Topologically associating domains (TADs) are genomic regions of self-interaction. Additionally, it is known that TAD boundaries are enriched in CTCF binding sites. In turn, CTCF sites are known to be asymmetric, whereby the convergent configuration of a pair of CTCF sites leads to the formation of a chromatin loop in vivo. However, to date, it has been unclear how to reconcile TAD structure with CTCF-based chromatin loops. We approach this problem by analysing CTCF binding site strengths and classifying clusters of CTCF sites along the genome on the basis of their relative orientation. Analysis of CTCF site orientation classes as a function of their spatial distribution along the human genome reveals that convergent CTCF site clusters are depleted while divergent CTCF clusters are enriched in the 5- to 100-kb range. We then analyse the distribution of CTCF binding sites as a function of TAD boundary conservation across seven primary human blood cell types. This reveals divergent CTCF site enrichment at TAD boundaries. Furthermore, convergent arrays of CTCF sites separate the left and right sections of TADs that harbour internal CTCF sites, resulting in unequal TAD ‘halves’. The orientation-based CTCF binding site cluster classification that we present reconciles TAD boundaries and CTCF site clusters in a mechanistically elegant fashion. This model suggests that the emergent structure of nuclear chromatin in the form of TADs relies on the obligate alternation of divergent and convergent CTCF site clusters that occur at different length scales along the genome.

中文翻译：

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CTCF 位点的空间模式定义了 TAD 的解剖结构及其边界

拓扑关联域 (TAD) 是自相互作用的基因组区域。此外，众所周知，TAD 边界富含 CTCF 结合位点。反过来，已知 CTCF 位点是不对称的，由此一对 CTCF 位点的会聚构型导致在体内形成染色质环。然而，迄今为止，尚不清楚如何协调 TAD 结构与基于 CTCF 的染色质环。我们通过分析 CTCF 结合位点强度并根据它们的相对方向对沿基因组的 CTCF 位点簇进行分类来解决这个问题。CTCF 位点方向类作为其沿人类基因组的空间分布的函数的分析表明，收敛的 CTCF 位点簇被耗尽，而发散的 CTCF 簇在 5 到 100 kb 范围内富集。然后，我们分析了 CTCF 结合位点的分布，作为跨七种主要人类血细胞类型的 TAD 边界守恒的函数。这揭示了 TAD 边界处不同的 CTCF 位点富集。此外，CTCF 位点的会聚阵列将包含内部 CTCF 位点的 TAD 的左右部分分开，导致不等的 TAD“一半”。我们提出的基于方向的 CTCF 结合位点簇分类以机械优雅的方式协调 TAD 边界和 CTCF 位点簇。该模型表明 TAD 形式的核染色质的突现结构依赖于沿基因组在不同长度尺度上发生的发散和会聚 CTCF 位点簇的专性交替。