Two Populations of Glucocorticoid Receptor-Binding Sites in the Male Rat Hippocampal Genome

Abstract

In the present study, genomic binding sites of glucocorticoid receptors (GR) were identified in vivo in the rat hippocampus applying chromatin immunoprecipitation followed by next-generation sequencing. We identified 2470 significant GR-binding sites (GBS) and were able to confirm GR binding to a random selection of these GBS covering a wide range of P values. Analysis of the genomic distribution of the significant GBS revealed a high prevalence of intragenic GBS. Gene ontology clusters involved in neuronal plasticity and other essential neuronal processes were overrepresented among the genes harboring a GBS or located in the vicinity of a GBS. Male adrenalectomized rats were challenged with increasing doses of the GR agonist corticosterone (CORT) ranging from 3 to 3000 μg/kg, resulting in clear differences in the GR-binding profile to individual GBS. Two groups of GBS could be distinguished: a low-CORT group that displayed GR binding across the full range of CORT concentrations, and a second high-CORT group that displayed significant GR binding only after administering the highest concentration of CORT. All validated GBS, in both the low-CORT and high-CORT groups, displayed mineralocorticoid receptor binding, which remained relatively constant from 30 μg/kg CORT upward. Motif analysis revealed that almost all GBS contained a glucocorticoid response element resembling the consensus motif in literature. In addition, motifs corresponding with new potential GR-interacting proteins were identified, such as zinc finger and BTB domain containing 3 (Zbtb3) and CUP (CG11181 gene product from transcript CG11181-RB), which may be involved in GR-dependent transactivation and transrepression, respectively. In conclusion, our results highlight the existence of 2 populations of GBS in the rat hippocampal genome.

Stress and corticosteroids regulate rat hippocampal mitochondrial DNA gene expression via the glucocorticoid receptor

“…43. Rats were adrenalectomized and injected with 300 or 3,000 μg/kg of corticosterone 1 h before they were killed and tissue was processed for ChIP.…”

30 YEARS OF THE MINERALOCORTICOID RECEPTOR: The brain mineralocorticoid receptor: a saga in three episodes

“…The gene patterns examined in laser-dissected hippocampal regions revealed that a history of chronic stress had profound consequences for the subsequent response to acute corticosterone challenge, differentially affecting the expression of several hundreds of genes as compared to challenged non-stressed control animals. The difference concerned an overrepresentation of genes involved in chromatin reorganisation and epigenetic processes in the stress group (Datson et al 2013).…”

Genome-wide coexpression of steroid receptors in the mouse brain: Identifying signaling pathways and functionally coordinated regions

“…Therefore, we set out to detect genomic binding of steroid receptors directly using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq). Previously, we used ChIP-Seq to identify genomic binding sites of GR in the rat hippocampus (28). Reanalyzing this data, we identified 694 corticosterone target genes with GR binding sites, of which 16 were within the top 200 genes coexpressed with Gr in the hippocampus (16 of 200; P = 9.97 × 10 −5 , one-sided Fisher's exact test; Table S4).…”