Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [AP_1 family]

The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to be coordinated by transcription factors (TFs), yet identifying and demonstrating the influence of different TFs has proven difficult. In this study we take a multi-omics approach to directly interrogate transient SWI/SNF interactors, chromatin targeting, and the plasticity of the resulting 3D epigenetic landscape. We utilized the novel proximity based labeling technique TurboID to identify the AP1 family as a critical interacting partner for endogenous SWI/SNF complexes. Validation through CUT&RUN profiling demonstrated SWI/SNF targeting enrichment at AP1 bound loci, and SWI/SNF – AP1 cooperation in chromatin targeting. Mapping of 3D chromatin structure via HiChIP revealed AP1-SWI/SNF dependent restructuring of promoter-enhancer architecture and generation of enhancer hubs, ultimately regulating transcription. Through direct interrogation of the SWI/SNF – AP1 interaction, we demonstrate a SWI/SNF functional dependency on AP1 mediated chromatin localization. We propose that pioneer factors such as AP1 bind and target SWI/SNF to inactive chromatin, where it restructures the genomic landscape into an active state through epigenetic rewiring spanning multiple dimensions. Time course CUT&RUN profiling of pJUN, JUND and JUNB in inducible SMARCB1 G401 cell line

长期以来，学界普遍推测，调控SWI/SNF复合物动态靶向的机制由转录因子（Transcription Factors, TFs）协同介导，但甄别并验证不同转录因子的调控作用始终极具挑战。本研究采用多组学研究策略，直接探究SWI/SNF复合物的瞬时互作蛋白、染色质靶向特征以及由此产生的三维表观遗传景观的可塑性。本研究借助新型邻近标记技术TurboID，将AP1家族（Activator Protein 1）鉴定为内源性SWI/SNF复合物的关键互作伙伴。通过CUT&RUN测序图谱进行验证的结果显示，SWI/SNF复合物在AP1结合位点呈现靶向富集现象，且SWI/SNF与AP1在染色质靶向过程中存在协同作用。通过HiChIP技术绘制三维染色质结构图谱后发现，AP1与SWI/SNF依赖的染色质重塑可介导启动子-增强子架构的重构，并催生增强子枢纽，最终实现转录调控。通过直接探究SWI/SNF与AP1的互作关系，本研究证实SWI/SNF的功能依赖于AP1介导的染色质定位。本研究提出，诸如AP1这类先驱因子（Pioneer Factors）可结合并靶向SWI/SNF至非活性染色质区域，通过跨多维度的表观遗传重编程将基因组景观重塑为活性状态。本研究在可诱导SMARCB1缺陷型G401细胞系中开展了针对pJUN、JUND及JUNB的时间梯度CUT&RUN测序分析。