CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells
CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells
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DOI：
10.1038/s41556-021-00722-w
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发表时间：
2021-07-29
影响因子：
21.3
通讯作者：
Galjart, Niels
中科院分区：
文献类型：
--
作者：
Soochit, Widia;Sleutels, Frank;Galjart, Niels
11锌指（ZF）蛋白CTCF通过选择性结合数千个基因组位点调节拓扑相关结构域的形成和转录。在这里，我们用绿色荧光蛋白标记的野生型或缺乏单个ZFs的突变蛋白替代小鼠胚胎干细胞中的内源性CTCF，以确定CTCF定位和功能的其他决定因素。虽然ZF1和ZF8- zf11不是细胞存活所必需的，但ZF8的缺失显著增加了突变CTCF的DNA结合off-rate，导致CTCF染色质停留时间减少。ZF8的缺失导致拓扑相关结构域的广泛减弱，基因表达异常和全基因组DNA甲基化增加。因此，重要的染色质模板化过程依赖于准确的CTCF染色质停留时间，我们认为这取决于局部序列和染色质背景以及全局CTCF蛋白浓度。Soochit等人报道CTCF在染色质上的停留时间由其锌指8结构域控制，并决定小鼠胚胎干细胞染色质组织、DNA甲基化和转录稳健性。
The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8-ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.Soochit et al. report that the residence time of CTCF on chromatin is controlled by its zinc finger 8 domain and determines chromatin organization, DNA methylation and transcriptional robustness in mouse embryonic stem cells.