101
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Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming. Nat Commun 2016; 7:12354. [PMID: 27507283 PMCID: PMC4987517 DOI: 10.1038/ncomms12354] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/24/2016] [Indexed: 12/17/2022] Open
Abstract
Erasure of epigenetic memory is required to convert somatic cells towards pluripotency. Reactivation of the inactive X chromosome (Xi) has been used to model epigenetic reprogramming in mouse, but human studies are hampered by Xi epigenetic instability and difficulties in tracking partially reprogrammed iPSCs. Here we use cell fusion to examine the earliest events in the reprogramming-induced Xi reactivation of human female fibroblasts. We show that a rapid and widespread loss of Xi-associated H3K27me3 and XIST occurs in fused cells and precedes the bi-allelic expression of selected Xi-genes by many heterokaryons (30–50%). After cell division, RNA-FISH and RNA-seq analyses confirm that Xi reactivation remains partial and that induction of human pluripotency-specific XACT transcripts is rare (1%). These data effectively separate pre- and post-mitotic events in reprogramming-induced Xi reactivation and reveal a complex hierarchy of epigenetic changes that are required to reactivate the genes on the human Xi chromosome. Reactivation of the inactive X chromosome (Xi) has modelled epigenetic reprogramming in mouse. Here, by using cell fusion between human female fibroblasts and mouse embryonic stem cells, the authors show a complex hierarchy of epigenetic changes that are required to reactivate the genes on the human Xi chromosome.
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102
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Goodrich L, Panning B, Leung KN. Activators and repressors: A balancing act for X-inactivation. Semin Cell Dev Biol 2016; 56:3-8. [DOI: 10.1016/j.semcdb.2016.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/06/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
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103
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Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J. Structural organization of the inactive X chromosome in the mouse. Nature 2016; 535:575-9. [PMID: 27437574 PMCID: PMC5443622 DOI: 10.1038/nature18589] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 05/18/2016] [Indexed: 12/23/2022]
Abstract
X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed. Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite. However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions,remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes indifferent neural progenitor clones are associated with the presence of different TAD-like structures after XCI. These findings suggest a key role for transcription and CTCF in the formation of TADs in the context of the Xi chromosome in neural progenitors.
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104
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Leone S, Santoro R. Challenges in the analysis of long noncoding RNA functionality. FEBS Lett 2016; 590:2342-53. [DOI: 10.1002/1873-3468.12308] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Sergio Leone
- Department of Molecular Mechanisms of Disease; University of Zurich; Switzerland
- Molecular Life Science Program; Life Science Zurich Graduate School; University of Zurich; Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease; University of Zurich; Switzerland
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105
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Vallot C, Ouimette JF, Rougeulle C. Establishment of X chromosome inactivation and epigenomic features of the inactive X depend on cellular contexts. Bioessays 2016; 38:869-80. [PMID: 27389958 DOI: 10.1002/bies.201600121] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
X chromosome inactivation (XCI) is an essential epigenetic process that ensures X-linked gene dosage equilibrium between sexes in mammals. XCI is dynamically regulated during development in a manner that is intimately linked to differentiation. Numerous studies, which we review here, have explored the dynamics of X inactivation and reactivation in the context of development, differentiation and diseases, and the phenotypic and molecular link between the inactive status, and the cellular context. Here, we also assess whether XCI is a uniform mechanism in mammals by analyzing epigenetic signatures of the inactive X (Xi) in different species and cellular contexts. It appears that the timing of XCI and the epigenetic signature of the inactive X greatly vary between species. Surprisingly, even within a given species, various Xi configurations are found across cellular states. We discuss possible mechanisms underlying these variations, and how they might influence the fate of the Xi.
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Affiliation(s)
- Céline Vallot
- Sorbonne Paris Cité, Epigenetics and Cell Fate, Université Paris Diderot, Paris, France
| | | | - Claire Rougeulle
- Sorbonne Paris Cité, Epigenetics and Cell Fate, Université Paris Diderot, Paris, France
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106
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Machiela MJ, Zhou W, Karlins E, Sampson JN, Freedman ND, Yang Q, Hicks B, Dagnall C, Hautman C, Jacobs KB, Abnet CC, Aldrich MC, Amos C, Amundadottir LT, Arslan AA, Beane-Freeman LE, Berndt SI, Black A, Blot WJ, Bock CH, Bracci PM, Brinton LA, Bueno-de-Mesquita HB, Burdett L, Buring JE, Butler MA, Canzian F, Carreón T, Chaffee KG, Chang IS, Chatterjee N, Chen C, Chen C, Chen K, Chung CC, Cook LS, Crous Bou M, Cullen M, Davis FG, De Vivo I, Ding T, Doherty J, Duell EJ, Epstein CG, Fan JH, Figueroa JD, Fraumeni JF, Friedenreich CM, Fuchs CS, Gallinger S, Gao YT, Gapstur SM, Garcia-Closas M, Gaudet MM, Gaziano JM, Giles GG, Gillanders EM, Giovannucci EL, Goldin L, Goldstein AM, Haiman CA, Hallmans G, Hankinson SE, Harris CC, Henriksson R, Holly EA, Hong YC, Hoover RN, Hsiung CA, Hu N, Hu W, Hunter DJ, Hutchinson A, Jenab M, Johansen C, Khaw KT, Kim HN, Kim YH, Kim YT, Klein AP, Klein R, Koh WP, Kolonel LN, Kooperberg C, Kraft P, Krogh V, Kurtz RC, LaCroix A, Lan Q, Landi MT, Marchand LL, Li D, Liang X, Liao LM, Lin D, Liu J, Lissowska J, Lu L, Magliocco AM, Malats N, Matsuo K, McNeill LH, McWilliams RR, Melin BS, Mirabello L, Moore L, Olson SH, Orlow I, Park JY, Patiño-Garcia A, Peplonska B, Peters U, Petersen GM, Pooler L, Prescott J, Prokunina-Olsson L, Purdue MP, Qiao YL, Rajaraman P, Real FX, Riboli E, Risch HA, Rodriguez-Santiago B, Ruder AM, Savage SA, Schumacher F, Schwartz AG, Schwartz KL, Seow A, Wendy Setiawan V, Severi G, Shen H, Sheng X, Shin MH, Shu XO, Silverman DT, Spitz MR, Stevens VL, Stolzenberg-Solomon R, Stram D, Tang ZZ, Taylor PR, Teras LR, Tobias GS, Van Den Berg D, Visvanathan K, Wacholder S, Wang JC, Wang Z, Wentzensen N, Wheeler W, White E, Wiencke JK, Wolpin BM, Wong MP, Wu C, Wu T, Wu X, Wu YL, Wunder JS, Xia L, Yang HP, Yang PC, Yu K, Zanetti KA, Zeleniuch-Jacquotte A, Zheng W, Zhou B, Ziegler RG, Perez-Jurado LA, Caporaso NE, Rothman N, Tucker M, Dean MC, Yeager M, Chanock SJ. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome. Nat Commun 2016; 7:11843. [PMID: 27291797 PMCID: PMC4909985 DOI: 10.1038/ncomms11843] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
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Affiliation(s)
- Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Joshua N. Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Casey Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Christopher Hautman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Kevin B. Jacobs
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
- Bioinformed, LLC, Gaithersburg, Maryland 20877, USA
| | - Christian C. Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Christopher Amos
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Laufey T. Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Alan A. Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, New York 10016, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016, USA
- New York University Cancer Institute, New York, New York 10016, USA
| | - Laura E. Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - Cathryn H. Bock
- Karmanos Cancer Institute and Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
| | - Paige M. Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
| | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - H Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), 3721 Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center, 3584 CX Utrecht, The Netherlands
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London SW7 2AZ, UK
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Julie E. Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Mary A. Butler
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio 45226, USA
| | - Federico Canzian
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tania Carreón
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio 45226, USA
| | - Kari G. Chaffee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Chu Chen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300040, China
| | - Charles C. Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Linda S. Cook
- University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Marta Crous Bou
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Faith G. Davis
- Department of Public Health Sciences, School of Public Health, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Jennifer Doherty
- Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03755, USA
| | - Eric J. Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute, Catalan Institute of Oncology (ICO-IDIBELL), 08908 Barcelona, Spain
| | - Caroline G. Epstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Jin-Hu Fan
- Shanghai Cancer Institute, Shanghai 200032, China
| | - Jonine D. Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Joseph F. Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Christine M. Friedenreich
- Department of Population Health Research, Cancer Control Alberta, Alberta Health Services, Calgary, Alberta, Canada T2N 2T9
| | - Charles S. Fuchs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Steven Gallinger
- Fred A Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada M5G 1X5
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotaong University School of Medicine, Shanghai 200032, China
| | - Susan M. Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Montserrat Garcia-Closas
- Division of Genetics and Epidemiology, and Breakthrough Breast Cancer Centre, Institute for Cancer Research, London SM2 5NG, UK
| | - Mia M. Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - J. Michael Gaziano
- Divisions of Preventive Medicine and Aging, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Massachusetts Veterans Epidemiology Research and Information Center/VA Cooperative Studies Programs, Veterans Affairs Boston Healthcare System, Boston, Massachusetts 02130, USA
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria & Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Elizabeth M. Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Edward L. Giovannucci
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Lynn Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine at the University of Southern California, Los Angeles, California 90033, USA
| | - Goran Hallmans
- Department of Public Health and Clinical Medicine/Nutritional Research, Umeå University, 901 87 Umeå, Sweden
| | - Susan E. Hankinson
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Biostatistics and Epidemiology, University of Massachusetts School of Public Health and Health Sciences, Amherst, Massachusetts 01003, USA
| | - Curtis C. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Roger Henriksson
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden
| | - Elizabeth A. Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 151-742, Republic of Korea
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Chao A. Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Mazda Jenab
- International Agency for Research on Cancer (IARC-WHO), 69372 Lyon, France
| | - Christoffer Johansen
