Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation (human cell)

ATP-dependent chromatin remodelers establish and arrange nucleosome distribution, modifying accessibility of DNA. Brg1 is exclusive ATPase subunit of mSWI/SNF complex. To understand the dosage dependent function of mSWI/SNF complex. We take an advantage of dTag system to precisely control abundancy of BRG1. We found overall Brg1-binding is sensitive to its abundance nevertheless OCT4-target or H3K27ac region, suggesting Brg1 genome-wide distribution rather than being actively recruited. We also reveal open chromatin dependency on BRG1. The chromatin accessibility of super enhancer shows buffered response on depletion of BRG1, whereas weak enhancer is sensitive. Finally, transcriptomic analysis identified that transcription shows buffered dependencies on BRG1 loss. Overall, our results highlight kinetics differences of BRG1-binding to transcriptome underline BRG1 dosage-sensitive mechanism. To study the kinetics of BRG1 binding, chromatin accessibility, and gene expression, we employed the dTAG system to precisely control Brg1 protein levels in BEAS-2B cell. We then used Cut&Run and ATAC-seq examine the kinetic changes under different Brg1 protein levels.

ATP依赖型染色质重塑因子（ATP-dependent chromatin remodelers）可建立并排布核小体分布，进而改变DNA的可及性。BRG1是mSWI/SNF复合物（mSWI/SNF complex）独有的ATP酶亚基。为阐明mSWI/SNF复合物的剂量依赖性功能，我们借助dTag系统（dTag system）精准调控BRG1的蛋白丰度。研究发现，整体BRG1结合事件对其自身丰度高度敏感，无论结合位点为OCT4靶位点（OCT4-target）还是H3K27乙酰化修饰区域（H3K27ac region），这提示BRG1主要以全基因组分布的形式存在，而非通过主动靶向招募至特定位点。我们还揭示了开放染色质的维持依赖于BRG1：超级增强子（super enhancer）的染色质可及性在BRG1耗竭时呈现缓冲性应答，而弱增强子（weak enhancer）则对BRG1丰度变化极为敏感。最终，转录组学分析结果显示，基因转录对BRG1缺失的依赖性同样存在缓冲特性。综上，本研究结果揭示了BRG1结合与转录组之间的动力学差异，阐明了BRG1剂量敏感的作用机制。为研究BRG1结合、染色质可及性与基因表达的动力学变化，我们利用dTag系统精准调控BEAS-2B细胞中BRG1的蛋白水平，并通过Cut&Run技术（Cut&Run）与ATAC-seq（ATAC-seq）检测不同BRG1丰度条件下的动力学改变。