Identification of dynamic glucocorticoid-induced methylation changes at the FKBP5 locus

Abstract

Background Epigenetic mechanisms may play a major role in the biological embedding of early-life stress (ELS). One proposed mechanism is that glucocorticoid (GC) release following ELS exposure induces long-lasting alterations in DNA methylation (DNAm) of important regulatory genes of the stress response. Here, we investigate the dynamics of GC-dependent methylation changes in key regulatory regions of the FKBP5 locus in which ELS-associated DNAm changes have been reported. Results We repeatedly measured DNAm in human peripheral blood samples from 2 independent cohorts exposed to the GC agonist dexamethasone (DEX) using a targeted bisulfite sequencing approach, complemented by data from Illumina 450K arrays. We detected differentially methylated CpGs in enhancers co-localizing with GC receptor binding sites after acute DEX treatment (1 h, 3 h, 6 h), which returned to baseline levels within 23 h. These changes withstood correction for immune cell count differences. While we observed main effects of sex, age, body mass index, smoking, and depression symptoms on FKBP5 methylation levels, only the functional FKBP5 SNP (rs1360780) moderated the dynamic changes following DEX. This genotype effect was observed in both cohorts and included sites previously shown to be associated with ELS. Conclusion Our study highlights that DNAm levels within regulatory regions of the FKBP5 locus show dynamic changes following a GC challenge and suggest that factors influencing the dynamics of this regulation may contribute to the previously reported alterations in DNAm associated with current and past ELS exposure. Electronic supplementary material The online version of this article (10.1186/s13148-019-0682-5) contains supplementary material, which is available to authorized users.

DNA methylation of FKBP5 in South African women: associations with obesity and insulin resistance

“…Furthermore, while it was beyond the scope of this study to elucidate the transcription factors that occupy and regulate this region, we note that CpG542 and CpG543 are located either directly within, or flank, biologically validated consensus glucocorticoid response elements (GREs), which have been shown to come into direct contact with the FKBP5 transcriptional start site and RNA polymerase II, via three-dimensional chromatin loops, and influence FKBP5 transcription [ 39 ]. In agreement with this are several reports demonstrating that exposure of human peripheral blood cells to dexamethasone, a GR agonist, can induce rapid demethylation and transcription of FKBP5 via these GREs [ 5 , 46 ]. Furthermore, while previous studies have shown that FKBP5 demethylation and mRNA induction by GR is influenced by the rs1360780 SNP in human peripheral blood from both African American and Caucasian populations [ 5 , 46 – 48 ], this was not observed in our study, albeit in a limited sample size.…”

“…In agreement with this are several reports demonstrating that exposure of human peripheral blood cells to dexamethasone, a GR agonist, can induce rapid demethylation and transcription of FKBP5 via these GREs [ 5 , 46 ]. Furthermore, while previous studies have shown that FKBP5 demethylation and mRNA induction by GR is influenced by the rs1360780 SNP in human peripheral blood from both African American and Caucasian populations [ 5 , 46 – 48 ], this was not observed in our study, albeit in a limited sample size. These findings may suggest that FKBP5 regulation is tissue-specific; however, confirmation of this in larger, more representative studies is required.…”

“…It is therefore possible that our analysis does not reflect the methylation effect of other genomic regions of GR and FKBP5 . In particular, FKBP5 contains numerous transcriptional regulatory regions which are distributed throughout the gene, including the promoter and other intronic enhancer regions which harbour functional GREs [ 5 , 46 ] as well as CCCTC-binding factor (CTCF) sites [ 46 ]. Our analysis of the effect of the rs1360780 SNP on FKBP5 methylation and gene expression levels should also be interpreted in the context of a small sample size, and larger, more representative studies will be required to confirm this finding.…”

Epigenetics and depression

“…The DMRs with GR binding motifs were more commonly demethylated than hypermethylated. Given that there is evidence that GRs can induce demethylation at glucocorticoid response elements (GREs), 56 the authors postulate that the molecular mechanisms underlying the observed methylation changes in this study are GRmediated. Further evidence of GR-mediated methylation changes will be discussed later in the review.…”

“…Highly dynamic GR-dependent changes in DNAm of CpGs in FKBP5 after acute GR activation have been shown to occur in adult peripheral blood cells, with de-and remethylation occurring within a period of 24 hours following GR activation. 56 However, as shown in a human hippocampal progenitor cell line, GR-induced demethylation can become stable when initiated during certain early developmental periods. 55 Such lasting changes in DNAm result in an altered set-point for transcriptional changes of FKBP5 upon subsequent GR activation.…”