- Oncology, Finsen Centre, Rigshospitalet, 2100 Copenhagen, Denmark
- Unit of Survivorship Research, The Danish Cancer Society Research Centre, 2100 Copenhagen, Denmark
| | - Kay-Tee Khaw
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - Hee Nam Kim
- Center for Creative Biomedical Scientists, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul 151-742, Republic of Korea
| | - Young Tae Kim
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Alison P. Klein
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Robert Klein
- Program in Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Woon-Puay Koh
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 119077, Singapore
| | - Laurence N. Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Vittorio Krogh
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milano 20133, Italy
| | - Robert C. Kurtz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Andrea LaCroix
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiaolin Liang
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Linda M. Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianjun Liu
- Department of Human Genetics, Genome Institute of Singapore 138672, Singapore
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Lingeng Lu
- Yale School of Public Health, New Haven, Connecticut 06510, USA
| | | | - Nuria Malats
- Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Lorna H. McNeill
- Department of Health Disparities Research, Division of OVP, Cancer Prevention and Population Sciences, and Center for Community-Engaged Translational Research, Duncan Family Institute, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Beatrice S. Melin
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Lee Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Sara H. Olson
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Irene Orlow
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu 101, Republic of Korea
| | - Ana Patiño-Garcia
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, IdiSNA, Navarra Institute for Health Research, Pamplona 31080, Spain
| | - Beata Peplonska
- Nofer Institute of Occupational Medicine, Lodz 91-348, Poland
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Gloria M. Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Loreall Pooler
- University of Southern California, Los Angeles, California 90007, USA
| | - Jennifer Prescott
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - You-Lin Qiao
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Francisco X. Real
- Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Elio Riboli
- Division of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Harvey A. Risch
- Yale School of Public Health, New Haven, Connecticut 06510, USA
| | - Benjamin Rodriguez-Santiago
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08002, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, 28029, Spain
- Quantitative Genomic Medicine Laboratory, qGenomics, Barcelona 08003, Spain
| | - Avima M. Ruder
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio 45226, USA
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine at the University of Southern California, Los Angeles, California 90033, USA
| | - Ann G. Schwartz
- Karmanos Cancer Institute and Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
| | - Kendra L. Schwartz
- Karmanos Cancer Institute and Department of Family Medicine and Public Health Sciences, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 119077, Singapore
| | - Veronica Wendy Setiawan
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine at the University of Southern California, Los Angeles, California 90033, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria & Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Human Genetics Foundation (HuGeF), Torino, 10126, Italy
| | - Hongbing Shen
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Nanjing Medical University, Nanjing 210029, China
- Department of Epidemiology, Nanjing Medical University School of Public Health, Nanjing 210029, China
| | - Xin Sheng
- University of Southern California, Los Angeles, California 90007, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwanju 501-746, Republic of Korea
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Debra T. Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | | | - Victoria L. Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Daniel Stram
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine at the University of Southern California, Los Angeles, California 90033, USA
| | - Ze-Zhong Tang
- Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Lauren R. Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Geoffrey S. Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - David Van Den Berg
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine at the University of Southern California, Los Angeles, California 90033, USA
| | - Kala Visvanathan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21218, USA
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Jiu-Cun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - William Wheeler
- Information Management Services Inc., Calverton, Maryland, 20904, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - John K. Wiencke
- University of California San Francisco, San Francisco, California 94143, USA
| | - Brian M. Wolpin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Maria Pik Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chen Wu
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Tangchun Wu
- Institute of Occupational Medicine and Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan 430400, China
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 515200, China
| | - Jay S. Wunder
- Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 515200, China
| | - Lucy Xia
- University of Southern California, Los Angeles, California 90007, USA
| | - Hannah P. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Pan-Chyr Yang
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Krista A. Zanetti
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Anne Zeleniuch-Jacquotte
- New York University Cancer Institute, New York, New York 10016, USA
- Department of Population Health, New York University School of Medicine, New York, New York 10016, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110001, China
| | - Regina G. Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Luis A. Perez-Jurado
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08002, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, 28029, Spain
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Michael C. Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland 20892, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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Keniry A, Gearing LJ, Jansz N, Liu J, Holik AZ, Hickey PF, Kinkel SA, Moore DL, Breslin K, Chen K, Liu R, Phillips C, Pakusch M, Biben C, Sheridan JM, Kile BT, Carmichael C, Ritchie ME, Hilton DJ, Blewitt ME. Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing. Epigenetics Chromatin 2016; 9:16. [PMID: 27195021 PMCID: PMC4870784 DOI: 10.1186/s13072-016-0064-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/31/2016] [Indexed: 11/16/2022] Open
Abstract
Background
The presence of histone 3 lysine 9 (H3K9) methylation on the mouse inactive X chromosome has been controversial over the last 15 years, and the functional role of H3K9 methylation in X chromosome inactivation in any species has remained largely unexplored. Results Here we report the first genomic analysis of H3K9 di- and tri-methylation on the inactive X: we find they are enriched at the intergenic, gene poor regions of the inactive X, interspersed between H3K27 tri-methylation domains found in the gene dense regions. Although H3K9 methylation is predominantly non-genic, we find that depletion of H3K9 methylation via depletion of H3K9 methyltransferase Set domain bifurcated 1 (Setdb1) during the establishment of X inactivation, results in failure of silencing for around 150 genes on the inactive X. By contrast, we find a very minor role for Setdb1-mediated H3K9 methylation once X inactivation is fully established. In addition to failed gene silencing, we observed a specific failure to silence X-linked long-terminal repeat class repetitive elements. Conclusions Here we have shown that H3K9 methylation clearly marks the murine inactive X chromosome. The role of this mark is most apparent during the establishment phase of gene silencing, with a more muted effect on maintenance of the silent state. Based on our data, we hypothesise that Setdb1-mediated H3K9 methylation plays a role in epigenetic silencing of the inactive X via silencing of the repeats, which itself facilitates gene silencing through alterations to the conformation of the whole inactive X chromosome. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0064-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Linden J Gearing
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Joy Liu
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Aliaksei Z Holik
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Sarah A Kinkel
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Darcy L Moore
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ruijie Liu
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Catherine Phillips
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Miha Pakusch
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Christine Biben
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Julie M Sheridan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Benjamin T Kile
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Catherine Carmichael
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.,Department of Genetics, University of Melbourne, Melbourne, VIC 3010 Australia
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Furlan G, Rougeulle C. Function and evolution of the long noncoding RNA circuitry orchestrating X-chromosome inactivation in mammals. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:702-22. [PMID: 27173581 DOI: 10.1002/wrna.1359] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 12/20/2022]
Abstract
X-chromosome inactivation (XCI) is a chromosome-wide regulatory process that ensures dosage compensation for X-linked genes in Theria. XCI is established during early embryogenesis and is developmentally regulated. Different XCI strategies exist in mammalian infraclasses and the regulation of this process varies also among closely related species. In Eutheria, initiation of XCI is orchestrated by a cis-acting locus, the X-inactivation center (Xic), which is particularly enriched in genes producing long noncoding RNAs (lncRNAs). Among these, Xist generates a master transcript that coats and propagates along the future inactive X-chromosome in cis, establishing X-chromosome wide transcriptional repression through interaction with several protein partners. Other lncRNAs also participate to the regulation of X-inactivation but the extent to which their function has been maintained in evolution is still poorly understood. In Metatheria, Xist is not conserved, but another, evolutionary independent lncRNA with similar properties, Rsx, has been identified, suggesting that lncRNA-mediated XCI represents an evolutionary advantage. Here, we review current knowledge on the interplay of X chromosome-encoded lncRNAs in ensuring proper establishment and maintenance of chromosome-wide silencing, and discuss the evolutionary implications of the emergence of species-specific lncRNAs in the control of XCI within Theria. WIREs RNA 2016, 7:702-722. doi: 10.1002/wrna.1359 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Giulia Furlan
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216 CNRS, Université Paris Diderot, Paris, France
| | - Claire Rougeulle
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216 CNRS, Université Paris Diderot, Paris, France
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109
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Payer B. Developmental regulation of X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:88-99. [PMID: 27112543 DOI: 10.1016/j.semcdb.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.
