phenotypic spectrum. Brain Dev 2022; 44:480-485. [PMID: 35461703 DOI: 10.1016/j.braindev.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Heterozygous POLR2A variants have been recently reported in patients with a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia. POLR2A encodes the highly conserved RBP1 protein, an essential subunit of the DNA-dependent RNA polymerase II. CASE PRESENTATION We investigated a 12-year-old girl presenting with an early-onset encephalopathy characterized by psychomotor delay, facial dysmorphism, refractory epilepsy with variable seizure types, behavioural abnormalities, and sleep disorder. Brain MRI showed a slowly progressive cerebellar atrophy. Trio-exome sequencing (Trio-ES) revealed the de novo germline variant NM_000937.5:c.1370T>C; p.(Ile457Thr) in POLR2A. This variant was previously reported in a subject with profound generalized hypotonia and muscular atrophy by Haijes et al. Our patient displayed instead a severe epileptic phenotype with refractory hypotonic seizures with impaired consciousness, myoclonic jerks, and drop attacks. CONCLUSION This case expands the clinical spectrum of POLR2A-related syndrome, highlighting its phenotypic variability and supporting the relevance of epilepsy as a core feature of this emerging condition.
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Affiliation(s)
- Thea Giacomini
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy; Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy.
| | - Giulia Nobile
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy.
| | | | - Domenico Tortora
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Lino Nobili
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy; Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy.
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy.
| | - Valeria Capra
- Medical Genetic Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | | | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy.
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- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
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Tønne E, Due-Tønnessen BJ, Vigeland MD, Amundsen SS, Ribarska T, Åsten PM, Sheng Y, Helseth E, Gilfillan GD, Mero IL, Heimdal KR. Whole-exome sequencing in syndromic craniosynostosis increases diagnostic yield and identifies candidate genes in osteogenic signaling pathways. Am J Med Genet A 2022; 188:1464-1475. [PMID: 35080095 DOI: 10.1002/ajmg.a.62663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/26/2021] [Accepted: 12/26/2021] [Indexed: 11/07/2022]
Abstract
Craniosynostosis (CS) is a common congenital anomaly defined by premature fusion of one or more cranial sutures. Syndromic CS involves additional organ anomalies or neurocognitive deficits and accounts for 25%-30% of the cases. In a recent population-based study by our group, 84% of the syndromic CS cases had a genetically verified diagnosis after targeted analyses. A number of different genetic causes were detected, confirming that syndromic CS is highly heterogeneous. In this study, we performed whole-exome sequencing of 10 children and parents from the same cohort where previous genetic results were negative. We detected pathogenic, or likely pathogenic, variants in four additional genes (NFIA, EXTL3, POLR2A, and FOXP2) associated with rare conditions. In two of these (POLR2A and FOXP2), CS has not previously been reported. We further detected a rare predicted damaging variant in SH3BP4, which has not previously been related to human disease. All findings were clustered in genes involved in the pathways of osteogenesis and suture patency. We conclude that whole-exome sequencing expands the list of genes associated with syndromic CS, and provides new candidate genes in osteogenic signaling pathways.
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Affiliation(s)
- Elin Tønne
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Norwegian National Unit for Craniofacial Surgery, Oslo University Hospital, Oslo, Norway
| | - Bernt Johan Due-Tønnessen
- Norwegian National Unit for Craniofacial Surgery, Oslo University Hospital, Oslo, Norway.,Department of Neurosurgery, Oslo University Hospital, Oslo, Norway
| | - Magnus Dehli Vigeland
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Teodora Ribarska
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eirik Helseth
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Neurosurgery, Oslo University Hospital, Oslo, Norway
| | - Gregor Duncan Gilfillan
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Inger-Lise Mero
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ketil Riddervold Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Norwegian National Unit for Craniofacial Surgery, Oslo University Hospital, Oslo, Norway
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3
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Boukas L, Bjornsson HT, Hansen KD. Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance. Am J Hum Genet 2020; 107:487-498. [PMID: 32800095 PMCID: PMC7477270 DOI: 10.1016/j.ajhg.2020.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022] Open
Abstract
The aggregation and joint analysis of large numbers of exome sequences has recently made it possible to derive estimates of intolerance to loss-of-function (LoF) variation for human genes. Here, we demonstrate strong and widespread coupling between genic LoF intolerance and promoter CpG density across the human genome. Genes downstream of the most CpG-rich promoters (top 10% CpG density) have a 67.2% probability of being highly LoF intolerant, using the LOEUF metric from gnomAD. This is in contrast to 7.4% of genes downstream of the most CpG-poor (bottom 10% CpG density) promoters. Combining promoter CpG density with exonic and promoter conservation explains 33.4% of the variation in LOEUF, and the contribution of CpG density exceeds the individual contributions of exonic and promoter conservation. We leverage this to train a simple and easily interpretable predictive model that outperforms other existing predictors and allows us to classify 1,760 genes-which are currently unascertained in gnomAD-as highly LoF intolerant or not. These predictions have the potential to aid in the interpretation of novel variants in the clinical setting. Moreover, our results reveal that high CpG density is not merely a generic feature of human promoters but is preferentially encountered at the promoters of the most selectively constrained genes, calling into question the prevailing view that CpG islands are not subject to selection.
