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

Abstract

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. The glucocorticoid receptor (GR) regulates a myriad of physiological functions, such as cell differentiation and metabolism, achieved through modulating transcription in a cell- and gene-specific manner. However, the determinants that specify cell- and gene-specific GR transcriptional regulation are not well established. We describe three properties that contribute to this specificity: (1) GR occupancy at genomic glucocorticoid response elements (GREs) appears to be a primary determinant of glucocorticoid responsiveness; (2) the DNA sequences bound by GR vary widely around a consensus, but the precise sequences of individual GREs are highly conserved, suggesting a role for these sequences in gene-specific GR transcriptional regulation; and (3) native chromosomal GREs were generally found to be composite elements, comprised of multiple factor binding sites that were highly variable in composition, but as with the GR binding sequences, highly conserved at individual GREs. In addition, we discovered that most GREs were positioned far from their GR target genes and that they were equally distributed upstream and downstream of the target genes. These findings, which may be applicable to other regulatory factors, provide fundamental insights for understanding cell- and gene-specific transcriptional regulation.