DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

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DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

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Title: DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
Author: Xie, Mingchao; Hong, Chibo; Zhang, Bo; Lowdon, Rebecca; Xing, Xiaoyun; Li, Daofeng; Zhou, Xin; Lee, Hyung Joo; Maire, Cecile L.; Ligon, Keith L.; Gascard, Philippe; Sigaroudinia, Mahvash; Tlsty, Thea D.; Kadlecek, Theresa; Weiss, Arthur; O’Geen, Henriette; Farnham, Peggy J.; Madden, Pamela A.F.; Mungall, Andrew J.; Tam, Angela; Kamoh, Baljit; Cho, Stephanie; Moore, Richard; Hirst, Martin; Marra, Marco A.; Costello, Joseph F.; Wang, Ting

Note: Order does not necessarily reflect citation order of authors.

Citation: Xie, M., C. Hong, B. Zhang, R. Lowdon, X. Xing, D. Li, X. Zhou, et al. 2013. “DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.” Nature genetics 45 (7): 10.1038/ng.2649. doi:10.1038/ng.2649. http://dx.doi.org/10.1038/ng.2649.
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Abstract: Introduction: Transposable element (TE) derived sequences comprise half of our genome and DNA methylome, and are presumed densely methylated and inactive. Examination of the genome-wide DNA methylation status within 928 TE subfamilies in human embryonic and adult tissues revealed unexpected tissue-specific and subfamily-specific hypomethylation signatures. Genes proximal to tissue-specific hypomethylated TE sequences were enriched for functions important for the tissue type and their expression correlated strongly with hypomethylation of the TEs. When hypomethylated, these TE sequences gained tissue-specific enhancer marks including H3K4me1 and occupancy by p300, and a majority exhibited enhancer activity in reporter gene assays. Many such TEs also harbored binding sites for transcription factors that are important for tissue-specific functions and exhibited evidence for evolutionary selection. These data suggest that sequences derived from TEs may be responsible for wiring tissue type-specific regulatory networks, and have acquired tissue-specific epigenetic regulation.
Published Version: doi:10.1038/ng.2649
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695047/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879711
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