Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells

We generated base-resolution DNA methylomes of a series of DNMT knockout (KO) ES cells with improved coverage at highly repetitive elements. We find that DNMT1- and DNMT3a/3b-dependent activities actually work complementarily and simultaneously to establish symmetric CG methylation and CHH (H=A, T or C) methylation, and unexpectedly have “division of labor” to suppress retrotransposon long terminal repeats (LTRs) and long interspersed elements (LINEs), respectively. Our data also reveal CG density number of 30 seems like a ''threshold'' to predetermine the level of methylation in wild type cells and the magnitude of methylation reduction in KO cells. Only genes with low CG number are either induced or surprisingly suppressed in hypomethylated genome. Our data unveil the concerted action of DNMT enzymes in the establishment/maintenance of methylation patterns. Overall design: Genomic DNA from four different cell lines were treated with bisulfite and sequenced with the Illumina HiSeq platform using paired end reads.

我们构建了一系列DNA甲基转移酶（DNMT）敲除（KO）胚胎干细胞（ES细胞）的碱基分辨率（base-resolution）DNA甲基化组（DNA methylome），该数据集在高度重复元件区域具备更优异的测序覆盖度。研究发现，DNMT1与DNMT3a/3b依赖的酶活性并非独立发挥作用，而是以互补且同步的方式共同建立对称的CG甲基化与CHH（H为A、T或C）甲基化；且二者存在出人意料的“分工”，分别抑制逆转录转座子长末端重复序列（long terminal repeats, LTRs）与长散在核元件（long interspersed elements, LINEs）。我们的数据还显示，CG密度阈值为30似乎可预先决定野生型细胞的甲基化水平，以及敲除细胞中甲基化的降低幅度。在低甲基化基因组中，仅CG含量较低的基因会出现表达上调，或出人意料地出现表达下调。本研究揭示了DNMT家族酶类在甲基化模式建立与维持过程中的协同作用。实验整体设计：对四种不同细胞系的基因组DNA进行亚硫酸氢盐（bisulfite）处理，随后采用Illumina HiSeq测序平台开展双端测序（paired end reads）。