Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [CAPIP-seq]. Mus musculus

In mammals, DNA methylation occurs mainly at 5mC of CpG dinucleotides. The methylation on the promoter leads to the suppression of gene expression, while the functional role of gene body DNA methylation in highly expressed genes has yet to be clarified. Here, we show that the Dnmt3b-dependent intragenic DNA methylation protects the gene body from RNA Polymerase II (RNA Pol II) spurious entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that loss of Dnmt3b leads to an increase of the RNA Pol II engagement within gene bodies and spurious intragenic transcription initiation events. Furthermore, inhibition of RNA Pol II spurious entry depends on the enzymatic activity of the Dnmt3b recruited by H3K36me3. Thus, elongating RNA Pol II triggers an epigenetic crosstalk that involves SetD2, H3K36me3, Dnmt3b, and DNA methylation to ensure gene transcription initiation fidelity with implications for intragenic hypomethylation in cancer. Overall design: Genome-wide analysis of Dnmt3b role in mouse ESCs using CAPIP-seq.

在哺乳动物中，DNA甲基化主要发生于CpG二核苷酸的5-甲基胞嘧啶（5mC）位点。启动子区域的甲基化会抑制基因表达，而基因体DNA甲基化在高表达基因中的功能作用仍有待阐明。本研究表明，依赖于DNA甲基转移酶3b（Dnmt3b）的基因体DNA甲基化，可保护基因体免受RNA聚合酶II（RNA Pol II）的错误侵入与隐秘转录起始的影响。通过多种全基因组分析手段，本研究证实，Dnmt3b缺失会导致RNA Pol II在基因体内的结合增加，并引发大量错误的基因体内转录起始事件。此外，对RNA Pol II错误侵入的抑制作用，依赖于由组蛋白H3赖氨酸36三甲基化（H3K36me3）招募的Dnmt3b的酶促活性。因此，正在延伸的RNA Pol II会触发一套涉及SetD2、H3K36me3、Dnmt3b与DNA甲基化的表观遗传串扰机制，以此保障基因转录起始的保真度，该机制对癌症中基因体低甲基化的研究具有重要启示意义。整体实验设计：利用CAPIP测序技术对小鼠胚胎干细胞（ESCs）中Dnmt3b的功能开展全基因组分析。