Xu Difei, Ma Rongsheng, Zhang Jiahai, Liu Zhijun, Wu Bo, Peng Junhui, Zhai Yanan, Gong Qingguo, Shi Yunyu, Wu Jihui, Wu Qiang, Zhang Zhiyong, Ruan Ke
Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , P. R. China.
National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , P. R. China.
J Phys Chem Lett. 2018 Jul 19;9(14):4020-4028. doi: 10.1021/acs.jpclett.8b01440. Epub 2018 Jul 6.
The 11 zinc fingers (ZFs) of the transcription factor CTCF play a versatile role in the regulation of gene expression. CTCF binds to numerous genomic sites to form chromatin loops and topologically associated domains and thus mediates the 3D architecture of chromatin. Although CTCF inter-ZF plasticity is essential for the recognition of multiple genomic sites, the dynamic nature of its 11 ZFs remains unknown. We assigned the chemical shifts of the CTCF ZFs 1-11 and solved the solution structures of each ZF. NMR backbone dynamics, residual dipolar couplings, and small-angle X-ray scattering experiments suggest a high inter-ZF plasticity of the free-form ZFs 1-11. As exemplified by two different protocadherin DNA sequences, the titration of DNAs to N-labeled CTCF ZFs 1-11 enabled systematic mapping of binding of CTCF ZFs to various chromatin sites. Our work paves the way for illustrating the molecular basis of the versatile DNA recognized by CTCF and has interesting implications for its conformational transition during DNA binding.
转录因子CTCF的11个锌指（ZF）在基因表达调控中发挥着多种作用。CTCF与众多基因组位点结合，形成染色质环和拓扑相关结构域，从而介导染色质的三维结构。尽管CTCF锌指间的可塑性对于识别多个基因组位点至关重要，但其11个锌指的动态特性仍不清楚。我们确定了CTCF锌指1 - 11的化学位移，并解析了每个锌指的溶液结构。核磁共振主链动力学、残余偶极耦合和小角X射线散射实验表明，游离形式的锌指1 - 11具有高度的锌指间可塑性。以两种不同的原钙黏蛋白DNA序列为例，将DNA滴定至N标记的CTCF锌指1 - 11能够系统地绘制CTCF锌指与各种染色质位点的结合图谱。我们的工作为阐明CTCF识别多种DNA的分子基础铺平了道路，并对其在DNA结合过程中的构象转变具有有趣的启示。
