Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
Babraham Institute, Epigenetics ISP, Babraham, CB22 3AT, UK.
Epigenetics Chromatin. 2019 Aug 9;12(1):49. doi: 10.1186/s13072-019-0295-4.
KRAB zinc finger proteins (KZFPs) represent one of the largest families of DNA-binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. ZFP57 is required to maintain the post-fertilization DNA methylation memory of parental origin at genomic imprints. Here we conduct RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant mouse ES cells to understand the relative importance of ZFP57 at imprints, unique and repetitive regions of the genome.
Over 80% of ZFP57 targets are TEs, however, ZFP57 is not essential for their repression. The remaining targets lie within unique imprinted and non-imprinted sequences. Though the loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and very few exhibit alterations in expression. Comparison of ZFP57 mutants with DNA methyltransferase-deleted ES cells (TKO) identifies a remarkably similar pattern of H3K9me3 loss across the genome. These data define regions where H3K9me3 is secondary to DNA methylation and we propose that ZFP57 is the principal if not sole methylation-sensitive KZFP in mouse ES cells. Finally, we examine dynamics of DNA and H3K9 methylation during pre-implantation development and show that sites bound by ZFP57 in ES cells maintain DNA methylation and H3K9me3 at imprints and at non-imprinted regions on the maternally inherited chromosome throughout preimplantation development.
Our analyses suggest the evolution of a rare DNA methylation-sensitive KZFP that is not essential for repeat silencing, but whose primary function is to maintain DNA methylation and repressive histone marks at germline-derived imprinting control regions.
KRAB 锌指蛋白（KZFPs）是脊椎动物基因组中最大的 DNA 结合蛋白家族之一，似乎通过序列特异性靶向抑制性染色质状态进化而来，以沉默转座元件（TEs），包括内源性逆转录病毒。ZFP57 是维持基因组印记中亲本来源的受精后 DNA 甲基化记忆所必需的。在这里，我们在正常和 ZFP57 突变体小鼠胚胎干细胞中进行 RNA-seq 和 ChIP-seq 分析，以了解 ZFP57 在印记、基因组独特和重复区域的相对重要性。
超过 80%的 ZFP57 靶标是 TEs，然而，ZFP57 对于它们的抑制并非必不可少。其余的靶标位于独特的印记和非印记序列内。尽管 ZFP57 的缺失如预期那样影响印记基因，但大多数独特的基因靶标失去 H3K9me3，对 DNA 甲基化影响很小，很少有表现出表达改变。与缺失 DNA 甲基转移酶的胚胎干细胞（TKO）的 ZFP57 突变体进行比较，确定了整个基因组中 H3K9me3 丢失的惊人相似模式。这些数据定义了 H3K9me3 是 DNA 甲基化的次要因素的区域，我们提出 ZFP57 是小鼠胚胎干细胞中主要的（如果不是唯一的）甲基化敏感的 KZFP。最后，我们检查了植入前发育过程中 DNA 和 H3K9 甲基化的动态变化，并表明在胚胎干细胞中由 ZFP57 结合的位点在整个植入前发育过程中保持印迹和母源遗传染色体上非印迹区域的 DNA 甲基化和 H3K9me3。
我们的分析表明，一种罕见的 DNA 甲基化敏感 KZFP 的进化，它对于重复沉默不是必需的，但它的主要功能是维持生殖系衍生的印记控制区域的 DNA 甲基化和抑制性组蛋白标记。
