OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide (RNA-Seq)

The O-GlcNAc transferase OGT interacts robustly with all three mammalian TET methylcytosine dioxygenases. We show here that deletion of theOgtgene in mouse embryonic stem cells (mESC) results in a widespread increase in the TET product 5-hydroxymethylcytosine (5hmC) in both euchromatic and heterochromatic compartments, with concomitant reduction of the TET substrate 5-methylcytosine (5mC) at the same genomic regions. mESC engineered to abolish the TET1-OGT interaction likewise displayed a genome-wide decrease of 5mC. DNA hypomethylation in OGT-deficient cells was accompanied by de-repression of transposable elements (TEs) predominantly located in heterochromatin, and this increase in TE expression was sometimes accompanied by increased cis-expression of genes and exons located 3' of the expressed TE. Thus, the TET-OGT interaction prevents DNA demethylation and TE expression in heterochromatin by restraining TET activity genome-wide. We suggest that OGT protects the genome against DNA hypomethylation and impaired heterochromatin integrity, preventing the aberrant increase in TE expression observed in cancer, autoimmune-inflammatory diseases, cellular senescence and ageing. Overall design: In this study, we examine the impact of Ogt-iKO and disrupted TET1-OGT interaction in mouse embryonic stem cells (mESCs). Our analysis focuses on changes in DNA methylation patterns, specifically alterations in 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) levels. We also explore the expression of transposable elements (TEs), especially in heterochromatin regions, and assess the cis-expression of neighboring genes and exons. This research aims to understand the genetic mechanisms underlying DNA methylation and TE expression in mESCs.

O-连接β-N-乙酰葡糖胺转移酶（O-GlcNAc transferase, OGT）可与所有三种哺乳动物TET甲基胞嘧啶双加氧酶（TET methylcytosine dioxygenases）发生稳定相互作用。本研究证实，在小鼠胚胎干细胞（mouse embryonic stem cells, mESC）中敲除Ogt基因，会导致常染色质与异染色质区域内TET催化产物5-羟甲基胞嘧啶（5-hydroxymethylcytosine, 5hmC）广泛升高，同时同一基因组区域内TET的底物5-甲基胞嘧啶（5-methylcytosine, 5mC）水平随之降低。经基因工程改造以阻断TET1与OGT相互作用的mESC，同样呈现全基因组范围内的5mC水平下降。OGT缺陷细胞中的DNA低甲基化，伴随主要定位于异染色质的转座元件（transposable elements, TEs）的去抑制；而TE表达的这种升高，有时会伴随表达TE的3'端下游区域的基因及外显子的顺式表达增加。综上，TET-OGT相互作用可通过在全基因组范围内抑制TET活性，阻止异染色质中的DNA去甲基化与TE表达。我们认为，OGT可保护基因组免受DNA低甲基化与异染色质完整性受损的影响，从而阻断癌症、自身免疫炎症性疾病、细胞衰老及衰老过程中出现的TE表达异常升高。本研究总体设计如下：本研究探究了Ogt诱导型敲除（Ogt-iKO）以及TET1-OGT相互作用破坏对小鼠胚胎干细胞（mESCs）的影响。分析重点聚焦于DNA甲基化模式的变化，尤其是5-羟甲基胞嘧啶（5hmC）与5-甲基胞嘧啶（5mC）水平的改变。本研究同时探讨转座元件（TEs）的表达情况，尤其是异染色质区域的TE表达，并对邻近基因及外显子的顺式表达进行评估。本研究旨在阐明小鼠胚胎干细胞中DNA甲基化与TE表达的潜在遗传机制。