Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea.
Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, South Korea.
Nucleic Acids Res. 2020 Sep 4;48(15):8431-8444. doi: 10.1093/nar/gkaa584.
Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.
在卵裂期的小鼠胚胎中，基因组范围的被动 DNA 去甲基化与维持甲基转移酶 DNMT1 的细胞质定位有关。然而，最近的研究提供了 DNMT1 核定位及其对早期胚胎印迹区域和其他基因组位点甲基化水平维持的证据。使用 DNA 腺嘌呤甲基酶鉴定方法，我们在四细胞和八细胞胚胎中鉴定了 Dnmt1 结合区域。Dnmt1 峰在基因区域（启动子和 CpG 岛）中的无偏分布以及 Dnmt1 峰与峰相关基因的表达水平之间没有相关性，这反驳了 Dnmt1 在早期发育阶段基因转录调控中的积极参与。相反，Dnmt1 被发现以极大的偏向方式与基因组反转录元件相关联，特别是与 LINE1（长散布核元件）和 ERVK（内源性逆转录病毒类型 K）序列相关联。转录组分析显示，富含 Dnmt1 的反转录元件的转录本在 Dnmt1 敲低胚胎中过度表达。最后，甲基-CpG 结合域测序证明，在野生型胚胎中高度甲基化的富含 Dnmt1 的反转录元件在 Dnmt1 耗尽的胚胎中去甲基化。我们的结果表明，在早期小鼠发育过程中，Dnmt1 通过 DNA 甲基化参与了对反转录元件的抑制。
