Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release

Abstract

SUMMARY Distal enhancers characterized by H3K4me1 mark play critical roles in developmental and transcriptional programs. However, potential roles of specific distal regulatory elements in regulating RNA Polymerase II (Pol II) promoter-proximal pause release remain poorly investigated. Here we report that a unique cohort of jumonji C domain-containing protein 6 (JMJD6) and bromodomain-containing protein 4 (Brd4) co-bound distal enhancers, termed anti-pause enhancers (A-PEs), regulate promoter-proximal pause release of a large subset of transcription units via long-range interactions. Brd4-dependent JMJD6 recruitment on A-PEs mediates erasure of H4R3me2(s), which is directly read by 7SK snRNA, and decapping/demethylation of 7SK snRNA, ensuring the dismissal of the 7SKsnRNA/HEXIM inhibitory complex. The interactions of both JMJD6 and Brd4 with the P-TEFb complex permit its activation and pause release of regulated coding genes. The functions of JMJD6/ Brd4-associated dual histone and RNA demethylase activity on anti-pause enhancers have intriguing implications for these proteins in development, homeostasis and disease.

Clipping of arginine-methylated histone tails by JMJD5 and JMJD7

“…While many members of the JmjC protein family have been characterized biochemically, the functions of several members, including JMJD4-JMJD8 and HSPBAP1 remain uncharacterized or controversial. For example, JMJD6 has been reported variously to be an arginine demethylase (10,11), a hydroxylase (12,13), a single-stranded RNA-binding protein (14), or RNA demethylase (11). Although JMJD6 has been reported to possess histone arginine demethylase activity (10,11), we and others have been unable to replicate this result (12,(14)(15)(16)(17).…”

“…For example, JMJD6 has been reported variously to be an arginine demethylase (10,11), a hydroxylase (12,13), a single-stranded RNA-binding protein (14), or RNA demethylase (11). Although JMJD6 has been reported to possess histone arginine demethylase activity (10,11), we and others have been unable to replicate this result (12,(14)(15)(16)(17). Thus, the identities of proteins that reverse methylation of arginine residues, either through conventional demethylation or others, have not been resolved.…”

GC skew defines distinct RNA polymerase pause sites in CpG island promoters

“…Several recent studies suggest that enhancers may function to regulate transcription in part by modulating Pol II pausing (Krumm et al 1995;Brown et al 1996;Core and Lis 2009;Zippo et al 2009;Anand et al 2013;Liu et al 2013;Loven et al 2013). We used chromatin conformation capture (3C) to probe the relationship between enhancer-promoter looping interactions and pausing class in MCF7 cells transiently exposed to estradiol (E2).…”

“…The role of active enhancers in mediating promoter-proximal pause release is incompletely understood but has been attributed to the delivery of the P-TEFb complex to the promoter, enhancer-mediated liberation of P-TEFb complex from local HEXIM1-mediated sequestration, and, most recently, a mechanism involving competition for promoter-bound NELF complex by enhancer-derived eRNAs (Anand et al 2013;Liu et al 2013;Loven et al 2013;Schaukowitch et al 2014). It is tempting to speculate that at distally paused genes, the enhancer might bring in factors capable of resolving R-loops or other physical constraints (e.g., supercoiling).…”

“…Enhancers are cis-acting regulatory elements that control transcription from a distance through the formation of contacts between the enhancer-bound transcription factors and promoter-bound Pol II and the looping out of intervening chromatin (Kagey et al 2010b). BRD4 and components of the P-TEFb complex have been shown to colocalize with elongating (serine-2-phosphorylated) Pol II at both the promoters and enhancers of active genes, and inhibition of either suppresses not only elongation of promoter-derived mRNAs but also that of noncoding "eRNAs" arising at distal enhancers (Zhang et al 2012;Anand et al 2013;Liu et al 2013;Loven et al 2013;Kanno et al 2014). In addition, long-range chromatin looping interactions have been shown to correlate with paused Pol II during Drosophila development (Ghavi-Helm et al 2014).…”