Chromatin accessibility is a key factor influencing gene expression. We optimized the Omni-ATAC-seq protocol and used it together with RNA-seq to investigate cis-regulatory elements in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs were mapped to differentially expressed (DE) genes enriched in distinct biological processes in each tissue. Randomly selected DE genes were validated by qPCR. Top enriched motifs in DARs predicted binding sites for transcription factors (TFs) showing tissue-specific up-regulation. The correlation between differential chromatin accessibility at a given TF binding motif and differential expression of target genes further supported the functional relevance of that motif. Our study identified cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.

染色质可及性是影响基因表达的关键因素。我们优化了 Omni-ATAC-seq 方案，并将其与 RNA-seq 一起使用来研究大鼠白色脂肪和骨骼肌（两种具有对比代谢功能的组织）中的顺式调控元件。虽然启动子可及性与 RNA 表达相关，但两个数据集的整合确定了主要位于基因间和内含子区域的组织特异性差异可及性区域 (DAR)。DAR 被映射到富含每个组织中不同生物过程的差异表达 (DE) 基因。通过 qPCR 验证随机选择的 DE 基因。DAR 中最富集的基序预测转录因子 (TF) 的结合位点，显示组织特异性上调。给定 TF 结合基序的染色质可及性差异与靶基因差异表达之间的相关性进一步支持了该基序的功能相关性。我们的研究确定了顺式调控区域，它们可能在脂肪和肌肉中组织特异性基因表达的调控中发挥重要作用。