Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion [4C-seq]

Structural loops are known to collapse in the absence of cohesin, whereas regulatory loops largely persist with only minor transcriptional changes, leaving unresolved questions about cohesin's role in establishing regulatory interactions during cell state transitions. To investigate this, we degraded RAD21, a core cohesin subunit, in mouse embryonic stem cells (ESCs) transitioning from mitosis to G1 under self-renewal or differentiation conditions. We performed high-resolution in situ 4C-seq around the promoters of cohesin-sensitive genes (Klf4, Tbx3, Myc, and Fosl2) in ESCs and EpiLCs. Overall design: 4C-seq for selected genes in ESCs and EpiLCs with or without RAD21 depletion

已知在缺乏黏连蛋白（cohesin）的情况下，结构环会发生解离，而调控环则大多保持完整，仅伴随轻微的转录变化，这使得黏连蛋白在细胞状态转换过程中建立调控相互作用的功能仍存在未解决的疑问。为探究这一问题，我们在处于有丝分裂向G1期转换的小鼠胚胎干细胞（ESCs）中降解了黏连蛋白的核心亚基RAD21，实验分别在自我更新或分化培养条件下进行。我们分别在ESCs和上皮样干细胞（EpiLCs）中，针对黏连蛋白敏感基因（Klf4、Tbx3、Myc及Fosl2）的启动子区域开展了高分辨率原位4C-seq实验。实验整体设计：在存在或不存在RAD21降解的情况下，对ESCs和EpiLCs中的目标基因开展4C-seq检测。