Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [ATAC-Seq]

3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of how rapid transcriptional responses, transcriptional memory, and integration of different environmental signals are orchestrated in the 3D genome is limited. Here, we study various aspects of the inflammatory response in macrophages using transcriptomic, epigenomic, and genome conformation mapping technologies, including high-resolution Micro-Capture C. We report that interleukine-4 (IL-4) stably rewires the 3D genome conformation of macrophages and juxtaposes endotoxin-, interferon-gamma-, and dexamethasone-activated enhancers to cognate gene promoters to support enhanced gene expression. IL-4-driven conformational change is indispensable for the integration of IL-4- and endotoxin-induced enhanced and synergistic transcriptional responses, provides short-term transcriptional memory, and can occur in the absence of IL-4-induced epigenetic and transcriptional changes. Our work reveals that IL-4-driven 3D genome conformation is required to shape macrophage plasticity to subsequent immunological responses, integrate distinct inflammatory signals, and provides memory. Overall design: Examination of TFs binding during macrophage responses to polarizing cytokines.

三维基因组构象（3D genome conformation）是基因表达调控的核心机制，然而目前我们对于快速转录应答、转录记忆以及不同环境信号的整合如何在三维基因组中被协同调控的理解仍十分有限。本研究利用转录组学、表观基因组学及包括高分辨率Micro-Capture C在内的基因组构象图谱技术，针对巨噬细胞炎症应答的多个方面展开研究。我们发现，白细胞介素4（interleukin-4，IL-4）可稳定重塑巨噬细胞的三维基因组构象，并将内毒素、干扰素-γ与地塞米松激活的增强子与对应基因启动子进行空间并置，以支持基因表达增强。IL-4介导的构象改变对于整合IL-4与内毒素诱导的增强型协同转录应答不可或缺，同时可介导短期转录记忆；即便不存在IL-4诱导的表观遗传与转录变化，该构象改变仍可发生。本研究揭示，IL-4驱动的三维基因组构象重塑是塑造巨噬细胞对后续免疫应答的可塑性、整合不同炎症信号并建立转录记忆所必需的。整体实验设计：检测巨噬细胞在应答极化细胞因子过程中的转录因子（Transcription Factors，TFs）结合情况。