Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages

Abstract

Glucocorticoids are potent anti-inflammatory drugs; however, their molecular mode of action remains complex and elusive. They bind to the glucocorticoid receptor (GR), a nuclear receptor that controls gene expression in almost all tissues in a cell type-specific manner. While GR’s transcriptional targets mediate beneficial reactions in immune cells, they also harbor the potential of adverse metabolic effects in other cell types such as hepatocytes. Here, we have profiled nascent transcription upon glucocorticoid stimulation in LPS-activated primary murine macrophages using 4sU-seq. We compared our results to publicly available nascent transcriptomics data from murine liver and bioinformatically identified non-coding RNAs transcribed from intergenic GR binding sites in a tissue-specific fashion. These tissue-specific enhancer RNAs (eRNAs) correlate with target gene expression, reflecting cell type-specific glucocorticoid responses. We further associate GR-mediated eRNA expression with changes in H3K27 acetylation and BRD4 recruitment in inflammatory macrophages upon glucocorticoid treatment. In summary, we propose a common mechanism by which GR-bound enhancers regulate target gene expression by changes in histone acetylation, BRD4 recruitment and eRNA expression. We argue that local eRNAs are potential therapeutic targets downstream of GR signaling which may modulate glucocorticoid response in a cell type-specific way.

Dimerization of the Glucocorticoid Receptor and Its Importance in (Patho)physiology: A Primer

“…Some genes do indeed have several GREs, which work together in order to regulate expression. Many GRE sites are more related to enhancer activity then direct transcriptional induction and have been found to modulate the expression level of genes under the control of enhancer regions [ 121 , 122 ].…”

Machine learning reveals STAT motifs as predictors for GR-mediated gene repression

“…a set of target genes). To this end we utilized previously published data [13] of 4-thiouridine labeled nascent transcripts in mouse bone marrow derived macrophages and compared nascent transcript levels of samples treated with the pro-inflammatory molecule lipopolysaccharide (LPS) for 2 h to samples treated with a combination of the GR agonist Dexamethasone for 2.5 h and LPS for 2 h (Dex+LPS) (see Methods Section 2.4 ). Dexamethasone binding allows GR to dimerize and translocate to the nucleus where we can monitor the expression of nascent transcripts without the preexisting transcript confounding the RNA levels.…”

“…H3K27ac (GSE136070) [14] . 4sU-seq (GSE186629) [13] . ATACseq data (GSE186511) and GR ChIPseq (GSE1865112) [25] .…”

Natural antisense transcripts as drug targets

“…Notably, eRNA expression patterns are known to be tissuespecific. Such local eRNAs represent potential therapeutic targets downstream of glucocorticoid receptor (GR), for example, and can be used to modulate glucocorticoid response in a cell typespecific manner to reduce the possibility of side effects (Greulich et al, 2021).…”