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110
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Pinter SF. A Tale of Two Cities: How Xist and its partners localize to and silence the bicompartmental X. Semin Cell Dev Biol 2016; 56:19-34. [PMID: 27072488 DOI: 10.1016/j.semcdb.2016.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
Abstract
Sex chromosomal dosage compensation in mammals takes the form of X chromosome inactivation (XCI), driven by the non-coding RNA Xist. In contrast to dosage compensation systems of flies and worms, mammalian XCI has to restrict its function to the Xist-producing X chromosome, while leaving autosomes and active X untouched. The mechanisms behind the long-range yet cis-specific localization and silencing activities of Xist have long been enigmatic, but genomics, proteomics, super-resolution microscopy, and innovative genetic approaches have produced significant new insights in recent years. In this review, I summarize and integrate these findings with a particular focus on the redundant yet mutually reinforcing pathways that enable long-term transcriptional repression throughout the soma. This includes an exploration of concurrent epigenetic changes acting in parallel within two distinct compartments of the inactive X. I also examine how Polycomb repressive complexes 1 and 2 and macroH2A may bridge XCI establishment and maintenance. XCI is a remarkable phenomenon that operates across multiple scales, combining changes in nuclear architecture, chromosome topology, chromatin compaction, and nucleosome/nucleotide-level epigenetic cues. Learning how these pathways act in concert likely holds the answer to the riddle posed by Cattanach's and other autosomal translocations: What makes the X especially receptive to XCI?
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Affiliation(s)
- Stefan F Pinter
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06030-6403, USA.
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111
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Pandya-Jones A, Plath K. The "lnc" between 3D chromatin structure and X chromosome inactivation. Semin Cell Dev Biol 2016; 56:35-47. [PMID: 27062886 DOI: 10.1016/j.semcdb.2016.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/01/2022]
Abstract
The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions.
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Affiliation(s)
- Amy Pandya-Jones
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA.
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112
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Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X. Proc Natl Acad Sci U S A 2016; 113:E2029-38. [PMID: 27001848 DOI: 10.1073/pnas.1520113113] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Females have a greater immunological advantage than men, yet they are more prone to autoimmune disorders. The basis for this sex bias lies in the X chromosome, which contains many immunity-related genes. Female mammals use X chromosome inactivation (XCI) to generate a transcriptionally silent inactive X chromosome (Xi) enriched with heterochromatic modifications and XIST/Xist RNA, which equalizes gene expression between the sexes. Here, we examine the maintenance of XCI in lymphocytes from females in mice and humans. Strikingly, we find that mature naïve T and B cells have dispersed patterns of XIST/Xist RNA, and they lack the typical heterochromatic modifications of the Xi. In vitro activation of lymphocytes triggers the return of XIST/Xist RNA transcripts and some chromatin marks (H3K27me3, ubiquitin-H2A) to the Xi. Single-cell RNA FISH analysis of female T cells revealed that the X-linked immunity genes CD40LG and CXCR3 are biallelically expressed in some cells. Using knockout and knockdown approaches, we find that Xist RNA-binding proteins, YY1 and hnRNPU, are critical for recruitment of XIST/Xist RNA back to the Xi. Furthermore, we examined B cells from patients with systemic lupus erythematosus, an autoimmune disorder with a strong female bias, and observed different XIST RNA localization patterns, evidence of biallelic expression of immunity-related genes, and increased transcription of these genes. We propose that the Xi in female lymphocytes is predisposed to become partially reactivated and to overexpress immunity-related genes, providing the first mechanistic evidence to our knowledge for the enhanced immunity of females and their increased susceptibility for autoimmunity.
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113
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Impaired imprinted X chromosome inactivation is responsible for the skewed sex ratio following in vitro fertilization. Proc Natl Acad Sci U S A 2016; 113:3197-202. [PMID: 26951653 DOI: 10.1073/pnas.1523538113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dynamic epigenetic reprogramming occurs during normal embryonic development at the preimplantation stage. Erroneous epigenetic modifications due to environmental perturbations such as manipulation and culture of embryos during in vitro fertilization (IVF) are linked to various short- or long-term consequences. Among these, the skewed sex ratio, an indicator of reproductive hazards, was reported in bovine and porcine embryos and even human IVF newborns. However, since the first case of sex skewing reported in 1991, the underlying mechanisms remain unclear. We reported herein that sex ratio is skewed in mouse IVF offspring, and this was a result of female-biased peri-implantation developmental defects that were originated from impaired imprinted X chromosome inactivation (iXCI) through reduced ring finger protein 12 (Rnf12)/X-inactive specific transcript (Xist) expression. Compensation of impaired iXCI by overexpression of Rnf12 to up-regulate Xist significantly rescued female-biased developmental defects and corrected sex ratio in IVF offspring. Moreover, supplementation of an epigenetic modulator retinoic acid in embryo culture medium up-regulated Rnf12/Xist expression, improved iXCI, and successfully redeemed the skewed sex ratio to nearly 50% in mouse IVF offspring. Thus, our data show that iXCI is one of the major epigenetic barriers for the developmental competence of female embryos during preimplantation stage, and targeting erroneous epigenetic modifications may provide a potential approach for preventing IVF-associated complications.
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114
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Pluripotent stem cells and livestock genetic engineering. Transgenic Res 2016; 25:289-306. [PMID: 26894405 DOI: 10.1007/s11248-016-9929-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/06/2016] [Indexed: 01/12/2023]
Abstract
The unlimited proliferative ability and capacity to contribute to germline chimeras make pluripotent embryonic stem cells (ESCs) perfect candidates for complex genetic engineering. The utility of ESCs is best exemplified by the numerous genetic models that have been developed in mice, for which such cells are readily available. However, the traditional systems for mouse genetic engineering may not be practical for livestock species, as it requires several generations of mating and selection in order to establish homozygous founders. Nevertheless, the self-renewal and pluripotent characteristics of ESCs could provide advantages for livestock genetic engineering such as ease of genetic manipulation and improved efficiency of cloning by nuclear transplantation. These advantages have resulted in many attempts to isolate livestock ESCs, yet it has been generally concluded that the culture conditions tested so far are not supportive of livestock ESCs self-renewal and proliferation. In contrast, there are numerous reports of derivation of livestock induced pluripotent stem cells (iPSCs), with demonstrated capacity for long term proliferation and in vivo pluripotency, as indicated by teratoma formation assay. However, to what extent these iPSCs represent fully reprogrammed PSCs remains controversial, as most livestock iPSCs depend on continuous expression of reprogramming factors. Moreover, germline chimerism has not been robustly demonstrated, with only one successful report with very low efficiency. Therefore, even 34 years after derivation of mouse ESCs and their extensive use in the generation of genetic models, the livestock genetic engineering field can stand to gain enormously from continued investigations into the derivation and application of ESCs and iPSCs.
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Maduro C, de Hoon B, Gribnau J. Fitting the Puzzle Pieces: the Bigger Picture of XCI. Trends Biochem Sci 2016; 41:138-147. [DOI: 10.1016/j.tibs.2015.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/08/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023]
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116
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RNA binding proteins implicated in Xist-mediated chromosome silencing. Semin Cell Dev Biol 2016; 56:58-70. [PMID: 26816113 DOI: 10.1016/j.semcdb.2016.01.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 11/20/2022]
Abstract
Chromosome silencing by Xist RNA occurs in two steps; localisation in cis within the nuclear matrix to form a domain that corresponds to the territory of the inactive X chromosome elect, and transduction of silencing signals from Xist RNA to the underlying chromatin. Key factors that mediate these processes have been identified in a series of recent studies that harnessed comprehensive proteomic or genetic screening strategies. In this review we discuss these findings in light of prior knowledge both of Xist-mediated silencing and known functions/properties of the novel factors.
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117
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Abstract
X-inactive specific transcript (Xist) long noncoding RNA (lncRNA) is thought to catalyze silencing of X-linked genes in cis during X-chromosome inactivation, which equalizes X-linked gene dosage between male and female mammals. To test the impact of Xist RNA on X-linked gene silencing, we ectopically induced endogenous Xist by ablating the antisense repressor Tsix in mice. We find that ectopic Xist RNA induction and subsequent X-linked gene silencing is sex specific in embryos and in differentiating embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs). A higher frequency of X(ΔTsix)Y male cells displayed ectopic Xist RNA coating compared with X(ΔTsix)X female cells. This increase reflected the inability of X(ΔTsix)Y cells to efficiently silence X-linked genes compared with X(ΔTsix)X cells, despite equivalent Xist RNA induction and coating. Silencing of genes on both Xs resulted in significantly reduced proliferation and increased cell death in X(ΔTsix)X female cells relative to X(ΔTsix)Y male cells. Thus, whereas Xist RNA can inactivate the X chromosome in females it may not do so in males. We further found comparable silencing in differentiating X(ΔTsix)Y and 39,X(ΔTsix) (X(ΔTsix)O) ESCs, excluding the Y chromosome and instead implicating the X-chromosome dose as the source of the sex-specific differences. Because X(ΔTsix)X female embryonic epiblast cells and EpiSCs harbor an inactivated X chromosome prior to ectopic inactivation of the active X(ΔTsix) X chromosome, we propose that the increased expression of one or more X-inactivation escapees activates Xist and, separately, helps trigger X-linked gene silencing.
