BackgroundCTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive.ResultsWe carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation.ConclusionsDynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.

中文翻译：

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聚类 CTCF 绑定是一种维持拓扑关联域的进化机制

背景CTCF结合通过划定大规模拓扑关联域（TAD）的边界，有助于建立更高阶的基因组结构。然而，尽管 TAD 的重要性和保守性，CTCF 结合在其进化和稳定性中的作用仍然难以捉摸。结果我们进行了一项实验和计算研究，利用五个密切相关的物种的自然遗传变异来评估 CTCF 结合模式如何稳定固定每个物种的进化有助于 TAD 边界的建立和进化动态。我们在多个小鼠物种中执行 CTCF ChIP-seq，以创建全基因组结合谱并将它们与 TAD 边界相关联。我们的分析表明，通过选择性约束和动态进化过程的平衡，CTCF 结合保持在 TAD 边界。无论跨物种的保护如何，与其他 CTCF 位点相比，TAD 边界的 CTCF 结合位点受到更强的序列和功能限制。TAD 边界经常包含动态进化的集群，其中包含进化上古老的和年轻的 CTCF 位点，这是由于反复获得接近保守位点的新物种特异性位点的结果。绝大多数聚集的 CTCF 位点与 cohesin 共定位，并且比非聚集的 CTCF 位点更接近基因转录起始位点，这表明 CTCF 簇特别有助于 cohesin 的稳定和转录调控。