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

被引：61

作者：

Amin, Viren ^{[1
]}

Harris, R. Alan ^{[1
]}

Onuchic, Vitor ^{[1
]}

Jackson, Andrew R. ^{[1
]}

Charnecki, Tim ^{[1
]}

Paithankar, Sameer ^{[1
]}

Subramanian, Sai Lakshmi ^{[1
]}

Riehle, Kevin ^{[1
]}

Coarfa, Cristian ^{[1
]}

Milosavljevic, Aleksandar ^{[1
]}

机构：

[1] Baylor Coll Med, Dept Mol & Human, Epigenome Ctr, Bioinformat Res Lab,Genet, Houston, TX 77030 USA

来源：

NATURE COMMUNICATIONS | 2015年 / 6卷

基金：

美国国家卫生研究院;

关键词：

NONCODING RNA; DIFFERENTIATION; ANNOTATION; EXPRESSION; ENHANCERS; PATTERNS; DISTINCT; PACKAGE; PROTEIN; MARKER;

D O I：

10.1038/ncomms7370

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：10

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