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118
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How Many Non-coding RNAs Does It Take to Compensate Male/Female Genetic Imbalance? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 886:33-49. [PMID: 26659486 DOI: 10.1007/978-94-017-7417-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genetic sex determination in mammals relies on dimorphic sex chromosomes that confer phenotypic/physiologic differences between males and females. In this heterogametic system, X and Y chromosomes diverged from an ancestral pair of autosomes, creating a genetic disequilibrium between XX females and XY males. Dosage compensation mechanisms alleviate intrinsic gene dosage imbalance, leading to equal expression levels of most X-linked genes in the two sexes. In therian mammals, this is achieved through inactivation of one of the two X chromosomes in females. Failure to undergo X-chromosome inactivation (XCI) results in developmental arrest and death. Although fundamental for survival, a surprising loose conservation in the mechanisms to achieve XCI during development in therian lineage has been, and continues, to be uncovered. XCI involves the concerted action of non-coding RNAs (ncRNAs), including the well-known Xist RNA, and has thus become a classical paradigm to study the mode of action of this particular class of transcripts. In this chapter, we will describe the processes coping with sex chromosome genetic imbalance and how ncRNAs underlie dosage compensation mechanisms and influence male-female differences in mammals. Moreover, we will discuss how ncRNAs have been tinkered with during therian evolution to adapt XCI mechanistic to species-specific constraints.
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119
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Hwang JY, Oh JN, Park CH, Lee DK, Lee CK. Dosage compensation of X-chromosome inactivation center-linked genes in porcine preimplantation embryos: Non-chromosome-wide initiation of X-chromosome inactivation in blastocysts. Mech Dev 2015; 138 Pt 3:246-55. [DOI: 10.1016/j.mod.2015.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 10/05/2015] [Accepted: 10/23/2015] [Indexed: 11/25/2022]
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120
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Ohhata T, Matsumoto M, Leeb M, Shibata S, Sakai S, Kitagawa K, Niida H, Kitagawa M, Wutz A. Histone H3 Lysine 36 Trimethylation Is Established over the Xist Promoter by Antisense Tsix Transcription and Contributes to Repressing Xist Expression. Mol Cell Biol 2015; 35:3909-20. [PMID: 26370508 PMCID: PMC4609750 DOI: 10.1128/mcb.00561-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/10/2015] [Accepted: 09/04/2015] [Indexed: 12/18/2022] Open
Abstract
One of the two X chromosomes in female mammals is inactivated by the noncoding Xist RNA. In mice, X chromosome inactivation (XCI) is regulated by the antisense RNA Tsix, which represses Xist on the active X chromosome. In the absence of Tsix, PRC2-mediated histone H3 lysine 27 trimethylation (H3K27me3) is established over the Xist promoter. Simultaneous disruption of Tsix and PRC2 leads to derepression of Xist and in turn silencing of the single X chromosome in male embryonic stem cells. Here, we identified histone H3 lysine 36 trimethylation (H3K36me3) as a modification that is recruited by Tsix cotranscriptionally and extends over the Xist promoter. Reduction of H3K36me3 by expression of a mutated histone H3.3 with a substitution of methionine for lysine at position 36 causes a significant derepression of Xist. Moreover, depletion of the H3K36 methylase Setd2 leads to upregulation of Xist, suggesting H3K36me3 as a modification that contributes to the mechanism of Tsix function in regulating XCI. Furthermore, we found that reduction of H3K36me3 does not facilitate an increase in H3K27me3 over the Xist promoter, indicating that additional mechanisms exist by which Tsix blocks PRC2 recruitment to the Xist promoter.
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Affiliation(s)
- Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan WT and MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mika Matsumoto
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Martin Leeb
- WT and MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Shinwa Shibata
- Department of Stem Cell Biology, Graduate School of Medicine, Kanazawa University, Kanazawa, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kyoko Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Anton Wutz
- WT and MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom Institute of Molecular Health Sciences, ETH, Zurich, Switzerland
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121
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Minkovsky A, Sahakyan A, Bonora G, Damoiseaux R, Dimitrova E, Rubbi L, Pellegrini M, Radu CG, Plath K. A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2'-dC upon inhibition of ribonucleotide reductase. Epigenetics Chromatin 2015; 8:42. [PMID: 26468331 PMCID: PMC4604769 DOI: 10.1186/s13072-015-0034-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is important for the maintenance of the silent state of genes on the inactive X chromosome (Xi). Here, we screened for siRNAs and chemicals that reactivate an Xi-linked reporter in the presence of 5-aza-2'-deoxycytidine (5-aza-2'-dC), an inhibitor of DNA methyltransferase 1, at a concentration that, on its own, is not sufficient for Xi-reactivation. RESULTS We found that inhibition of ribonucleotide reductase (RNR) induced expression of the reporter. RNR inhibition potentiated the effect of 5-aza-2'-dC by enhancing its DNA incorporation, thereby decreasing DNA methylation levels genome-wide. Since both 5-aza-2'-dC and RNR-inhibitors are used in the treatment of hematological malignancies, we treated myeloid leukemia cell lines with 5-aza-2'-dC and the RNR-inhibitor hydroxyurea, and observed synergistic inhibition of cell growth and a decrease in genome-wide DNA methylation. CONCLUSIONS Taken together, our study identifies a drug combination that enhances DNA demethylation by altering nucleotide metabolism. This demonstrates that Xi-reactivation assays can be used to optimize the epigenetic activity of drug combinations.
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Affiliation(s)
- Alissa Minkovsky
- Department of Biological Chemistry, David Geffen School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, 90095 USA
| | - Anna Sahakyan
- Department of Biological Chemistry, David Geffen School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, 90095 USA
| | - Giancarlo Bonora
- Department of Biological Chemistry, David Geffen School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, 90095 USA
| | - Robert Damoiseaux
- Department of Molecular and Medicinal Chemistry and California NanoSystems Institute, University of California, Los Angeles, 90095 USA
| | - Elizabeth Dimitrova
- Ahmanson Translational Imaging Division, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, 90095 USA
| | - Liudmilla Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 90095 USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 90095 USA
| | - Caius G Radu
- Ahmanson Translational Imaging Division, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, 90095 USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, 90095 USA
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122
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Kelsey AD, Yang C, Leung D, Minks J, Dixon-McDougall T, Baldry SEL, Bogutz AB, Lefebvre L, Brown CJ. Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST. Genome Biol 2015; 16:208. [PMID: 26429547 PMCID: PMC4591629 DOI: 10.1186/s13059-015-0774-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/10/2015] [Indexed: 01/07/2023] Open
Abstract
Background X-chromosome inactivation is a striking example of epigenetic silencing in which expression of the long non-coding RNA XIST initiates the heterochromatinization and silencing of one of the pair of X chromosomes in mammalian females. To understand how the RNA can establish silencing across millions of basepairs of DNA we have modelled the process by inducing expression of XIST from nine different locations in human HT1080 cells. Results Localization of XIST, depletion of Cot-1 RNA, perinuclear localization, and ubiquitination of H2A occurs at all sites examined, while recruitment of H3K9me3 was not observed. Recruitment of the heterochromatic features SMCHD1, macroH2A, H3K27me3, and H4K20me1 occurs independently of each other in an integration site-dependent manner. Silencing of flanking reporter genes occurs at all sites, but the spread of silencing to flanking endogenous human genes is variable in extent of silencing as well as extent of spread, with silencing able to skip regions. The spread of H3K27me3 and loss of H3K27ac correlates with the pre-existing levels of the modifications, and overall the extent of silencing correlates with the ability to recruit additional heterochromatic features. Conclusions The non-coding RNA XIST functions as a cis-acting silencer when expressed from nine different locations throughout the genome. A hierarchy among the features of heterochromatin reveals the importance of interaction with the local chromatin neighborhood for optimal spread of silencing, as well as the independent yet cooperative nature of the establishment of heterochromatin by the non-coding XIST RNA. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0774-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angela D Kelsey
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Christine Yang
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Danny Leung
- Ludwig Institute for Cancer Research, University of California at San Diego School of Medicine, La Jolla, CA, USA. .,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| | - Jakub Minks
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Thomas Dixon-McDougall
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Sarah E L Baldry
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Aaron B Bogutz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
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123
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Abstract
X chromosome inactivation (XCI) is the dosage compensation mechanism that evolved in female mammals to correct the genetic imbalance of X-linked genes between sexes. X chromosome inactivation occurs in early development when one of the two X chromosomes of females is nearly-completely silenced. Differentiating Embryonic Stem cells (ESC) are regarded as a useful tool to study XCI, since they recapitulate many events occurring during early development. In this review we aim to summarise the advances in the field and to discuss the close connection between cell differentiation and X chromosome inactivation, with a particular focus on mouse ESCs.