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Affiliation(s)
- Leandros Boukas
- Human Genetics Training Program, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, 1800 Orleans Street, Baltimore, MD 21287, USA; Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland; Landspitali University Hospital, Hringbraut, 101 Reykjavik, Iceland.
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA.
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4
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Haijes HA, Koster MJE, Rehmann H, Li D, Hakonarson H, Cappuccio G, Hancarova M, Lehalle D, Reardon W, Schaefer GB, Lehman A, van de Laar IMBH, Tesselaar CD, Turner C, Goldenberg A, Patrier S, Thevenon J, Pinelli M, Brunetti-Pierri N, Prchalová D, Havlovicová M, Vlckova M, Sedláček Z, Lopez E, Ragoussis V, Pagnamenta AT, Kini U, Vos HR, van Es RM, van Schaik RFMA, van Essen TAJ, Kibaek M, Taylor JC, Sullivan J, Shashi V, Petrovski S, Fagerberg C, Martin DM, van Gassen KLI, Pfundt R, Falk MJ, McCormick EM, Timmers HTM, van Hasselt PM. De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia. Am J Hum Genet 2019; 105:283-301. [PMID: 31353023 PMCID: PMC6699192 DOI: 10.1016/j.ajhg.2019.06.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/30/2019] [Indexed: 11/26/2022] Open
Abstract
The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.
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Affiliation(s)
- Hanneke A Haijes
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Maria J E Koster
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Holger Rehmann
- Expertise Center for Structural Biology, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Dong Li
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Daphne Lehalle
- Department of Genetics, Centre Hospitalier Universitaire de Dijon, 21000 Dijon, France
| | - Willie Reardon
- Department of Clinical and Medical Genetics, Our Lady's Hospital for Sick Children, D12 N512 Dublin, Ireland
| | - G Bradley Schaefer
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, AR 72223, USA
| | - Anna Lehman
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus Medical University Center Rotterdam, 3000 CA Rotterdam, the Netherlands
| | - Coranne D Tesselaar
- Department of Pediatrics, Amphia Hospital Breda, 4818 CK Breda, the Netherlands
| | - Clesson Turner
- Department of Clinical Genetics and Pediatrics, Walter Reed National Military Medical Center, Bethesda, Maryland, MD 20814, USA
| | - Alice Goldenberg
- Department of Genetics, Rouen University Hospital, Centre de Référence Anomalies du Développement, Normandy Centre for Genomic and Personalized Medicine, 76000 Rouen, France
| | - Sophie Patrier
- Department of Pathology, Rouen University Hospital, Centre de Référence Anomalies du Développement, 76000 Rouen, France
| | - Julien Thevenon
- Department of Genetics and Reproduction, Centre Hospitalier Universitaire de Grenoble, 38700 Grenoble, France
| | - Michele Pinelli
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Darina Prchalová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Vlckova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Zdeněk Sedláček
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Elena Lopez
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Vassilis Ragoussis
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Alistair T Pagnamenta
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Usha Kini
- Department of Genomic Medicine, Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, OX3 7LE Oxford, UK
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Robert M van Es
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Richard F M A van Schaik
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Ton A J van Essen
- Department of Clinical Genetics, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Maria Kibaek
- H.C. Andersen Children Hospital, Odense University Hospital, 5000 Odense, Denmark
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Slave Petrovski
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA; AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, CB4 0WG Cambridge, United Kingdom; Department of Medicine, the University of Melbourne, VIC 3010 Melbourne, Australia
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, MI 48109, USA
| | - Koen L I van Gassen
- Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center Nijmegen, 6525 HR Nijmegen, the Netherlands
| | - Marni J Falk
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Department of Urology, University Medical Center Freiburg, University of Freiburg, 79110 Freiburg, Germany
| | - Peter M van Hasselt
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands.
