Dynamic enhancer–gene body contacts during transcription elongation

Abstract

Enhancers govern transcription through multiple mechanisms, including the regulation of elongation by RNA polymerase II (RNAPII). We characterized the dynamics of looped enhancer contacts during synchronous transcription elongation. We found that two model enhancers form stable contacts with their target promoters during the entire interval of elongation. Notably, we detected additional dynamic enhancer contacts throughout the gene bodies that track with elongating RNAPII and the leading edge of RNA synthesis. These results support a model in which the gene body changes its position relative to a stable enhancer-promoter complex, which has broad ramifications for enhancer function and architectural models of transcriptional elongation.Supplemental material is available for this article.Received November 1, 2014; revised version accepted September 9, 2015. Enhancers are regulatory elements that stimulate transcription of genes in response to signaling events or developmental cues. A great deal has been learned about how enhancers function, and it has become clear that their mechanisms of actions are not uniform (Bulger and Groudine 2011;Liu et al. 2013). Enhancers can promote gene expression by altering chromatin structure and histone modifications, influencing the location of the target gene within the nucleus, and aiding in the recruitment of basal/general transcription factors (GTFs). In addition, enhancers have been reported to promote transcription elongation (Sawado et al. 2003;Liu et al. 2013). Since a large fraction of enhancers is occupied by BET family proteins that bind and activate P-TEFb to promote transcription elongation (Yang et al. 2005;Zhang et al. 2012) and since numerous genes display promoter-proximally paused RNA polymerase II (RNAPII) (Adelman and Lis 2012), it is possible that overcoming the pause might be a widespread mechanism of enhancer action (Hargreaves et al. 2009;Zippo et al. 2009;Liu et al. 2013).Enhancer elements can reside close to the promoters that they control, hundreds of kilobases away, or within the gene bodies. Despite varied positioning, a feature shared among many enhancers is direct physical contact with target promoters via chromatin looping (Sanyal et al. 2012). Looped contacts among regulatory elements can be highly dynamic, as revealed by experiments using conditional activation of transcription factors (Drissen et al. 2004;Vakoc et al. 2005), and can occur during both gene activation and repression (Jing et al. 2008). Another notable feature of a subset of extragenic enhancers is the presence of high levels of GTFs (Szutorisz et al. 2005;Koch et al. 2011) and RNAP (De Santa et al. 2010;Koch et al. 2011;Hah et al. 2013;Schaaf et al. 2013), including its elongation-competent forms (Louie et al. 2003;Wang et al. 2005;Zippo et al. 2009;Zhang et al. 2012). Moreover, there are reports of transcription elongation factors occupying active enhancer elements (Song et al. 2010;Lin et al. 2011Lin et al. , 2013Kellner et al. 2013). Examples of RNAPII occupancy at active enh...

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

“…However, loss of the LCR in whole animals left chromatin accessibility, histone acetylation and transcription factor occupancy at the promoters largely intact (Epner et al, 1998; Reik et al, 1998; Song et al, 2010; Vakoc et al, 2005). The LCR may also contribute to burst size by stimulating transcription elongation via physical contacts with the gene body (Kolovos et al, 2012; Larkin et al, 2012; Lee et al, 2015). Our forced looping approach predominantly facilitates enhancer contacts with the promoter, while increasing gene body contacts less than GATA1 induced maturation does (Deng et al 2012).…”

The 3D Genome as Moderator of Chromosomal Communication

“…For instance, RNAP polymerase II is obviously tracking along the chromatin while transcribing genes. In an interesting recent study Blobel and co-workers found evidence that the moving polymerase may remain associated also with the promoter leading to dynamic loop formation between the promoters and body of gene (Lee et al, 2015). Tracking and extruding genes by active polymerases has also been reported by the Cook laboratory (Larkin et al, 2013).…”

A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

“…See Supplemental Figure S14 for browser tracks. These enhancers were described in prior studies: Cd47 −20 kb was described in Dogan et al (2015), Kit −114 kb was described in Jing et al (2008) and Lee et al (2015), the Hba-a1 −34-kb R2 region was described in Hughes et al (2005), and the Hbb-b1 +32.5-kb locus control region was described in Bender et al (2000). The Y-axis is the normalized Capture-C contact frequency as described in C. Error bars and the number of replicates are as described in C, except for Hbb-b1, which represents n = 2 separate ligation libraries.…”