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. Overall design: Time course CUT&RUN profiling of pJUN, JUND and JUNB in inducible SMARCB1 G401 cell line

长期以来，学界推测SWI/SNF复合物（SWI/SNF）的动态靶向调控机制由转录因子（transcription factors, TFs）协同介导，但此前鉴定并验证不同转录因子的作用颇具难度。本研究采用多组学策略，直接探究SWI/SNF的瞬时互作蛋白、染色质靶向特性以及由此产生的三维表观遗传景观的可塑性。我们借助新型邻近标记技术TurboID，鉴定出AP1家族为内源性SWI/SNF复合物的关键互作伴侣。通过CUT&RUN谱分析验证，发现SWI/SNF在AP1结合位点处存在靶向富集，且SWI/SNF与AP1在染色质靶向过程中存在协同作用。通过HiChIP技术解析三维染色质结构，我们发现AP1与SWI/SNF可介导启动子-增强子架构重塑及增强子枢纽的形成，最终实现转录调控。通过直接探究SWI/SNF与AP1的互作关系，我们证实SWI/SNF的功能依赖于AP1介导的染色质定位。我们提出，诸如AP1这类先驱因子（pioneer factors）可结合并将SWI/SNF靶向至非活性染色质，随后SWI/SNF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。实验整体设计：在可诱导SMARCB1 G401细胞系中，对pJUN、JUND及JUNB开展时间梯度CUT&RUN谱分析。