Intermediate DNA methylation is a conserved signature of genome regulation
The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples. We report 18,452...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
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Nature Publishing Group
2018
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| Online Access: | http://hdl.handle.net/1721.1/115440 |
| _version_ | 1826207047081787392 |
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| author | Elliott, GiNell Hong, Chibo Xing, Xiaoyun Zhou, Xin Li, Daofeng Coarfa, Cristian Bell, Robert J.A. Maire, Cecile L. Ligon, Keith L. Sigaroudinia, Mahvash Gascard, Philippe Tlsty, Thea D. Harris, R. Alan Schalkwyk, Leonard C. Bilenky, Misha Mill, Jonathan Farnham, Peggy J. Kellis, Manolis Marra, Marco A. Milosavljevic, Aleksandar Hirst, Martin Stormo, Gary D. Wang, Ting Costello, Joseph F. |
| author2 | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science |
| author_facet | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Elliott, GiNell Hong, Chibo Xing, Xiaoyun Zhou, Xin Li, Daofeng Coarfa, Cristian Bell, Robert J.A. Maire, Cecile L. Ligon, Keith L. Sigaroudinia, Mahvash Gascard, Philippe Tlsty, Thea D. Harris, R. Alan Schalkwyk, Leonard C. Bilenky, Misha Mill, Jonathan Farnham, Peggy J. Kellis, Manolis Marra, Marco A. Milosavljevic, Aleksandar Hirst, Martin Stormo, Gary D. Wang, Ting Costello, Joseph F. |
| author_sort | Elliott, GiNell |
| collection | MIT |
| description | The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples. We report 18,452 intermediate methylation regions located near 36% of genes and enriched at enhancers, exons and DNase I hypersensitivity sites. Intermediate methylation regions average 57% methylation, are predominantly allele-independent and are conserved across individuals and between mouse and human, suggesting a conserved function. These regions have an intermediate level of active chromatin marks and their associated genes have intermediate transcriptional activity. Exonic intermediate methylation correlates with exon inclusion at a level between that of fully methylated and unmethylated exons, highlighting gene context-dependent functions. We conclude that intermediate DNA methylation is a conserved signature of gene regulation and exon usage. |
| first_indexed | 2024-09-23T13:42:39Z |
| format | Article |
| id | mit-1721.1/115440 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T13:42:39Z |
| publishDate | 2018 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/1154402022-09-28T15:44:48Z Intermediate DNA methylation is a conserved signature of genome regulation Elliott, GiNell Hong, Chibo Xing, Xiaoyun Zhou, Xin Li, Daofeng Coarfa, Cristian Bell, Robert J.A. Maire, Cecile L. Ligon, Keith L. Sigaroudinia, Mahvash Gascard, Philippe Tlsty, Thea D. Harris, R. Alan Schalkwyk, Leonard C. Bilenky, Misha Mill, Jonathan Farnham, Peggy J. Kellis, Manolis Marra, Marco A. Milosavljevic, Aleksandar Hirst, Martin Stormo, Gary D. Wang, Ting Costello, Joseph F. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kellis, Manolis The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples. We report 18,452 intermediate methylation regions located near 36% of genes and enriched at enhancers, exons and DNase I hypersensitivity sites. Intermediate methylation regions average 57% methylation, are predominantly allele-independent and are conserved across individuals and between mouse and human, suggesting a conserved function. These regions have an intermediate level of active chromatin marks and their associated genes have intermediate transcriptional activity. Exonic intermediate methylation correlates with exon inclusion at a level between that of fully methylated and unmethylated exons, highlighting gene context-dependent functions. We conclude that intermediate DNA methylation is a conserved signature of gene regulation and exon usage. 2018-05-17T18:55:07Z 2018-05-17T18:55:07Z 2015-02 2014-11 2018-05-10T16:59:59Z Article http://purl.org/eprint/type/JournalArticle 2041-1723 http://hdl.handle.net/1721.1/115440 Elliott, GiNell et al. “Intermediate DNA Methylation Is a Conserved Signature of Genome Regulation.” Nature Communications 6, 1 (February 2015): 6363 © 2015 Macmillan Publishers Limited http://dx.doi.org/10.1038/NCOMMS7363 Nature Communications Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ application/pdf Nature Publishing Group Nature |
| spellingShingle | Elliott, GiNell Hong, Chibo Xing, Xiaoyun Zhou, Xin Li, Daofeng Coarfa, Cristian Bell, Robert J.A. Maire, Cecile L. Ligon, Keith L. Sigaroudinia, Mahvash Gascard, Philippe Tlsty, Thea D. Harris, R. Alan Schalkwyk, Leonard C. Bilenky, Misha Mill, Jonathan Farnham, Peggy J. Kellis, Manolis Marra, Marco A. Milosavljevic, Aleksandar Hirst, Martin Stormo, Gary D. Wang, Ting Costello, Joseph F. Intermediate DNA methylation is a conserved signature of genome regulation |
| title | Intermediate DNA methylation is a conserved signature of genome regulation |
| title_full | Intermediate DNA methylation is a conserved signature of genome regulation |
| title_fullStr | Intermediate DNA methylation is a conserved signature of genome regulation |
| title_full_unstemmed | Intermediate DNA methylation is a conserved signature of genome regulation |
| title_short | Intermediate DNA methylation is a conserved signature of genome regulation |
| title_sort | intermediate dna methylation is a conserved signature of genome regulation |
| url | http://hdl.handle.net/1721.1/115440 |
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