Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Nat Cell Biol. 2021 Aug;23(8):881-893. doi: 10.1038/s41556-021-00722-w. Epub 2021 Jul 29.
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.
11 锌指 (ZF) 蛋白 CTCF 通过选择性结合到数千个基因组位点来调节拓扑关联域的形成和转录。在这里，我们用绿色荧光蛋白标记的野生型或突变蛋白替代内源性 CTCF 在小鼠胚胎干细胞中，以鉴定 CTCF 定位和功能的其他决定因素。虽然 ZF1 和 ZF8-ZF11 对于细胞存活不是必需的，但 ZF8 缺失显著增加了突变 CTCF 的 DNA 结合解吸率，导致 CTCF 染色质居留时间减少。ZF8 的缺失导致拓扑关联域广泛减弱、基因表达异常和全基因组 DNA 甲基化增加。因此，重要的染色质模板过程依赖于准确的 CTCF 染色质居留时间，我们提出这取决于局部序列和染色质背景以及全局 CTCF 蛋白浓度。
