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DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells

Authors :
Tianpeng Gu
Xueqiu Lin
Sean M. Cullen
Min Luo
Mira Jeong
Marcos Estecio
Jianjun Shen
Swanand Hardikar
Deqiang Sun
Jianzhong Su
Danielle Rux
Anna Guzman
Minjung Lee
Lei Stanley Qi
Jia-Jia Chen
Michael Kyba
Yun Huang
Taiping Chen
Wei Li
Margaret A. Goodell
Source :
Genome Biology, Vol 19, Iss 1, Pp 1-15 (2018)
Publication Year :
2018
Publisher :
BMC, 2018.

Abstract

Abstract Background DNA methylation is a heritable epigenetic mark, enabling stable but reversible gene repression. In mammalian cells, DNA methyltransferases (DNMTs) are responsible for modifying cytosine to 5-methylcytosine (5mC), which can be further oxidized by the TET dioxygenases to ultimately cause DNA demethylation. However, the genome-wide cooperation and functions of these two families of proteins, especially at large under-methylated regions, called canyons, remain largely unknown. Results Here we demonstrate that DNMT3A and TET1 function in a complementary and competitive manner in mouse embryonic stem cells to mediate proper epigenetic landscapes and gene expression. The longer isoform of DNMT3A, DNMT3A1, exhibits significant enrichment at distal promoters and canyon edges, but is excluded from proximal promoters and canyons where TET1 shows prominent binding. Deletion of Tet1 increases DNMT3A1 binding capacity at and around genes with wild-type TET1 binding. However, deletion of Dnmt3a has a minor effect on TET1 binding on chromatin, indicating that TET1 may limit DNA methylation partially by protecting its targets from DNMT3A and establishing boundaries for DNA methylation. Local CpG density may determine their complementary binding patterns and therefore that the methylation landscape is encoded in the DNA sequence. Furthermore, DNMT3A and TET1 impact histone modifications which in turn regulate gene expression. In particular, they regulate Polycomb Repressive Complex 2 (PRC2)-mediated H3K27me3 enrichment to constrain gene expression from bivalent promoters. Conclusions We conclude that DNMT3A and TET1 regulate the epigenome and gene expression at specific targets via their functional interplay.

Details

Language :
English
ISSN :
1474760X
Volume :
19
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Genome Biology
Publication Type :
Academic Journal
Accession number :
edsdoj.6fd2d3e46453433ea4d4e102f933e748
Document Type :
article
Full Text :
https://doi.org/10.1186/s13059-018-1464-7