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Nat Commun. 2015 Feb 18;6:6370. doi: 10.1038/ncomms7370.

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.

Author information

1
Epigenome Center, Bioinformatics Research Laboratory, Department of Molecular &Human, Genetics, Baylor College of Medicine, One Baylor Plaza, BCMD 400D, Houston, Texas 77030, USA.

Abstract

Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.

PMID:
25691256
PMCID:
PMC4335353
DOI:
10.1038/ncomms7370
[Indexed for MEDLINE]
Free PMC Article

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