CTCF, a conserved 3D genome architecture protein, determines proper genome-wide chromatin looping interactions through directional binding to specific sequence elements of four modules within numerous CTCF-binding sites (CBSs) by its 11 zinc fingers (ZFs). Here, we report four crystal structures of human CTCF in complex with CBSs of the protocadherin (Pcdh) clusters. We show that directional CTCF binding to cognate CBSs of the Pcdh enhancers and promoters is achieved through inserting its ZF3, ZFs 4-7, and ZFs 9-11 into the major groove along CBSs, resulting in a sequence-specific recognition of module 4, modules 3 and 2, and module 1, respectively; and ZF8 serves as a spacer element for variable distances between modules 1 and 2. In addition, the base contact with the asymmetric "A" in the central position of modules 2-3, is essential for directional recognition of the CBSs with symmetric core sequences but lacking module 1. Furthermore, CTCF tolerates base changes at specific positions within the degenerated CBS sequences, permitting genome-wide CTCF binding to a diverse range of CBSs. Together, these complex structures provide important insights into the molecular mechanisms for the directionality, diversity, flexibility, dynamics, and conservation of multivalent CTCF binding to its cognate sites across the entire human genome.

中文翻译：

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定向CTCF识别各种基因组位点的分子机制。

CTCF是一种保守的3D基因组结构蛋白，可通过其11个锌指（ZF）与许多CTCF结合位点（CBS）中的四个模块的特定序列元件进行定向结合，从而确定适当的全基因组染色质环相互作用。在这里，我们报告人类CTCF与原钙粘蛋白（Pcdh）群集的CBS复杂的四个晶体结构。我们显示定向CTCF结合到Pcdh增强子和启动子的同源CBS的实现是通过将其ZF3，ZF 4-7和ZF 9-11插入沿CBS的主要凹槽中实现的，从而导致对模块4的序列特异性识别模块3和2，以及模块1；ZF8和ZF8用作模块1和2之间可变距离的间隔元件。此外，在模块2-3的中心位置，基极与不对称的“ A”相接触，对于具有对称核心序列但缺少模块1的CBS定向识别至关重要。此外，CTCF可以耐受简并CBS序列内特定位置的碱基变化，从而使全基因组CTCF结合到多种CBS上。这些复杂的结构共同为分子机制的方向性，多样性，灵活性，动力学和多价CTCF与其整个人类基因组同源位点的结合保守提供了重要的见识。