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Affiliation(s)
- Greta Pintacuda
- />Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | - Andrea Cerase
- />EMBL Mouse Biology Unit, Monterotondo, 00015 RM Italy
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124
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Sen A, Heredia N, Senut MC, Land S, Hollocher K, Lu X, Dereski MO, Ruden DM. Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildren. Sci Rep 2015; 5:14466. [PMID: 26417717 PMCID: PMC4586440 DOI: 10.1038/srep14466] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/30/2015] [Indexed: 12/26/2022] Open
Abstract
We report that the DNA methylation profile of a child’s neonatal whole blood can be significantly influenced by his or her mother’s neonatal blood lead levels (BLL). We recruited 35 mother-infant pairs in Detroit and measured the whole blood lead (Pb) levels and DNA methylation levels at over 450,000 loci from current blood and neonatal blood from both the mother and the child. We found that mothers with high neonatal BLL correlate with altered DNA methylation at 564 loci in their children’s neonatal blood. Our results suggest that Pb exposure during pregnancy affects the DNA methylation status of the fetal germ cells, which leads to altered DNA methylation in grandchildren’s neonatal dried blood spots. This is the first demonstration that an environmental exposure in pregnant mothers can have an epigenetic effect on the DNA methylation pattern in the grandchildren.
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Affiliation(s)
- Arko Sen
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201.,Department of Pharmacology, Wayne State University, Detroit, MI 48201
| | - Nicole Heredia
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201
| | - Marie-Claude Senut
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201
| | - Susan Land
- C. S. Mott Centre for Human Growth and Development, Wayne State University, Detroit, MI 48201.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201
| | | | - Xiangyi Lu
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201
| | - Mary O Dereski
- Department of Biomedical Sciences, Oakland University William Beaumont School of Medicine, Rochester, MI 48309
| | - Douglas M Ruden
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201.,C. S. Mott Centre for Human Growth and Development, Wayne State University, Detroit, MI 48201.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201
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125
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Cerase A, Pintacuda G, Tattermusch A, Avner P. Xist localization and function: new insights from multiple levels. Genome Biol 2015; 16:166. [PMID: 26282267 PMCID: PMC4539689 DOI: 10.1186/s13059-015-0733-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/29/2015] [Indexed: 12/21/2022] Open
Abstract
In female mammals, one of the two X chromosomes in each cell is transcriptionally silenced in order to achieve dosage compensation between the genders in a process called X chromosome inactivation. The master regulator of this process is the long non-coding RNA Xist. During X-inactivation, Xist accumulates in cis on the future inactive X chromosome, triggering a cascade of events that provoke the stable silencing of the entire chromosome, with relatively few genes remaining active. How Xist spreads, what are its binding sites, how it recruits silencing factors and how it induces a specific topological and nuclear organization of the chromatin all remain largely unanswered questions. Recent studies have improved our understanding of Xist localization and the proteins with which it interacts, allowing a reappraisal of ideas about Xist function. We discuss recent advances in our knowledge of Xist-mediated silencing, focusing on Xist spreading, the nuclear organization of the inactive X chromosome, recruitment of the polycomb complex and the role of the nuclear matrix in the process of X chromosome inactivation.
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Affiliation(s)
- Andrea Cerase
- EMBL Mouse Biology Unit, Monterotondo, 00015 (RM), Italy.
| | - Greta Pintacuda
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Anna Tattermusch
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Philip Avner
- EMBL Mouse Biology Unit, Monterotondo, 00015 (RM), Italy. .,Institut Pasteur, Unite de Genetique Moleculaire Murine, CNRS, URA2578, Paris, France.
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126
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Marks H, Kerstens HHD, Barakat TS, Splinter E, Dirks RAM, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG. Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. Genome Biol 2015; 16:149. [PMID: 26235224 PMCID: PMC4546214 DOI: 10.1186/s13059-015-0698-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/18/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells, which contain a single X chromosome. Here, we use mouse female embryonic stem cells (ESCs) with non-random X chromosome inactivation (XCI) and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome by high-resolution allele-specific RNA-seq. RESULTS Induction of XCI by differentiation of female ESCs shows that genes proximal to the X-inactivation center are silenced earlier than distal genes, while lowly expressed genes show faster XCI dynamics than highly expressed genes. The active X chromosome shows a minor but significant increase in gene activity during differentiation, resulting in complete dosage compensation in differentiated cell types. Genes escaping XCI show little or no silencing during early propagation of XCI. Allele-specific RNA-seq of neural progenitor cells generated from the female ESCs identifies three regions distal to the X-inactivation center that escape XCI. These regions, which stably escape during propagation and maintenance of XCI, coincide with topologically associating domains (TADs) as present in the female ESCs. Also, the previously characterized gene clusters escaping XCI in human fibroblasts correlate with TADs. CONCLUSIONS The gene silencing observed during XCI provides further insight in the establishment of the repressive complex formed by the inactive X chromosome. The association of escape regions with TADs, in mouse and human, suggests that TADs are the primary targets during propagation of XCI over the X chromosome.
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Affiliation(s)
- Hendrik Marks
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Hindrik H D Kerstens
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tahsin Stefan Barakat
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Erik Splinter
- Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
| | - René A M Dirks
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Guido van Mierlo
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Onkar Joshi
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Shuang-Yin Wang
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tomas Babak
- Biology Department, Queen's University, Kingston, ON, Canada.
| | - Cornelis A Albers
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tüzer Kalkan
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Alice Jouneau
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Wouter de Laat
- Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Hendrik G Stunnenberg
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
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127
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Monfort A, Di Minin G, Postlmayr A, Freimann R, Arieti F, Thore S, Wutz A. Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells. Cell Rep 2015; 12:554-61. [PMID: 26190100 PMCID: PMC4530576 DOI: 10.1016/j.celrep.2015.06.067] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/22/2015] [Accepted: 06/23/2015] [Indexed: 01/21/2023] Open
Abstract
In mammals, the noncoding Xist RNA triggers transcriptional silencing of one of the two X chromosomes in female cells. Here, we report a genetic screen for silencing factors in X chromosome inactivation using haploid mouse embryonic stem cells (ESCs) that carry an engineered selectable reporter system. This system was able to identify several candidate factors that are genetically required for chromosomal repression by Xist. Among the list of candidates, we identify the RNA-binding protein Spen, the homolog of split ends. Independent validation through gene deletion in ESCs confirms that Spen is required for gene repression by Xist. However, Spen is not required for Xist RNA localization and the recruitment of chromatin modifications, including Polycomb protein Ezh2. The identification of Spen opens avenues for further investigation into the gene-silencing pathway of Xist and shows the usefulness of haploid ESCs for genetic screening of epigenetic pathways.
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Affiliation(s)
- Asun Monfort
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Giulio Di Minin
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Andreas Postlmayr
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Remo Freimann
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Fabiana Arieti
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 62500, Czech Republic
| | - Stéphane Thore
- University of Bordeaux, European Institute for Chemistry and Biology (IECB), ARNA Laboratory, Bordeaux 33000, France; Institut National de la Sante et de la Recherche Medicale, INSERM, U869, ARNA Laboratory, Bordeaux 33000, France
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.
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128
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Abstract
Female mammalian cells compensate dosage of X-linked gene expression through the inactivation of one of their two X chromosomes. X chromosome inactivation (XCI) in eutherians is dependent on the non-coding RNA Xist that is up-regulated from the future inactive X chromosome, coating it and recruiting factors involved in silencing and altering its chromatin state. Xist lies within the X-inactivation center (Xic), a region on the X that is required for XCI, and is regulated in cis by elements on the X chromosome and in trans by diffusible factors. In this review, we summarize the latest results in cis- and trans-regulation of the Xic. We discuss how the organization of the Xic in topologically associating domains is important for XCI (cis-regulation) and how proteins in the pluripotent state and upon development or differentiation of embryonic stem cells control proper inactivation of one X chromosome (trans-regulation).
