Effect of mithramycin on chromatin accessibility (ChIP-Seq)

Mammalian genome encodes approximately 1,700 transcription factors (TFs), 1,300 out of which have sequence specific binding motifs. Transcription in mammalian cells is regulated by the recruitment of TFs to specific cis-regulatory elements. In spite of consistent efforts on the function of individual TF, the question still remains how TFs bind to DNA and form enhancer. Here, we try to solve this problem by investigating the relationship between TF binding pattern and chromatin accessibility (ATAC-Seq). We first systematically acquired ATAC-Seq dataset as well as matched RNA-Seq dataset from different mouse primary tissues. A comprehensive TF binding map was built for each tissue/cell type by genomic approaches. Overall design: We displaced stripe factors with mithramycin in activated B cell and then checked effect on chromatin accessibility.

哺乳动物基因组编码约1700种转录因子（Transcription Factors, TFs），其中1300种具备序列特异性结合基序。哺乳动物细胞的转录过程通过将转录因子招募至特定顺式调控元件而得以调控。尽管学界已针对单个转录因子的功能开展了诸多持续性研究，但转录因子如何结合DNA并形成增强子这一核心问题仍悬而未决。本研究通过探究转录因子结合模式与染色质可及性（ATAC-Seq）之间的关联，尝试解答上述问题。我们首先从不同小鼠原代组织中系统性获取了ATAC-Seq数据集与匹配的RNA测序（RNA-Seq）数据集，并通过基因组学手段为每种组织/细胞类型构建了全面的转录因子结合图谱。实验整体设计：本研究在活化B细胞中用光神霉素（mithramycin）置换条纹因子（stripe factors），随后检测其对染色质可及性的影响。