Glucocorticoid Receptor-Dependent Gene Regulatory Networks

Abstract

While the molecular mechanisms of glucocorticoid regulation of transcription have been studied in detail, the global networks regulated by the glucocorticoid receptor (GR) remain unknown. To address this question, we performed an orthogonal analysis to identify direct targets of the GR. First, we analyzed the expression profile of mouse livers in the presence or absence of exogenous glucocorticoid, resulting in over 1,300 differentially expressed genes. We then executed genome-wide location analysis on chromatin from the same livers, identifying more than 300 promoters that are bound by the GR. Intersecting the two lists yielded 53 genes whose expression is functionally dependent upon the ligand-bound GR. Further network and sequence analysis of the functional targets enabled us to suggest interactions between the GR and other transcription factors at specific target genes. Together, our results further our understanding of the GR and its targets, and provide the basis for more targeted glucocorticoid therapies. Glucocorticoids are essential steroid hormones, and synthetic glucocorticoids are widely prescribed for a variety of medical conditions. Understanding the mechanism by which glucocorticoids act requires knowing the direct target genes whose expression levels are modulated by the glucocorticoid signaling pathway. In this publication, Le and colleagues have utilized two high-throughput techniques to determine genes directly regulated in vivo by the glucocorticoid receptor (GR). RNA and chromatin were extracted from the livers of mice injected with the synthetic glucocorticoid dexamethasone and compared to control littermates. The analysis of RNA expression levels generated a list of genes differentially expressed after addition of dexamethasone. The analysis of the chromatin produced a list of gene promoter sequences where the GR was bound to DNA. By intersecting the two lists, the researchers obtained a list of genes that are directly controlled by the GR, including several previously known targets. This list of direct targets was then used as the basis for complex pathways and sequence analyses, which suggested several interactions between the GR and other transcription factors. This study provides an evaluation of a medically important signaling pathway and serves as a model for future analyses of transcriptional regulation.