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129
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A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing. Cell Rep 2015; 12:562-72. [PMID: 26190105 PMCID: PMC4534822 DOI: 10.1016/j.celrep.2015.06.053] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/21/2015] [Accepted: 06/15/2015] [Indexed: 11/24/2022] Open
Abstract
X-chromosome inactivation is the process that evolved in mammals to equalize levels of X-linked gene expression in XX females relative to XY males. Silencing of a single X chromosome in female cells is mediated by the non-coding RNA Xist. Although progress has been made toward identifying factors that function in the maintenance of X inactivation, the primary silencing factors are largely undefined. We developed an shRNA screening strategy to produce a ranked list of candidate primary silencing factors. Validation experiments performed on several of the top hits identified the SPOC domain RNA binding proteins Rbm15 and Spen and Wtap, a component of the m6A RNA methyltransferase complex, as playing an important role in the establishment of Xist-mediated silencing. Localization analysis using super-resolution 3D-SIM microscopy demonstrates that these factors co-localize with Xist RNA within the nuclear matrix subcompartment, consistent with a direct interaction. An shRNA screen identifies factors implicated in chromosome silencing by Xist RNA Rbm15, Wtap, and Spen are required for Xist-mediated silencing Rbm15 is important for efficient deposition of H3K27me3 on the inactive chromosome Rbm15, Wtap, and Spen co-localize with Xist RNA in perichromatin spaces
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130
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Chen Q, Gao S, He W, Kou X, Zhao Y, Wang H, Gao S. Xist repression shows time-dependent effects on the reprogramming of female somatic cells to induced pluripotent stem cells. Stem Cells 2015; 32:2642-56. [PMID: 24965076 DOI: 10.1002/stem.1775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 05/17/2014] [Accepted: 05/23/2014] [Indexed: 11/10/2022]
Abstract
Although the reactivation of silenced X chromosomes has been observed as part of the process of reprogramming female somatic cells into induced pluripotent stem cells (iPSCs), it remains unknown whether repression of the X-inactive specific transcript (Xist) can greatly enhance female iPSC induction similar to that observed in somatic cell nuclear transfer studies. In this study, we discovered that the repression of Xist plays opposite roles in the early and late phases of female iPSCs induction. Our results demonstrate that the downregulation of Xist by an isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible short hairpin RNA (shRNA) system can greatly impair the mesenchymal-to-epithelial transition (MET) in the early phase of iPSC induction but can significantly promote the transition of pre-iPSCs to iPSCs in the late phase. Furthermore, we demonstrate that although the knockdown of Xist did not affect the H3K27me3 modification on the X chromosome, macroH2A was released from the inactivated X chromosome (Xi). This enables the X chromosome silencing to be a reversible event. Moreover, we demonstrate that the supplementation of vitamin C (Vc) can augment and stabilize the reversible X chromosome by preventing the relocalization of macroH2A to the Xi. Therefore, our study reveals an opposite role of Xist repression in the early and late stages of reprogramming female somatic cells to pluripotency and demonstrates that the release of macroH2A by Xist repression enables the transition from pre-iPSCs to iPSCs.
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Affiliation(s)
- Qi Chen
- School of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences (NIBS), Beijing, China
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131
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Vallot C, Ouimette JF, Makhlouf M, Féraud O, Pontis J, Côme J, Martinat C, Bennaceur-Griscelli A, Lalande M, Rougeulle C. Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape. Cell Stem Cell 2015; 16:533-46. [PMID: 25921272 DOI: 10.1016/j.stem.2015.03.016] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 01/07/2015] [Accepted: 03/22/2015] [Indexed: 10/23/2022]
Abstract
Human pluripotent stem cells (hPSCs) display extensive epigenetic instability, particularly on the X chromosome. In this study, we show that, in hPSCs, the inactive X chromosome has a specific heterochromatin landscape that predisposes it to erosion of X chromosome inactivation (XCI), a process that occurs spontaneously in hPSCs. Heterochromatin remodeling and gene reactivation occur in a non-random fashion and are confined to specific H3K27me3-enriched domains, leaving H3K9me3-marked regions unaffected. Using single-cell monitoring of XCI erosion, we show that this instability only occurs in pluripotent cells. We also provide evidence that loss of XIST expression is not the primary cause of XCI instability and that gene reactivation from the inactive X (Xi) precedes loss of XIST coating. Notably, expression and coating by the long non-coding RNA XACT are early events in XCI erosion and, therefore, may play a role in mediating this process.
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Affiliation(s)
- Céline Vallot
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Jean-François Ouimette
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Mélanie Makhlouf
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Olivier Féraud
- ESTeam Paris Sud, INSERM U935, Université Paris Sud 11, AP-HP, Villejuif 94802, France
| | - Julien Pontis
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Julien Côme
- INSERM/UEVE UMR 861, ISTEM, AFM, 91030 Evry Cedex, France
| | | | | | - Marc Lalande
- Stem Cell and Systems Genomics Institutes, University of Connecticut, Farmington, CT 06030, USA
| | - Claire Rougeulle
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France.
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132
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Systematic discovery of Xist RNA binding proteins. Cell 2015; 161:404-16. [PMID: 25843628 DOI: 10.1016/j.cell.2015.03.025] [Citation(s) in RCA: 753] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/29/2015] [Accepted: 03/11/2015] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA-protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3' RNA processing machinery. Xist, an essential lncRNA for X chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK, which participates in Xist-mediated gene silencing and histone modifications but not Xist localization, and Drosophila Split ends homolog Spen, which interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing.
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Abstract
Many organisms show major chromosomal differences between sexes. In mammals, females have two copies of a large, gene-rich chromosome, the X, whereas males have one X and a small, gene-poor Y. The imbalance in expression of several hundred genes is lethal if not dealt with by dosage compensation. The male-female difference is addressed by silencing of genes on one female X early in development. However, both males and females now have only one active X chromosome. This is compensated by twofold up-regulation of genes on the active X. This complex system continues to provide important insights into mechanisms of epigenetic regulation.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford Oxford OX1 3QU, United Kingdom
| | - Bryan M Turner
- School of Cancer Sciences, Institute of Biomedical Research, University of Birmingham Medical School, Birmingham B15 2TT, United Kingdom
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134
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Lin IH, Chen DT, Chang YF, Lee YL, Su CH, Cheng C, Tsai YC, Ng SC, Chen HT, Lee MC, Chen HW, Suen SH, Chen YC, Liu TT, Chang CH, Hsu MT. Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes. PLoS One 2015; 10:e0118453. [PMID: 25706888 PMCID: PMC4338251 DOI: 10.1371/journal.pone.0118453] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/20/2015] [Indexed: 01/18/2023] Open
Abstract
Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.
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Affiliation(s)
- I-Hsuan Lin
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Dow-Tien Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Feng Chang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Ling Lee
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Hsin Su
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Ching Cheng
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chien Tsai
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Swee-Chuan Ng
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Hsiao-Tan Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Mei-Chen Lee
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Hong-Wei Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Hui Suen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Cheng Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Tze-Tze Liu
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Chuan-Hsiung Chang
- Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Ta Hsu
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- * E-mail:
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135
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Pasque V, Tchieu J, Karnik R, Uyeda M, Sadhu Dimashkie A, Case D, Papp B, Bonora G, Patel S, Ho R, Schmidt R, McKee R, Sado T, Tada T, Meissner A, Plath K. X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency. Cell 2015; 159:1681-97. [PMID: 25525883 DOI: 10.1016/j.cell.2014.11.040] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/30/2014] [Accepted: 11/12/2014] [Indexed: 12/16/2022]
Abstract
Reprogramming to iPSCs resets the epigenome of somatic cells, including the reversal of X chromosome inactivation. We sought to gain insight into the steps underlying the reprogramming process by examining the means by which reprogramming leads to X chromosome reactivation (XCR). Analyzing single cells in situ, we found that hallmarks of the inactive X (Xi) change sequentially, providing a direct readout of reprogramming progression. Several epigenetic changes on the Xi occur in the inverse order of developmental X inactivation, whereas others are uncoupled from this sequence. Among the latter, DNA methylation has an extraordinary long persistence on the Xi during reprogramming, and, like Xist expression, is erased only after pluripotency genes are activated. Mechanistically, XCR requires both DNA demethylation and Xist silencing, ensuring that only cells undergoing faithful reprogramming initiate XCR. Our study defines the epigenetic state of multiple sequential reprogramming intermediates and establishes a paradigm for studying cell fate transitions during reprogramming.
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Affiliation(s)
- Vincent Pasque
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Tchieu
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Molly Uyeda
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Anupama Sadhu Dimashkie
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Dana Case
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernadett Papp
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Giancarlo Bonora
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sanjeet Patel
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ritchie Ho
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ryan Schmidt
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Robin McKee
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kinki University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Takashi Tada
- Department of Stem Cell Engineering, Stem Cell Research Center, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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136
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System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions. Sci Rep 2015; 5:8283. [PMID: 25655563 PMCID: PMC4319166 DOI: 10.1038/srep08283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/09/2015] [Indexed: 11/24/2022] Open
Abstract
We present a system-wide transcriptional network structure that controls cell types in the context of expression pattern transitions that correspond to cell type transitions. Co-expression based analyses uncovered a system-wide, ladder-like transcription factor cluster structure composed of nearly 1,600 transcription factors in a human transcriptional network. Computer simulations based on a transcriptional regulatory model deduced from the system-wide, ladder-like transcription factor cluster structure reproduced expression pattern transitions when human THP-1 myelomonocytic leukaemia cells cease proliferation and differentiate under phorbol myristate acetate stimulation. The behaviour of MYC, a reprogramming Yamanaka factor that was suggested to be essential for induced pluripotent stem cells during dedifferentiation, could be interpreted based on the transcriptional regulation predicted by the system-wide, ladder-like transcription factor cluster structure. This study introduces a novel system-wide structure to transcriptional networks that provides new insights into network topology.
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137
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Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 2015; 36:25-64. [PMID: 25426780 PMCID: PMC4309736 DOI: 10.1210/er.2014-1034] [Citation(s) in RCA: 314] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases.
