Determinants of Cell- and Gene-Specific Transcriptional Regulation by the Glucocorticoid Receptor

The glucocorticoid receptor (GR) associates with glucocorticoid response elements (GREs) and regulates selective gene transcription in a cell-specific manner. Native GREs are typically thought to be composite elements that recruit GR as well as other regulatory factors into functional complexes. We assessed whether GR occupancy is commonly a limiting determinant of GRE function as well as the extent to which core GR binding sequences and GRE architecture are conserved at functional loci. We surveyed 100-kb regions surrounding each of 548 known or potentially glucocorticoid-responsive genes in A549 human lung cells for GR-occupied GREs. We found that GR was bound in A549 cells predominately near genes responsive to glucocorticoids in those cells and not at genes regulated by GR in other cells. The GREs were positionally conserved at each responsive gene but across the set of responsive genes were distributed equally upstream and downstream of the transcription start sites, with 63% of them >10 kb from those sites. Strikingly, although the core GR binding sequences across the set of GREs varied extensively around a consensus, the precise sequence at an individual GRE was conserved across four mammalian species. Similarly, sequences flanking the core GR binding sites also varied among GREs but were conserved at individual GREs. We conclude that GR occupancy is a primary determinant of glucocorticoid responsiveness in A549 cells and that core GR binding sequences as well as GRE architecture likely harbor gene-specific regulatory information.

糖皮质激素受体（glucocorticoid receptor, GR）可结合糖皮质激素应答元件（glucocorticoid response elements, GREs），并以细胞特异性方式调控选择性基因转录。传统观点认为，天然GREs多为复合元件，可招募GR及其他调控因子形成功能复合物。本研究旨在评估GR结合是否普遍为GRE功能发挥的限制性决定因素，同时探究功能性位点处GR核心结合序列与GRE结构的保守程度。我们针对人肺腺癌细胞A549中548个已知或潜在糖皮质激素应答基因的周边100千碱基区域，筛查了结合GR的GREs。结果显示，在A549细胞中，GR结合位点主要富集于该细胞内对糖皮质激素产生应答的基因附近，而非其他细胞中受GR调控的基因区域。GREs在各应答基因上均呈现位置保守性，但在所有应答基因集合中，其分布在转录起始位点的上下游区域均等，其中63%的GREs距离转录起始位点超过10千碱基。值得注意的是，尽管所有GRE的核心GR结合序列围绕共识序列存在广泛变异，但单个GRE的精确序列在四种哺乳动物物种中均保持保守。类似地，GR核心结合位点的侧翼序列在不同GRE间存在差异，但在单个GRE中同样具有物种保守性。综上，我们得出结论：GR结合是A549细胞中糖皮质激素应答性的主要决定因素，且GR核心结合序列与GRE结构可能携带有基因特异性的调控信息。