Nair Venugopalan D, Vasoya Mital, Nair Vishnu, Smith Gregory R, Pincas Hanna, Ge Yongchao, Douglas Collin M, Esser Karyn A, Sealfon Stuart C
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Genomics. 2021 Nov;113(6):3827-3841. doi: 10.1016/j.ygeno.2021.09.013. Epub 2021 Sep 20.
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。我们优化了全基因组转座酶可及染色质测序（Omni-ATAC-seq）方案，并将其与RNA测序结合使用，以研究大鼠白色脂肪组织和骨骼肌中的顺式调控元件，这两种组织具有截然不同的代谢功能。虽然启动子可及性与RNA表达相关，但两个数据集的整合鉴定出了组织特异性差异可及区域（DAR），这些区域主要位于基因间区和内含子区域。DAR被映射到在每个组织中富集于不同生物学过程的差异表达（DE）基因。通过定量聚合酶链反应（qPCR）对随机选择的DE基因进行了验证。DAR中富集程度最高的基序预测了显示组织特异性上调的转录因子（TF）的结合位点。给定TF结合基序处的差异染色质可及性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。我们的研究确定了可能在脂肪组织和肌肉中组织特异性基因表达调控中起主要作用的顺式调控区域。
