Abstract 460: Base resolution epigenomic analysis reveals a role for Tet2 in modulating enhancer activity (2014)

Abstract Cytosine methylation (5mC) is a well-established epigenetic mechanism essential for genomic imprinting, silencing of retrotransposons, and lineage-specific expression of developmental genes. This epigenetic mark is extensively remodeled during mammalian development through the action of several DNA methyltransferases (DNMT) and the Ten-Eleven-Translocation (TET) family of protein dioxygenases. TET proteins function in DNA de-methylation by catalyzing the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and other oxidized intermediates. Recurrent loss of function mutations of Tet2 are found in 27% of acute myeloid leukemia patients. In mouse models, TET2 loss is sufficient to cause myeloid malignancy through defects in hematopoietic stem cell differentiation. However, it remains unclear how TET2-dependent de-methylation regulates differentiation, a process often disrupted in tumorigenesis. Base-resolution methylomes have revealed that 5mC is dynamically regulated in a cell-type specific manner. Notably, DNA methylation is depleted at distal regulatory elements such as enhancers, where reduction of 5mC is correlated with the activity of these sequences. 5hmC is also significantly enriched at distal cis-regulatory sequences, suggesting that dynamic DNA methylation at these regions is likely mediated by interplays between DNMT-mediated methylation and TET-mediated de-methylation. Despite these discoveries, several open questions remain. First, are the different TET proteins functionally redundant? Does Tet2 uniquely modulate the methylome? If so, how? Second, what is the precise role of DNA hypomethylation and hydroxymethylation at enhancers? Do these modifications play active roles in gene regulation? We have employed genome-wide technologies to examine the effects of loss of Tet1 and Tet2 genes on DNA methylation, chromatin modification and gene expression landscapes in mouse embryonic stem cells. We generated base resolution DNA methylation and hydroxymethylation maps in wild type and Tet1 or Tet2 mutant mES cells, and determined the genomic regions where dynamic DNA methylation depends on either Tet1 or Tet2. Loss of Tet2 leads to dramatic reduction of DNA hydroxymethylation genome-wide, and local hypermethylation predominantly at enhancers. Furthermore, we observed reduced activities of re-methylated enhancers in Tet2-/- mES cells, supporting an active role for Tet2 and DNA hypomethylation at enhancers. Together, our results clarify the distinct functions of Tet1 and Tet2 in mammalian cells and highlight an active role of DNA hypomethylation at enhancers. Citation Format: Gary Hon, Chun-Xiao Song, Fulai Jin, Siddarth Selvaraj, Ah Young Lee, Chia-an Yen, Zhen Ye, Shi-Qing Mao, Bang-An Wang, Samantha Kuan, Lee Edsall, Boxuan Simen Zhao, Guo-Liang Xu, Chuan He, Bing Ren. Base resolution epigenomic analysis reveals a role for Tet2 in modulating enhancer activity. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 460. doi:10.1158/1538-7445.AM2014-460