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Affiliation(s)
- Miao Sun
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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138
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Richard JLC, Ogawa Y. Understanding the Complex Circuitry of lncRNAs at the X-inactivation Center and Its Implications in Disease Conditions. Curr Top Microbiol Immunol 2015; 394:1-27. [PMID: 25982976 DOI: 10.1007/82_2015_443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Balanced gene expression is a high priority in order to maintain optimal functioning since alterations and variations could result in acute consequences. X chromosome inactivation (X-inactivation) is one such strategy utilized by mammalian species to silence the extra X chromosome in females to uphold a similar level of expression between the two sexes. A functionally versatile class of molecules called long noncoding RNA (lncRNA) has emerged as key regulators of gene expression and plays important roles during development. An lncRNA that is indispensable for X-inactivation is X-inactive specific transcript (Xist), which induces a repressive epigenetic landscape and creates the inactive X chromosome (Xi). With recent advents in the field of X-inactivation, novel positive and negative lncRNA regulators of Xist such as Jpx and Tsix, respectively, have broadened the regulatory network of X-inactivation. Xist expression failure or dysregulation has been implicated in producing developmental anomalies and disease states. Subsequently, reactivation of the Xi at a later stage of development has also been associated with certain tumors. With the recent influx of information about lncRNA biology and advancements in methods to probe lncRNA, we can now attempt to understand this complex network of Xist regulation in development and disease. It has become clear that the presence of an extra set of genes could be fatal for the organism. Only by understanding the precise ways in which lncRNAs function can treatments be developed to bring aberrations under control. This chapter summarizes our current understanding and knowledge with regard to how lncRNAs are orchestrated at the X-inactivation center (Xic), with a special focus on how genetic diseases come about as a consequence of lncRNA dysregulation.
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Affiliation(s)
- John Lalith Charles Richard
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Yuya Ogawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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139
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Abstract
In many animals, males have one X and females have two X chromosomes. The difference in X chromosome dosage between the two sexes is compensated by mechanisms that regulate X chromosome transcription. Recent advances in genomic techniques have provided new insights into the molecular mechanisms of X chromosome dosage compensation. In this review, I summarize our current understanding of dosage imbalance in general, and then review the molecular mechanisms of X chromosome dosage compensation with an emphasis on the parallels and differences between the three well-studied model systems, M. musculus, D. melanogaster and C. elegans.
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Affiliation(s)
- Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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140
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Rodriguez RM, Suarez-Alvarez B, Mosén-Ansorena D, García-Peydró M, Fuentes P, García-León MJ, Gonzalez-Lahera A, Macias-Camara N, Toribio ML, Aransay AM, Lopez-Larrea C. Regulation of the transcriptional program by DNA methylation during human αβ T-cell development. Nucleic Acids Res 2014; 43:760-74. [PMID: 25539926 PMCID: PMC4333391 DOI: 10.1093/nar/gku1340] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Thymocyte differentiation is a complex process involving well-defined sequential developmental stages that ultimately result in the generation of mature T-cells. In this study, we analyzed DNA methylation and gene expression profiles at successive human thymus developmental stages. Gain and loss of methylation occurred during thymocyte differentiation, but DNA demethylation was much more frequent than de novo methylation and more strongly correlated with gene expression. These changes took place in CpG-poor regions and were closely associated with T-cell differentiation and TCR function. Up to 88 genes that encode transcriptional regulators, some of whose functions in T-cell development are as yet unknown, were differentially methylated during differentiation. Interestingly, no reversion of accumulated DNA methylation changes was observed as differentiation progressed, except in a very small subset of key genes (RAG1, RAG2, CD8A, PTCRA, etc.), indicating that methylation changes are mostly unique and irreversible events. Our study explores the contribution of DNA methylation to T-cell lymphopoiesis and provides a fine-scale map of differentially methylated regions associated with gene expression changes. These can lay the molecular foundations for a better interpretation of the regulatory networks driving human thymopoiesis.
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Affiliation(s)
- Ramon M Rodriguez
- Department of Immunology, Hospital Universitario Central de Asturias, 33006 Oviedo, Spain
| | - Beatriz Suarez-Alvarez
- Cellular Biology in Renal Diseases Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David Mosén-Ansorena
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Marina García-Peydró
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Patricia Fuentes
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María J García-León
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Aintzane Gonzalez-Lahera
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Nuria Macias-Camara
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - María L Toribio
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Carlos Lopez-Larrea
- Department of Immunology, Hospital Universitario Central de Asturias, 33006 Oviedo, Spain Fundación Renal 'Íñigo Álvarez de Toledo', 28003 Madrid, Spain
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141
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Kota SK, Roy Chowdhury D, Rao LK, Padmalatha V, Singh L, Bhadra U. Uncoupling of X-linked gene silencing from XIST binding by DICER1 and chromatin modulation on human inactive X chromosome. Chromosoma 2014; 124:249-62. [PMID: 25428210 DOI: 10.1007/s00412-014-0495-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 10/24/2014] [Accepted: 11/07/2014] [Indexed: 12/18/2022]
Abstract
In mammals, X-inactivation process is achieved by the cis-spreading of long noncoding Xist RNA over one of the female X chromosomes. The Xist binding accumulates histones H3 methylation and H4 hypoacetylation required for X inactivation that leads to proper dosage compensation of the X-linked genes. Co-transcription of Tsix, an antisense copy of Xist, blocks the Xist coating on the Xi. In mice ES cells, an RNase III enzyme Dicer1 disrupts Xist binding and methylated H3K27me3 accumulation on the Xi. Later, multiple reports opposed these findings raising a question regarding the possible role of Dicer1 in murine X silencing. Here, we show that reduction of DICER1 in human female cells increases XIST transcripts without compromising the binding of the XIST and histone tail modifications on the Xi. Moreover, DICER1-depleted cells show differential upregulation of many human X-linked genes by binding different amounts of acetylated histone predominantly on their active promoter sites. Therefore, X-linked gene silencing, which is thought to be coupled with the accumulation of XIST and heterochromatin markers on Xi can be disrupted in DICER1 depleted human cells. These results suggest that DICER1 has no apparent effect on the recruitment of heterochromatic markers on the Xi but is required for inactivation of differentially regulated genes for the maintenance of proper dosage compensation in differentiated cells.
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Affiliation(s)
- Satya Keerthi Kota
- Functional Genomics and Gene Silencing Group, Centre For Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
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142
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Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol 2014; 24:651-63. [PMID: 25441720 DOI: 10.1016/j.tcb.2014.08.009] [Citation(s) in RCA: 242] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 02/07/2023]
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs) that play important roles in diverse biological processes. As a class, lncRNAs are generally enriched in the nucleus and, specifically, within the chromatin-associated fraction. Consistent with their localization, many lncRNAs have been implicated in the regulation of gene expression and in shaping 3D nuclear organization. In this review, we discuss the evidence that many nuclear-retained lncRNAs can interact with various chromatin regulatory proteins and recruit them to specific sites on DNA to regulate gene expression. Furthermore, we discuss the role of specific lncRNAs in shaping nuclear organization and their emerging mechanisms. Based on these examples, we propose a model that explains how lncRNAs may shape aspects of nuclear organization to regulate gene expression.
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143
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Genetic and pharmacological reactivation of the mammalian inactive X chromosome. Proc Natl Acad Sci U S A 2014; 111:12591-8. [PMID: 25136103 DOI: 10.1073/pnas.1413620111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
X-chromosome inactivation (XCI), the random transcriptional silencing of one X chromosome in somatic cells of female mammals, is a mechanism that ensures equal expression of X-linked genes in both sexes. XCI is initiated in cis by the noncoding Xist RNA, which coats the inactive X chromosome (Xi) from which it is produced. However, trans-acting factors that mediate XCI remain largely unknown. Here, we perform a large-scale RNA interference screen to identify trans-acting XCI factors (XCIFs) that comprise regulators of cell signaling and transcription, including the DNA methyltransferase, DNMT1. The expression pattern of the XCIFs explains the selective onset of XCI following differentiation. The XCIFs function, at least in part, by promoting expression and/or localization of Xist to the Xi. Surprisingly, we find that DNMT1, which is generally a transcriptional repressor, is an activator of Xist transcription. Small-molecule inhibitors of two of the XCIFs can reversibly reactivate the Xi, which has implications for treatment of Rett syndrome and other dominant X-linked diseases. A homozygous mouse knockout of one of the XCIFs, stanniocalcin 1 (STC1), has an expected XCI defect but surprisingly is phenotypically normal. Remarkably, X-linked genes are not overexpressed in female Stc1(-/-) mice, revealing the existence of a mechanism(s) that can compensate for a persistent XCI deficiency to regulate X-linked gene expression.
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144
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Maclary E, Hinten M, Harris C, Kalantry S. Long nonoding RNAs in the X-inactivation center. Chromosome Res 2014; 21:601-614. [PMID: 24297756 DOI: 10.1007/s10577-013-9396-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The X-inactivation center is a hotbed of functional long noncoding RNAs in eutherian mammals. These RNAs are thought to help orchestrate the epigenetic transcriptional states of the two X-chromosomes in females as well as of the single X-chromosome in males. To balance X-linked gene expression between the sexes, females undergo transcriptional silencing of most genes on one of the two X-chromosomes in a process termed X-chromosome inactivation. While one X-chromosome is inactivated, the other X-chromosome remains active. Moreover, with a few notable exceptions, the originally established epigenetic transcriptional profiles of the two X-chromosomes is maintained as such through many rounds of cell division, essentially for the life of the organism. The stable and divergent transcriptional fates of the two X-chromosomes, despite residing in a shared nucleoplasm, make X-inactivation a paradigm of epigenetic transcriptional regulation. Originally proposed in 1961 by Mary Lyon, the X-inactivation hypothesis has been validated through much experimentation. In the last 25 years, the discovery and functional characterization has firmly established X-linked long noncoding RNAs as key players in choreographing X-chromosome inactivation.