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Zhang LQ, Li QZ. Estimating the effects of transcription factors binding and histone modifications on gene expression levels in human cells. Oncotarget 2018; 8:40090-40103. [PMID: 28454114 PMCID: PMC5522221 DOI: 10.18632/oncotarget.16988] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/11/2017] [Indexed: 12/22/2022] Open
Abstract
Transcription factors and histone modifications are vital for the regulation of gene expression. Hence, to estimate the effects of transcription factors binding and histone modifications on gene expression, we construct a statistical model for the genome-wide 15 transcription factors binding data, 10 histone modifications profiles and DNase-I hypersensitivity data in three mammalian. Remarkably, our results show POLR2A and H3K36me3 can highly and consistently predict gene expression in three cell lines. And H3K4me3, H3K27me3 and H3K9ac are more reliable predictors than other histone modifications in human embryonic stem cells. Moreover, genome-wide statistical redundancies exist within and between transcription factors and histone modifications, and these phenomena may be caused by the regulation mechanism. In further study, we find that even though transcription factors and histone modifications offer similar effects on expression levels of genome-wide genes, the effects of transcription factors and histone modifications on predictive abilities are different for genes in independent biological processes.
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Affiliation(s)
- Lu-Qiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
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6
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Uzbekova S, Roy-Sabau M, Dalbiès-Tran R, Perreau C, Papillier P, Mompart F, Thelie A, Pennetier S, Cognie J, Cadoret V, Royere D, Monget P, Mermillod P. Zygote arrest 1 gene in pig, cattle and human: evidence of different transcript variants in male and female germ cells. Reprod Biol Endocrinol 2006; 4:12. [PMID: 16551357 PMCID: PMC1435755 DOI: 10.1186/1477-7827-4-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 03/21/2006] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Zygote arrest 1 (ZAR1) is one of the few known oocyte-specific maternal-effect genes essential for the beginning of embryo development discovered in mice. This gene is evolutionary conserved in vertebrates and ZAR1 protein is characterized by the presence of atypical plant homeobox zing finger domain, suggesting its role in transcription regulation. This work was aimed at the study of this gene, which could be one of the key regulators of successful preimplantation development of domestic animals, in pig and cattle, as compared with human. METHODS Screenings of somatic cell hybrid panels and in silico research were performed to characterize ZAR1 chromosome localization and sequences. Rapid amplification of cDNA ends was used to obtain full-length cDNAs. Spatio-temporal mRNA expression patterns were studied using Northern blot, reverse transcription coupled to polymerase chain reaction and in situ hybridization. RESULTS We demonstrated that ZAR1 is a single copy gene, positioned on chromosome 8 in pig and 6 in cattle, and several variants of correspondent cDNA were cloned from oocytes. Sequence analysis of ZAR1 cDNAs evidenced numerous short inverted repeats within the coding sequences and putative Pumilio-binding and embryo-deadenylation elements within the 3'-untranslated regions, indicating the potential regulation ways. We showed that ZAR1 expressed exclusively in oocytes in pig ovary, persisted during first cleavages in embryos developed in vivo and declined sharply in morulae and blastocysts. ZAR1 mRNA was also detected in testis, and, at lower level, in hypothalamus and pituitary in both species. For the first time, ZAR1 was localized in testicular germ cells, notably in round spermatids. In addition, in pig, cattle and human only shorter ZAR1 transcript variants resulting from alternative splicing were found in testis as compared to oocyte. CONCLUSION Our data suggest that in addition to its role in early embryo development highlighted by expression pattern of full-length transcript in oocytes and early embryos, ZAR1 could also be implicated in the regulation of meiosis and post meiotic differentiation of male and female germ cells through expression of shorter splicing variants. Species conservation of ZAR1 expression and regulation underlines the central role of this gene in early reproductive processes.
