Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

• DOI: 10.1038/s41467-018-08006-y
• Publication Date: 2018-12-28T12:32:36Z
• Authors: Jiangping He; Xiuling Fu; Meng Zhang; Fangfang He; Wenjuan Li; Mazid Md. Abdul; Jianguo Zhou; Li Sun; Chen Chang; Yuhao Li; He Liu; Kaixin Wu; Isaac A. Babarinde; Qiang Zhuang; Yuin-Han Loh; Jiekai Chen; Miguel A. Esteban; Andrew P. Hutchins
• Keywords: Bivalent chromatin; Epigenomics; Polycomb-group proteins

Abstract The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs increasingly recognized for their important biological functions, they a potential danger genomic stability and carefully regulated by the epigenetic system. However, full complexity this regulatory system is not understood. Here, using mouse embryonic stem cells, we show that suppressed heterochromatic marks like H3K9me3, also labelled all major types chromatin modification in complex patterns, including bivalent activatory repressive marks. We identified 29 modifiers significantly deregulated at least one type TE. loss Setdb1 , Ncor2 Rnf2 Kat5 Prmt5 Uhrf1 Rrp8 caused widespread changes TE expression accessibility. These effects were context-specific, with different regulating accessibility specific subsets TEs. Our work reveals patterns regulation