Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [ChIP-Seq]

We used a differential open chromatin approach, coupled with active enhancer mark ,transcriptomic and computational TFs binding analysis to map cell-type-specific active enhancers in cardiac fibroblasts and cardiomyocytes, and outline the TFs that control them. We identified Tead, Sox9, Smad, Tcf, Meis, Rbpj, and Runx1 as the main cardiac fibroblasts TF groups. Our analysis shows that in cardiomyocytes and cardiac fibroblasts, distal enhancers, containing concentrated combinatorial clusters of multiple tissue expressed TFs recognition motifs, are combinatorically clustered around tissue specific genes. We examined 3 different biological samples ('cardioPE', 'cardioSFM' (cardiomyocytes in different conditions) and 'cardiacFibro'), in duplicates, to identify histone modification by using ChIP-seq assay.

本研究采用差异开放染色质方法，结合活性增强子标记、转录组学与计算转录因子（Transcription Factors, TFs）结合分析，对心脏成纤维细胞与心肌细胞中的细胞类型特异性活性增强子进行定位，并阐明调控这些增强子的转录因子。我们鉴定出Tead、Sox9、Smad、Tcf、Meis、Rbpj及Runx1为心脏成纤维细胞的主要转录因子家族。分析结果显示，在心肌细胞与心脏成纤维细胞中，携带多种组织表达转录因子识别基序的浓缩组合簇的远端增强子，会在组织特异性基因周围形成组合式聚集区域。我们针对3种不同生物学样本——'cardioPE'、'cardioSFM'（即不同培养条件下的心肌细胞）及'cardiacFibro'——设置双生物学重复实验，通过染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）技术鉴定组蛋白修饰情况。