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Affiliation(s)
- Svetlana Uzbekova
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Monica Roy-Sabau
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Rozenn Dalbiès-Tran
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Christine Perreau
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Pascal Papillier
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Florence Mompart
- Laboratoire de Génétique Cellulaire, INRA, Chemin de Borde-Rouge – Auzeville, BP 52627 31326 Castanet-Tolosan Cedex, France
| | - Aurore Thelie
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Sophie Pennetier
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Juliette Cognie
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Veronique Cadoret
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
- Service de Médecine et Biologie de la Reproduction, UMR 6175, Centre Hospitalier Universitaire Bretonneau, 37044 Tours, France
| | - Dominique Royere
- Service de Médecine et Biologie de la Reproduction, UMR 6175, Centre Hospitalier Universitaire Bretonneau, 37044 Tours, France
| | - Philippe Monget
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Pascal Mermillod
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
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7
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Grandemange S, Schaller S, Yamano S, Du Manoir S, Shpakovski GV, Mattei MG, Kedinger C, Vigneron M. A human RNA polymerase II subunit is encoded by a recently generated multigene family. BMC Mol Biol 2001; 2:14. [PMID: 11747469 PMCID: PMC61041 DOI: 10.1186/1471-2199-2-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2001] [Accepted: 11/30/2001] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The sequences encoding the yeast RNA polymerase II (RPB) subunits are single copy genes. RESULTS While those characterized so far for the human (h) RPB are also unique, we show that hRPB subunit 11 (hRPB11) is encoded by a multigene family, mapping on chromosome 7 at loci p12, q11.23 and q22. We focused on two members of this family, hRPB11a and hRPB11b: the first encodes subunit hRPB11a, which represents the major RPB11 component of the mammalian RPB complex; the second generates polypeptides hRPB11balpha and hRPB11bbeta through differential splicing of its transcript and shares homologies with components of the hPMS2L multigene family related to genes involved in mismatch-repair functions (MMR). Both hRPB11a and b genes are transcribed in all human tissues tested. Using an inter-species complementation assay, we show that only hRPB11balpha is functional in yeast. In marked contrast, we found that the unique murine homolog of RPB11 gene maps on chromosome 5 (band G), and encodes a single polypeptide which is identical to subunit hRPB11a. CONCLUSIONS The type hRPB11b gene appears to result from recent genomic recombination events in the evolution of primates, involving sequence elements related to the MMR apparatus.
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Affiliation(s)
- Sylvie Grandemange
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Sophie Schaller
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Shigeru Yamano
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Stanislas Du Manoir
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP-7, 117997 Moscow, Russia
| | - Marie-Geneviève Mattei
- U.491/INSERM, Faculté de médecine Timone, 27 bd Jean Moulin, F-13385 Marseille Cedex 5, France
| | - Claude Kedinger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Marc Vigneron
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
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8
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Sugaya K, Sasanuma S, Cook PR, Mita K. A mutation in the largest (catalytic) subunit of RNA polymerase II and its relation to the arrest of the cell cycle in G(1) phase. Gene 2001; 274:77-81. [PMID: 11674999 DOI: 10.1016/s0378-1119(01)00615-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transcriptional activity of RNA polymerase II is modulated during the cell cycle. We previously identified a temperature-sensitive mutation in the largest (catalytic) subunit of RNA polymerase II (RPB1) that causes cell cycle arrest and genome instability. We now characterize a different cell line that has a temperature-sensitive defect in cell cycle progression, and find that it also has a mutation in RPB1. The temperature-sensitive mutant, tsAF8, of the Syrian hamster cell line, BHK21, arrests at the non-permissive temperature in the mid-G(1) phase. We show that RPB1 in tsAF8--which is found exclusively in the nucleus at the permissive temperature--is also found in the cytoplasm at the non-permissive temperature. Comparison of the DNA sequences of the RPB1 gene in the wild-type and mutant shows the mutant phenotype results from a (hemizygous) C-to-A variation at nucleotide 944 in one RPB1 allele; this gives rise to an ala-to-asp substitution at residue 315 in the protein. Aligning the amino acid sequences from various species reveals that ala(315) is highly conserved in eukaryotes.
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Affiliation(s)
- K Sugaya
- Genome Research Group, National Institute of Radiological Sciences, 4-9-1, Anagawa, Chiba, 263-8555, Japan.
