Discovery and characterization of chromatin states for systematic annotation of the human genome
A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, thei...
| Main Authors: | , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2012
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| Online Access: | http://hdl.handle.net/1721.1/73004 |
| _version_ | 1826196423018807296 |
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| author | Ernst, Jason Kellis, Manolis |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Ernst, Jason Kellis, Manolis |
| author_sort | Ernst, Jason |
| collection | MIT |
| description | A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, their combinatorial patterns are still unresolved and their potential for systematic de novo genome annotation remains untapped. Here, we use a multivariate Hidden Markov Model to reveal 'chromatin states' in human T cells, based on recurrent and spatially coherent combinations of chromatin marks. We define 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, large-scale repressed and repeat-associated states. Each chromatin state shows specific enrichments in functional annotations, sequence motifs and specific experimentally observed characteristics, suggesting distinct biological roles. This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function. |
| first_indexed | 2024-09-23T10:26:16Z |
| format | Article |
| id | mit-1721.1/73004 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:26:16Z |
| publishDate | 2012 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/730042022-09-26T17:53:59Z Discovery and characterization of chromatin states for systematic annotation of the human genome Ernst, Jason Kellis, Manolis Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kellis, Manolis Ernst, Jason Kellis, Manolis A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, their combinatorial patterns are still unresolved and their potential for systematic de novo genome annotation remains untapped. Here, we use a multivariate Hidden Markov Model to reveal 'chromatin states' in human T cells, based on recurrent and spatially coherent combinations of chromatin marks. We define 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, large-scale repressed and repeat-associated states. Each chromatin state shows specific enrichments in functional annotations, sequence motifs and specific experimentally observed characteristics, suggesting distinct biological roles. This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function. National Science Foundation (U.S.). (Award 0905968) National Human Genome Research Institute (U.S.) (Award U54-HG004570) National Human Genome Research Institute (U.S.) (Award RC1-HG005334) 2012-09-17T17:14:40Z 2012-09-17T17:14:40Z 2010-07 Article http://purl.org/eprint/type/JournalArticle 1087-0156 1546-1696 http://hdl.handle.net/1721.1/73004 Ernst, Jason, and Manolis Kellis. “Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome.” Nature Biotechnology 28.8 (2010): 817–825. en_US http://dx.doi.org/10.1038/nbt.1662 Nature Biotechnology Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Nature Publishing Group PubMed Central |
| spellingShingle | Ernst, Jason Kellis, Manolis Discovery and characterization of chromatin states for systematic annotation of the human genome |
| title | Discovery and characterization of chromatin states for systematic annotation of the human genome |
| title_full | Discovery and characterization of chromatin states for systematic annotation of the human genome |
| title_fullStr | Discovery and characterization of chromatin states for systematic annotation of the human genome |
| title_full_unstemmed | Discovery and characterization of chromatin states for systematic annotation of the human genome |
| title_short | Discovery and characterization of chromatin states for systematic annotation of the human genome |
| title_sort | discovery and characterization of chromatin states for systematic annotation of the human genome |
| url | http://hdl.handle.net/1721.1/73004 |
| work_keys_str_mv | AT ernstjason discoveryandcharacterizationofchromatinstatesforsystematicannotationofthehumangenome AT kellismanolis discoveryandcharacterizationofchromatinstatesforsystematicannotationofthehumangenome |