Behera Vivek, Evans Perry, Face Carolyne J, Hamagami Nicole, Sankaranarayanan Laavanya, Keller Cheryl A, Giardine Belinda, Tan Kai, Hardison Ross C, Shi Junwei, Blobel Gerd A
University of Pennsylvania, Philadelphia, PA, 19104, USA.
Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Nat Commun. 2018 Feb 22;9(1):782. doi: 10.1038/s41467-018-03082-6.
Single-nucleotide variants that underlie phenotypic variation can affect chromatin occupancy of transcription factors (TFs). To delineate determinants of in vivo TF binding and chromatin accessibility, we introduce an approach that compares ChIP-seq and DNase-seq data sets from genetically divergent murine erythroid cell lines. The impact of discriminatory single-nucleotide variants on TF ChIP signal enables definition at single base resolution of in vivo binding characteristics of nuclear factors GATA1, TAL1, and CTCF. We further develop a facile complementary approach to more deeply test the requirements of critical nucleotide positions for TF binding by combining CRISPR-Cas9-mediated mutagenesis with ChIP and targeted deep sequencing. Finally, we extend our analytical pipeline to identify nearby contextual DNA elements that modulate chromatin binding by these three TFs, and to define sequences that impact kb-scale chromatin accessibility. Combined, our approaches reveal insights into the genetic basis of TF occupancy and their interplay with chromatin features.
构成表型变异基础的单核苷酸变异可影响转录因子（TFs）与染色质的结合。为了阐明体内TF结合和染色质可及性的决定因素，我们引入了一种方法，该方法比较来自基因不同的小鼠红细胞系的ChIP-seq和DNase-seq数据集。鉴别性单核苷酸变异对TF ChIP信号的影响能够在单碱基分辨率下定义核因子GATA1、TAL1和CTCF的体内结合特征。我们进一步开发了一种简便的互补方法，通过将CRISPR-Cas9介导的诱变与ChIP和靶向深度测序相结合，更深入地测试关键核苷酸位置对TF结合的要求。最后，我们扩展了分析流程，以识别调节这三种TF与染色质结合的附近上下文DNA元件，并定义影响kb尺度染色质可及性的序列。综合起来，我们的方法揭示了对TF占据的遗传基础及其与染色质特征相互作用的见解。
