The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD.

中文翻译：

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OnTAD：分层域结构揭示了 TAD 和边界之间活动的差异

细胞核中染色质的空间组织与调节基因表达有关。染色质不同片段之间的高频相互作用图揭示了拓扑关联域 (TAD)，其中大多数调节相互作用被认为发生。TAD 不是同质的结构单元，但似乎被组织成一个层次结构。我们展示了 OnTAD，一个来自 Hi-C 数据的优化嵌套 TAD 调用程序，用于识别分层 TAD。OnTAD 揭示了对不同 TAD 水平、基因调控中的边界使用、环挤出模型和区室域的作用的新生物学见解。OnTAD 可在 https://github.com/anlin00007/OnTAD 获得。