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9
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Obexer P, Certa U, Kofler R, Helmberg A. Expression profiling of glucocorticoid-treated T-ALL cell lines: rapid repression of multiple genes involved in RNA-, protein- and nucleotide synthesis. Oncogene 2001; 20:4324-36. [PMID: 11466613 DOI: 10.1038/sj.onc.1204573] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2001] [Revised: 04/02/2001] [Accepted: 04/03/2001] [Indexed: 11/08/2022]
Abstract
To arrive at a better understanding of the effects of the glucocorticoid component of chemotherapy protocols on lymphocytic leukemia cells, we analysed early responses of T-lymphocytic leukemia cell lines Jurkat and CEM-C7, both of which undergo apoptosis in response to dexamethasone, via gene chips. Among genes identified as repressed, a notable cluster seemed to be of importance for the processes of transcription, mRNA splicing and protein synthesis. Consequently, we assessed time-resolved uptake of uridine and methionine to monitor RNA and protein synthesis, along with parameters quantifying apoptosis. Repression of uptake to about 65% of that in untreated cells preceded the first sign of apoptosis by several hours in both cell lines. In addition to this general repression of RNA and protein synthesis, several genes were found to be regulated that may contribute to synergistic action of glucocorticoids with other components of frequently used chemotherapy protocols such as antimetabolites, methotrexate and alkylating agents.
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Affiliation(s)
- P Obexer
- Institute of Pathophysiology, University of Innsbruck, Medical School, A 6020 Innsbruck, Austria
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10
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Sugaya K, Sasanuma S, Nohata J, Kimura T, Hongo E, Higashi T, Morimyo M, Tsuji H, Mita K. Cloning and sequencing for the largest subunit of Chinese hamster RNA polymerase II gene: identification of a mutation related to abnormal induction of sister chromatid exchanges. Gene 1997; 194:267-72. [PMID: 9272869 DOI: 10.1016/s0378-1119(97)00204-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In order to analyze the mutation sites related to abnormal induction of sister chromatid exchanges (SCEs) in the RNA polymerase II largest subunit (RpII LS) gene of the Chinese hamster CHO-KI cell mutant, we have completely sequenced the whole region of the RpII LS cDNAs obtained from normal and mutant cells. By comparing both sequences, a mutation that results in an amino acid (aa) change in the RpII LS gene was found. This aa change was Pro (CCC) to Ser (TCC) at position 1006. Multiple alignment for aa sequences of RpII LS from various species revealed that this Pro residue was highly conserved throughout the eukaryotes. Considering the differences in physico-chemical properties between Pro and Ser residues, the Pro-->Ser substitution may alter the RpII LS structure.
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Affiliation(s)
- K Sugaya
- Genome Research Group, National Institute of Radiological Sciences, Chiba, Japan.
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Schoen TJ, Chandrasekharappa SC, Guru SC, Mazuruk K, Chader GJ, Rodriguez IR. Human gene for the RNA polymerase II seventh subunit (hsRPB7): structure, expression and chromosomal localization. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1353:39-49. [PMID: 9256063 DOI: 10.1016/s0167-4781(97)00041-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human gene for the seventh largest subunit of RNA polymerase II complex, hsRPB7 was cloned, sequenced and mapped. This complex is an integral part of the transcription-coupled DNA repair mechanism and has been shown to be involved in several human genetic diseases and implicated in many others. The hsRPB7 gene consists of 8 exons and spans approximately 5.1 kb. Southern blots of genomic and cloned DNA suggest that hsRPB7 is coded for by a single gene. Using human radiation hybrids and YACs, the gene was localized to 11q13.1, within 70 kb of marker D11S1765. The sequence of the 5' flanking region does not contain a TATA element, but does contain several Sp1 binding sites, an AP-1 site and a novel inverted polymorphic GATA tandem repeat. This novel GATA repeat can be used for linkage analysis. The hsRPB7 gene seems to be highly conserved among eukaryotic species, showing general sequence conservation to yeast and Drosophila. Northern blot analysis reveals a high degree of tissue-specific expression. For example, adult retina, brain and kidney exhibit a relatively high level of expression. A moderate level of expression is observed in heart, lung, testis, cornea, retinal pigmented epithelium/choroid and placenta with a lower level of expression in the uterus, small intestine and skeletal muscle. A very low level of expression was observed in stomach and liver. Comparison between four fetal and adult tissues also demonstrate a surprising level of developmental specificity. Expression in fetal retina is considerably lower than fetal brain but similar to adult retina.
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Affiliation(s)
- T J Schoen
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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