Mitotic chromosome binding predicts transcription factor properties in interphase [ATAC-Seq]

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/ non-specific DNA binding affinity. How these properties affect the ability of TFs to occupy their specific binding sites in the genome and modify the epigenetic landscape is unclear. Here we combined live cell quantitative measurements of mitotic chromosome binding (MCB) of 502 TFs, measurements of TF mobility by fluorescence recovery after photobleaching, single molecule imaging of DNA binding in live cells, and genome-wide mapping of TF binding and chromatin accessibility. MCB scaled with interphase properties such as association with DNA-rich compartments, mobility, as well as large differences in genome-wide specific site occupancy that correlated with TF impact on chromatin accessibility. As MCB is largely mediated by electrostatic, non-specific TF-DNA interactions, our data suggests that non-specific DNA binding of TFs enhances their search for specific sites and thereby their impact on the accessible chromatin landscape. Overall design: NIH-3T3 cells overexpressing different transcription factors (or no overexpression control) were subjected to ATAC-seq by Tn5 transposition哺乳动物转录因子（transcription factors, TFs）在核迁移能力以及序列特异性/非特异性DNA结合亲和力方面存在广泛差异。目前尚不清楚这些性质如何影响转录因子在基因组中占据其特异性结合位点并修饰表观遗传景观的能力。本研究结合了502种转录因子的活细胞有丝分裂染色体结合（mitotic chromosome binding, MCB）定量检测、通过荧光漂白恢复技术测定的转录因子迁移能力、活细胞内DNA结合的单分子成像，以及转录因子结合与染色质可及性的全基因组定位分析。研究发现，MCB水平与间期相关特性（如与富DNA区室的关联、迁移能力），以及与转录因子对染色质可及性的影响相关的全基因组特异性位点占据度的显著差异均呈相关性。由于MCB主要由静电介导的非特异性转录因子-DNA相互作用所介导，本研究数据表明，转录因子的非特异性DNA结合能够增强其对特异性位点的搜寻效率，进而强化其对可及染色质景观的调控作用。整体实验设计：将过表达不同转录因子（或设置未过表达的对照组）的NIH-3T3细胞进行Tn5转座酶介导的ATAC-seq检测。