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Affiliation(s)
- Emily Maclary
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105
| | - Michael Hinten
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105
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145
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Abstract
Along the lines of established players like chromatin modifiers and transcription factors, noncoding RNA (ncRNA) are now widely accepted as one of the key regulatory molecules in epigenetic regulation of transcription. With increasing evidence of ncRNAs in the establishment of gene silencing through their ability to interact with major chromatin modifiers, in the current review, we discuss their prospective role in the area of inheritance and maintenance of these established silenced states which can be reversible or irreversible in nature. In addition, we attempt to understand and speculate how these RNA dependent or independent maintenance mechanisms differ between each other in a developmental stage, tissue, and gene-specific manner in different biological contexts by utilizing known/unknown regulatory factors.
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Affiliation(s)
- Tanmoy Mondal
- Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Medicinaregatan 9A, 40530, Gothenburg, Sweden
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146
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Abstract
In mammals, the process of X-chromosome inactivation ensures equivalent levels of X-linked gene expression between males and females through the silencing of one of the two X chromosomes in female cells. The process is established early in development and is initiated by a unique locus, which produces a long noncoding RNA, Xist. The Xist transcript triggers gene silencing in cis by coating the future inactive X chromosome. It also induces a cascade of chromatin changes, including posttranslational histone modifications and DNA methylation, and leads to the stable repression of all X-linked genes throughout development and adult life. We review here recent progress in our understanding of the molecular mechanisms involved in the initiation of Xist expression, the propagation of the Xist RNA along the chromosome, and the cis-elements and trans-acting factors involved in the maintenance of the repressed state. We also describe the diverse strategies used by nonplacental mammals for X-chromosome dosage compensation and highlight the common features and differences between eutherians and metatherians, in particular regarding the involvement of long noncoding RNAs.
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Affiliation(s)
- Anne-Valerie Gendrel
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, 75248 Paris, France;
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147
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Minkovsky A, Sahakyan A, Rankin-Gee E, Bonora G, Patel S, Plath K. The Mbd1-Atf7ip-Setdb1 pathway contributes to the maintenance of X chromosome inactivation. Epigenetics Chromatin 2014; 7:12. [PMID: 25028596 PMCID: PMC4099106 DOI: 10.1186/1756-8935-7-12] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/05/2014] [Indexed: 01/08/2023] Open
Abstract
Background X chromosome inactivation (XCI) is a developmental program of heterochromatin formation that initiates during early female mammalian embryonic development and is maintained through a lifetime of cell divisions in somatic cells. Despite identification of the crucial long non-coding RNA Xist and involvement of specific chromatin modifiers in the establishment and maintenance of the heterochromatin of the inactive X chromosome (Xi), interference with known pathways only partially reactivates the Xi once silencing has been established. Here, we studied ATF7IP (MCAF1), a protein previously characterized to coordinate DNA methylation and histone H3K9 methylation through interactions with the methyl-DNA binding protein MBD1 and the histone H3K9 methyltransferase SETDB1, as a candidate maintenance factor of the Xi. Results We found that siRNA-mediated knockdown of Atf7ip in mouse embryonic fibroblasts (MEFs) induces the activation of silenced reporter genes on the Xi in a low number of cells. Additional inhibition of two pathways known to contribute to Xi maintenance, DNA methylation and Xist RNA coating of the X chromosome, strongly increased the number of cells expressing Xi-linked genes upon Atf7ip knockdown. Despite its functional importance in Xi maintenance, ATF7IP does not accumulate on the Xi in MEFs or differentiating mouse embryonic stem cells. However, we found that depletion of two known repressive biochemical interactors of ATF7IP, MBD1 and SETDB1, but not of other unrelated H3K9 methyltransferases, also induces the activation of an Xi-linked reporter in MEFs. Conclusions Together, these data indicate that Atf7ip acts in a synergistic fashion with DNA methylation and Xist RNA to maintain the silent state of the Xi in somatic cells, and that Mbd1 and Setdb1, similar to Atf7ip, play a functional role in Xi silencing. We therefore propose that ATF7IP links DNA methylation on the Xi to SETDB1-mediated H3K9 trimethylation via its interaction with MBD1, and that this function is a crucial feature of the stable silencing of the Xi in female mammalian cells.
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Affiliation(s)
- Alissa Minkovsky
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Elyse Rankin-Gee
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Giancarlo Bonora
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Sanjeet Patel
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
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148
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Zhang X, Moen EL, Liu C, Mu W, Gamazon ER, Delaney SM, Wing C, Godley LA, Dolan ME, Zhang W. Linking the genetic architecture of cytosine modifications with human complex traits. Hum Mol Genet 2014; 23:5893-905. [PMID: 24943591 DOI: 10.1093/hmg/ddu313] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interindividual variation in cytosine modifications could contribute to heterogeneity in disease risks and other complex traits. We assessed the genetic architecture of cytosine modifications at 283,540 CpG sites in lymphoblastoid cell lines (LCLs) derived from independent samples of European and African descent. Our study suggests that cytosine modification variation was primarily controlled in local by single major modification quantitative trait locus (mQTL) and additional minor loci. Local genetic epistasis was detectable for a small proportion of CpG sites, which were enriched by more than 9-fold for CpG sites mapped to population-specific mQTL. Genetically dependent CpG sites whose modification levels negatively (repressive sites) or positively (facilitative sites) correlated with gene expression levels significantly co-localized with transcription factor binding, with the repressive sites predominantly associated with active promoters whereas the facilitative sites rarely at active promoters. Genetically independent repressive or facilitative sites preferentially modulated gene expression variation by influencing local chromatin accessibility, with the facilitative sites primarily antagonizing H3K27me3 and H3K9me3 deposition. In comparison with expression quantitative trait loci (eQTL), mQTL detected from LCLs were enriched in associations for a broader range of disease categories including chronic inflammatory, autoimmune and psychiatric disorders, suggesting that cytosine modification variation, while possesses a degree of cell linage specificity, is more stably inherited over development than gene expression variation. About 11% of unique single-nucleotide polymorphisms reported in the Genome-Wide Association Study Catalog were annotated, 78% as mQTL and 31% as eQTL in LCLs, which covered 37% of the investigated diseases/traits and provided insights to the biological mechanisms.
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Affiliation(s)
- Xu Zhang
- Section of Hematology/Oncology, Department of Medicine
| | | | | | | | | | | | - Claudia Wing
- Section of Hematology/Oncology, Department of Medicine and
| | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine and Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA
| | - M Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine and Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA
| | - Wei Zhang
- Department of Pediatrics, Institute of Human Genetics, The University of Illinois, Chicago, IL 60612, USA,
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149
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Chaligné R, Heard E. X-chromosome inactivation in development and cancer. FEBS Lett 2014; 588:2514-22. [PMID: 24937141 DOI: 10.1016/j.febslet.2014.06.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation represents an epigenetics paradigm and a powerful model system of facultative heterochromatin formation triggered by a non-coding RNA, Xist, during development. Once established, the inactive state of the Xi is highly stable in somatic cells, thanks to a combination of chromatin associated proteins, DNA methylation and nuclear organization. However, sporadic reactivation of X-linked genes has been reported during ageing and in transformed cells and disappearance of the Barr body is frequently observed in cancer cells. In this review we summarise current knowledge on the epigenetic changes that accompany X inactivation and discuss the extent to which the inactive X chromosome may be epigenetically or genetically perturbed in breast cancer.
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Affiliation(s)
- Ronan Chaligné
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France
| | - Edith Heard
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France.
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150
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Peeters SB, Cotton AM, Brown CJ. Variable escape from X-chromosome inactivation: identifying factors that tip the scales towards expression. Bioessays 2014; 36:746-56. [PMID: 24913292 PMCID: PMC4143967 DOI: 10.1002/bies.201400032] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In humans over 15% of X-linked genes have been shown to ‘escape’ from X-chromosome inactivation (XCI): they continue to be expressed to some extent from the inactive X chromosome. Mono-allelic expression is anticipated within a cell for genes subject to XCI, but random XCI usually results in expression of both alleles in a cell population. Using a study of allelic expression from cultured lymphoblasts and fibroblasts, many of which showed substantial skewing of XCI, we recently reported that the expression of genes lies on a contiunuum between those that are subject to inactivation, and those that escape. We now review allelic expression studies from mouse, and discuss the variability in escape seen in both humans and mice in genic expression levels, between X chromosomes and between tissues. We also discuss current knowledge of the heterochromatic features, DNA elements and three-dimensional topology of the inactive X that contribute to the balance of expression from the otherwise inactive X chromosome.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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