3D Chromosome Regulatory Landscape of Human Pluripotent Cells
In this study, we describe the 3D chromosome regulatory landscape of human naive and primed embryonic stem cells. To devise this map, we identified transcriptional enhancers and insulators in these cells and placed them within the context of cohesin-associated CTCF-CTCF loops using cohesin ChIA-PET...
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| Format: | Article |
| Language: | en_US |
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Elsevier
2017
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| Online Access: | http://hdl.handle.net/1721.1/107115 https://orcid.org/0000-0002-7256-3158 https://orcid.org/0000-0002-1650-2289 https://orcid.org/0000-0003-0998-9882 https://orcid.org/0000-0001-8855-8647 |
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| author | Ji, Xiong Powell, Benjamin E. Shachar, Sigal Hnisz, Denes Pegoraro, Gianluca Lee, Tong Ihn Misteli, Tom Dadon, Daniel Benjamin Fan, Zi Peng Borges-Rivera, Diego Ramon Weintraub, Abraham Selby Jaenisch, Rudolf Young, Richard A. |
| author2 | Massachusetts Institute of Technology. Computational and Systems Biology Program |
| author_facet | Massachusetts Institute of Technology. Computational and Systems Biology Program Ji, Xiong Powell, Benjamin E. Shachar, Sigal Hnisz, Denes Pegoraro, Gianluca Lee, Tong Ihn Misteli, Tom Dadon, Daniel Benjamin Fan, Zi Peng Borges-Rivera, Diego Ramon Weintraub, Abraham Selby Jaenisch, Rudolf Young, Richard A. |
| author_sort | Ji, Xiong |
| collection | MIT |
| description | In this study, we describe the 3D chromosome regulatory landscape of human naive and primed embryonic stem cells. To devise this map, we identified transcriptional enhancers and insulators in these cells and placed them within the context of cohesin-associated CTCF-CTCF loops using cohesin ChIA-PET data. The CTCF-CTCF loops we identified form a chromosomal framework of insulated neighborhoods, which in turn form topologically associating domains (TADs) that are largely preserved during the transition between the naive and primed states. Regulatory changes in enhancer-promoter interactions occur within insulated neighborhoods during cell state transition. The CTCF anchor regions we identified are conserved across species, influence gene expression, and are a frequent site of mutations in cancer cells, underscoring their functional importance in cellular regulation. These 3D regulatory maps of human pluripotent cells therefore provide a foundation for future interrogation of the relationships between chromosome structure and gene control in development and disease. |
| first_indexed | 2024-09-23T08:01:05Z |
| format | Article |
| id | mit-1721.1/107115 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:01:05Z |
| publishDate | 2017 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/1071152022-09-23T10:20:51Z 3D Chromosome Regulatory Landscape of Human Pluripotent Cells Ji, Xiong Powell, Benjamin E. Shachar, Sigal Hnisz, Denes Pegoraro, Gianluca Lee, Tong Ihn Misteli, Tom Dadon, Daniel Benjamin Fan, Zi Peng Borges-Rivera, Diego Ramon Weintraub, Abraham Selby Jaenisch, Rudolf Young, Richard A. Massachusetts Institute of Technology. Computational and Systems Biology Program Massachusetts Institute of Technology. Department of Biology Dadon, Daniel Benjamin Fan, Zi Peng Borges-Rivera, Diego Ramon Weintraub, Abraham Selby Jaenisch, Rudolf Young, Richard A In this study, we describe the 3D chromosome regulatory landscape of human naive and primed embryonic stem cells. To devise this map, we identified transcriptional enhancers and insulators in these cells and placed them within the context of cohesin-associated CTCF-CTCF loops using cohesin ChIA-PET data. The CTCF-CTCF loops we identified form a chromosomal framework of insulated neighborhoods, which in turn form topologically associating domains (TADs) that are largely preserved during the transition between the naive and primed states. Regulatory changes in enhancer-promoter interactions occur within insulated neighborhoods during cell state transition. The CTCF anchor regions we identified are conserved across species, influence gene expression, and are a frequent site of mutations in cancer cells, underscoring their functional importance in cellular regulation. These 3D regulatory maps of human pluripotent cells therefore provide a foundation for future interrogation of the relationships between chromosome structure and gene control in development and disease. Center for Cancer Research (National Cancer Institute (U.S.)) National Institutes of Health (U.S.). Intramural Research Program Virginia and Daniel K. Ludwig Graduate Fellowship National Institutes of Health (U.S.) (Grants HG002668 and HD 045022) Simons Foundation (Grant SFLIFE 286977) 2017-02-23T15:24:41Z 2017-02-23T15:24:41Z 2015-12 2015-10 Article http://purl.org/eprint/type/JournalArticle 1934-5909 http://hdl.handle.net/1721.1/107115 Ji, Xiong et al. “3D Chromosome Regulatory Landscape of Human Pluripotent Cells.” Cell Stem Cell 18.2 (2016): 262–275. https://orcid.org/0000-0002-7256-3158 https://orcid.org/0000-0002-1650-2289 https://orcid.org/0000-0003-0998-9882 https://orcid.org/0000-0001-8855-8647 en_US http://dx.doi.org/10.1016/j.stem.2015.11.007 Cell Stem Cell Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Elsevier PMC |
| spellingShingle | Ji, Xiong Powell, Benjamin E. Shachar, Sigal Hnisz, Denes Pegoraro, Gianluca Lee, Tong Ihn Misteli, Tom Dadon, Daniel Benjamin Fan, Zi Peng Borges-Rivera, Diego Ramon Weintraub, Abraham Selby Jaenisch, Rudolf Young, Richard A. 3D Chromosome Regulatory Landscape of Human Pluripotent Cells |
| title | 3D Chromosome Regulatory Landscape of Human Pluripotent Cells |
| title_full | 3D Chromosome Regulatory Landscape of Human Pluripotent Cells |
| title_fullStr | 3D Chromosome Regulatory Landscape of Human Pluripotent Cells |
| title_full_unstemmed | 3D Chromosome Regulatory Landscape of Human Pluripotent Cells |
| title_short | 3D Chromosome Regulatory Landscape of Human Pluripotent Cells |
| title_sort | 3d chromosome regulatory landscape of human pluripotent cells |
| url | http://hdl.handle.net/1721.1/107115 https://orcid.org/0000-0002-7256-3158 https://orcid.org/0000-0002-1650-2289 https://orcid.org/0000-0003-0998-9882 https://orcid.org/0000-0001-8855-8647 |
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