Genetic, functional and molecular features of glucocorticoid receptor binding (expression). Homo sapiens

Glucocorticoids (GCs) are key mediators of stress response and are widely used as pharmacological agents to treat immune diseases, such as asthma and inflammatory bowel disease, and certain types of cancer. GCs act mainly by activating the GC receptor (GR), which interacts with other transcription factors to regulate gene expression. Here, we combined different functional genomics approaches to gain molecular insights into the mechanisms of action of GC. By profiling the transcriptional response to GC over time in 4 Yoruba (YRI) and 4 Tuscans (TSI) lymphoblastoid cell lines (LCLs), we suggest that the transcriptional response to GC is variable not only in time, but also in direction (positive or negative) depending on the presence of specific interacting TFs. Accordingly, when we performed ChIP-seq for GR and NF-kB in two YRI LCLs treated with GC or with vehicle control, we observed that features of GR binding sites differ for up- and down-regulated genes. Finally, we show that eQTLs that affect expression patterns only in the presence of GC are 1.9-fold more likely to occur in GR binding sites, compared to eQTLs that affect expression only in its absence. Our results indicate that genetic variation at GR and interacting transcription factors binding sites influences variability in gene expression, and attest to the power of combining different functional genomic approaches. Overall design: Total RNA obtained from lymphoblastoid cell lines treated with either dexamethasone or EtOH (vehicle for dexamethasone) for 2, 4, 8, 12, 16, or 24 hours.

糖皮质激素（Glucocorticoids, GCs）是应激反应的关键介导因子，被广泛用作药理制剂治疗哮喘、炎症性肠病等免疫疾病及部分类型癌症。GCs主要通过激活糖皮质激素受体（Glucocorticoid Receptor, GR）发挥作用，后者可与其他转录因子相互作用以调控基因表达。本研究整合多种功能基因组学手段，以解析GC的分子作用机制。我们对4株约鲁巴人（Yoruba, YRI）和4株托斯卡纳人（Tuscans, TSI）的淋巴母细胞系（Lymphoblastoid Cell Lines, LCLs）开展GC处理后的时序转录应答谱分析，结果显示GC的转录应答不仅存在时序差异，还会因特异性相互作用转录因子的存在而呈现正向或负向的调控方向差异。进一步地，我们对经GC或载体对照处理的2株YRI LCLs进行了GR与核因子κB（Nuclear Factor-kappa B, NF-κB）的染色质免疫共沉淀测序（ChIP-seq），观察到GR结合位点的特征在调控上调与下调基因时存在显著差异。最后，我们证实：相较于仅在无GC处理条件下影响基因表达的表达数量性状位点（expression Quantitative Trait Loci, eQTLs），仅在GC存在时调控基因表达模式的eQTLs在GR结合位点中出现的概率高出1.9倍。本研究结果表明，GR及相互作用转录因子结合位点处的遗传变异会影响基因表达的个体差异，同时验证了多类功能基因组学方法联用的研究效力。实验整体设计：提取经地塞米松或乙醇（地塞米松的溶剂载体）处理2、4、8、12、16或24小时的淋巴母细胞系的总RNA。