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Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, Zaugg JB, Snyder M. Landscape of cohesin-mediated chromatin loops in the human genome. Nature 2020; 583:737-743. [PMID: 32728247 PMCID: PMC7410831 DOI: 10.1038/s41586-020-2151-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/11/2019] [Indexed: 01/14/2023]
Abstract
Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.
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Affiliation(s)
- Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rohith Srivas
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Damek V Spacek
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mariana Ruiz-Velasco
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Peyton Greenside
- Biomedical Informatics Graduate Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anil Narasimha
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Qing Liu
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Benjamin Geller
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Akshay Sanghi
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael Kulik
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Silin Sa
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Stephen Dalton
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Judith B Zaugg
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA.
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Sailani MR, Chappell J, Jingga I, Narasimha A, Zia A, Lynch JL, Mazrouei S, Bernstein JA, Aryani O, Snyder MP. WISP3 mutation associated with pseudorheumatoid dysplasia. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a001990. [PMID: 29092958 PMCID: PMC5793776 DOI: 10.1101/mcs.a001990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 09/28/2017] [Indexed: 01/28/2023] Open
Abstract
Progressive pseudorheumatoid dysplasia (PPD) is a skeletal dysplasia characterized by predominant involvement of articular cartilage with progressive joint stiffness. Here we report genetic characterization of a consanguineous family segregating an uncharacterized from of skeletal dysplasia. Whole-exome sequencing of four affected siblings and their parents identified a loss-of-function homozygous mutation in the WISP3 gene, leading to diagnosis of PPD in the affected individuals. The identified variant (Chr6: 112382301; WISP3:c.156C>A p.Cys52*) is rare and predicted to cause premature termination of the WISP3 protein.
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Affiliation(s)
- M Reza Sailani
- Department of Genetics, Stanford University, Stanford, California 94304, USA
| | - James Chappell
- Department of Genetics, Stanford University, Stanford, California 94304, USA
| | - Inlora Jingga
- Department of Genetics, Stanford University, Stanford, California 94304, USA
| | - Anil Narasimha
- Department of Genetics, Stanford University, Stanford, California 94304, USA
| | - Amin Zia
- Department of Genetics, Stanford University, Stanford, California 94304, USA
| | - Janet Linnea Lynch
- Department of Genetics, Stanford University, Stanford, California 94304, USA
| | - Safoura Mazrouei
- Clinic of Internal Medicine, Department of Cardiology, University Heart Center, Jena University Hospital, 07747 Jena, Germany
| | | | - Omid Aryani
- Department of Neuroscience, Iran University of Medical Sciences, Tehran 1449614535, Iran.,Endocrinology and Metabolic Research Institute, Tehran University of Medical Sciences, Tehran 1599666615, Iran
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California 94304, USA
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Ang YS, Rivas RN, Ribeiro AJS, Srivas R, Rivera J, Stone NR, Pratt K, Mohamed TMA, Fu JD, Spencer CI, Tippens ND, Li M, Narasimha A, Radzinsky E, Moon-Grady AJ, Yu H, Pruitt BL, Snyder MP, Srivastava D. Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis. Cell 2017; 167:1734-1749.e22. [PMID: 27984724 DOI: 10.1016/j.cell.2016.11.033] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 08/09/2016] [Accepted: 11/17/2016] [Indexed: 12/12/2022]
Abstract
Mutation of highly conserved residues in transcription factors may affect protein-protein or protein-DNA interactions, leading to gene network dysregulation and human disease. Human mutations in GATA4, a cardiogenic transcription factor, cause cardiac septal defects and cardiomyopathy. Here, iPS-derived cardiomyocytes from subjects with a heterozygous GATA4-G296S missense mutation showed impaired contractility, calcium handling, and metabolic activity. In human cardiomyocytes, GATA4 broadly co-occupied cardiac enhancers with TBX5, another transcription factor that causes septal defects when mutated. The GATA4-G296S mutation disrupted TBX5 recruitment, particularly to cardiac super-enhancers, concomitant with dysregulation of genes related to the phenotypic abnormalities, including cardiac septation. Conversely, the GATA4-G296S mutation led to failure of GATA4 and TBX5-mediated repression at non-cardiac genes and enhanced open chromatin states at endothelial/endocardial promoters. These results reveal how disease-causing missense mutations can disrupt transcriptional cooperativity, leading to aberrant chromatin states and cellular dysfunction, including those related to morphogenetic defects.
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Affiliation(s)
- Yen-Sin Ang
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Renee N Rivas
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Rohith Srivas
- Department of Genetics and Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA 94305, USA
| | - Janell Rivera
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Nicole R Stone
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karishma Pratt
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Tamer M A Mohamed
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ji-Dong Fu
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - C Ian Spencer
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Nathaniel D Tippens
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Molong Li
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Anil Narasimha
- Department of Genetics and Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ethan Radzinsky
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Anita J Moon-Grady
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Beth L Pruitt
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics and Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA 94305, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
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