Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions [RNA-Seq]

One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the Cohesin in chromatin and identified transcription factors, RNA-binding proteins, and chromatin regulators associated with Cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to Cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with Cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in Cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of Cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with Cohesin that warrant further investigation. We performed ChIP-Seq, ChIP-MS, RNA-Seq, and Hi-C to investigate the roles of ZBTB transcription factors in 3D chromatin organization.

解析三维染色质结构的调控原理时，当前面临的一大瓶颈在于已知调控因子的稀缺性。黏连蛋白（Cohesin）是三维染色质组构的核心必需因子，其互作蛋白可作为候选调控因子。本研究对染色质中的黏连蛋白开展蛋白质组谱分析，鉴定出与黏连蛋白相关的转录因子、RNA结合蛋白及染色质调控因子。随后我们先后开展了急性蛋白降解、时序全基因组结合定量分析与BAT Hi-C实验，结果显示转录因子ZBTB21可参与调控黏连蛋白的染色质结合、三维染色质互作及转录抑制过程。值得注意的是，多组学分析揭示其余四类ZBTB家族转录因子均可与黏连蛋白互作，且联合降解ZBTB21与ZBTB7B可进一步降低黏连蛋白在染色质上的驻留丰度。本研究提出，多种ZBTB家族转录因子可协同调控黏连蛋白的染色质结合，进而调节染色质互作；同时我们整理了一批与黏连蛋白相关的额外蛋白目录，可供后续研究深入探究。本研究通过ChIP-Seq、ChIP-MS、RNA-Seq及Hi-C实验，探究ZBTB家族转录因子在三维染色质组构中的功能。