Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.
Nat Commun. 2020 Jun 24;11(1):3199. doi: 10.1038/s41467-020-16989-w.
De novo establishment of DNA methylation is accomplished by DNMT3A and DNMT3B. Here, we analyze de novo DNA methylation in mouse embryonic fibroblasts (2i-MEFs) derived from DNA-hypomethylated 2i/L ES cells with genetic ablation of Dnmt3a or Dnmt3b. We identify 355 and 333 uniquely unmethylated genes in Dnmt3a and Dnmt3b knockout (KO) 2i-MEFs, respectively. We find that Dnmt3a is exclusively required for de novo methylation at both TSS regions and gene bodies of Polycomb group (PcG) target developmental genes, while Dnmt3b has a dominant role on the X chromosome. Consistent with this, tissue-specific DNA methylation at PcG target genes is substantially reduced in Dnmt3a KO embryos. Finally, we find that human patients with DNMT3 mutations exhibit reduced DNA methylation at regions that are hypomethylated in Dnmt3 KO 2i-MEFs. In conclusion, here we report a set of unique de novo DNA methylation target sites for both DNMT3 enzymes during mammalian development that overlap with hypomethylated sites in human patients.
从头建立 DNA 甲基化是由 DNMT3A 和 DNMT3B 完成的。在这里，我们分析了从 DNA 低甲基化的 2i/L ES 细胞衍生的具有 Dnmt3a 或 Dnmt3b 基因缺失的小鼠胚胎成纤维细胞（2i-MEF）中的从头 DNA 甲基化。我们分别在 Dnmt3a 和 Dnmt3b 敲除（KO）2i-MEF 中鉴定出 355 个和 333 个独特的非甲基化基因。我们发现 Dnmt3a 仅在 TSS 区域和多梳组（PcG）靶发育基因的基因体处的从头甲基化是必需的，而 Dnmt3b 在 X 染色体上具有主导作用。与此一致的是，在 Dnmt3a KO 胚胎中，PcG 靶基因的组织特异性 DNA 甲基化显著降低。最后，我们发现 DNMT3 突变的人类患者在 Dnmt3 KO 2i-MEF 中低甲基化的区域表现出 DNA 甲基化减少。总之，在这里，我们报告了一套在哺乳动物发育过程中，DNMT3 酶的独特的从头 DNA 甲基化靶位点，这些位点与人类患者中低甲基化的位点重叠。
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