Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs

Abstract

Enhancers are critical genomic elements that define cellular and functional identity through the spatial and temporal regulation of gene expression. Recent studies suggest that key genes regulating cell type-specific functions reside in enhancer-dense genomic regions (i.e., super enhancers, stretch enhancers). Here we report that enhancer RNAs (eRNAs) identified by global nuclear run-on sequencing are extensively transcribed within super enhancers and are dynamically regulated in response to cellular signaling. Using Toll-like receptor 4 (TLR4) signaling in macrophages as a model system, we find that transcription of super enhancer-associated eRNAs is dynamically induced at most of the key genes driving innate immunity and inflammation. Unexpectedly, genes repressed by TLR4 signaling are also associated with super enhancer domains and accompanied by massive repression of eRNA transcription. Furthermore, we find each super enhancer acts as a single regulatory unit within which eRNA and genic transcripts are coordinately regulated. The key regulatory activity of these domains is further supported by the finding that super enhancer-associated transcription factor binding is twice as likely to be conserved between human and mouse than typical enhancer sites. Our study suggests that transcriptional activities at super enhancers are critical components to understand the dynamic gene regulatory network.super enhancers | enhancer RNAs | transcription factors | GRO-Seq | macrophage

Brd4 modulates the innate immune response through Mnk2–eIF4E pathway-dependent translational control of IκBα

“…Consistent with the previous finding that Brd4 acts as both a coactivator and corepressor for gene expression (16), many genes were either up-regulated or down-regulated in Brd4-deficient BMDMs (Fig. 4 C and D).…”

“…Inhibition of BET family proteins by small molecules such as JQ1 and I-BET has been shown to down-regulate the expression of inflammatory genes selectively (16,19,20). To understand better the specific contribution of Brd4 in LPS-stimulated gene expression, we performed geneexpression microarray analysis using RNA isolated from WT and Brd4-deficient BMDMs stimulated or not stimulated by LPS.…”

“…Induction of PRGs has been shown to be regulated at the level of transcriptional elongation and mRNA processing through the signal-dependent recruitment of CDK9 (17). Brd4 is recruited to the promoters of inflammatory genes via acetylated NF-κB or histones and regulates the NF-κB-dependent inflammatory gene expression by activating CDK9 (14)(15)(16)(17). Therefore, Brd4 deficiency would have a direct effect on the recruitment of CDK9, leading to the reduced transcription elongation for the PRGs.…”

“…Brd4 has recently emerged as a key transcription regulator of NF-κB-dependent inflammatory gene expression by activating CDK9 of P-TEFb (positive transcription elongation factor b) to facilitate the RNAPII-dependent transcription elongation (14)(15)(16)(17). Inhibition of Brd4 by small molecules suppresses NF-κB-dependent inflammatory gene expression and LPS-induced sepsis (16,(18)(19)(20).…”

“…Inhibition of Brd4 by small molecules suppresses NF-κB-dependent inflammatory gene expression and LPS-induced sepsis (16,(18)(19)(20). Brd4 also has been shown to regulate inflammatory gene expression by facilitating the transcription of enhancer RNA and super-enhancer formation (14,16,18).…”