RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene

Abstract

Since the discovery that many transcriptional enhancers are transcribed into long noncoding RNAs termed "enhancer RNAs" (eRNAs), their putative role in enhancer function has been debated. Very recent evidence has indicted that some eRNAs play a role in initiating or activating transcription, possibly by helping recruit and/or stabilize binding of the general transcription machinery to the proximal promoter of their target genes. The distal enhancer of the gonadotropin hormone α-subunit gene, chorionic gonadotropin alpha (Cga), is responsible for Cga cell-specific expression in gonadotropes and thyrotropes, and we show here that it encodes two bidirectional nonpolyadenylated RNAs whose levels are increased somewhat by exposure to gonadotropin-releasing hormone but are not necessarily linked to Cga transcriptional activity. Knockdown of the more distal eRNA led to a drop in Cga mRNA levels, initially without effect on the forward eRNA levels. With time, however, the repression on the Cga increased, and the forward eRNA levels were suppressed also. We demonstrate that the interaction of the enhancer with the promoter is lost after eRNA knockdown. Dramatic changes also were seen in the chromatin, with an increase in total histone H3 occupancy throughout this region and a virtual loss of histone H3 Lys 4 trimethylation at the promoter following the eRNA knockdown. Moreover, histone H3 Lys 27 (H3K27) acetylation, which was found at both enhancer and promoter in wild-type cells, appeared to have been replaced by H3K27 trimethylation at the enhancer. Thus, the Cga eRNA mediates the physical interaction between these genomic regions and determines the chromatin structure of the proximal promoter to allow gene expression.

JMJD6 Licenses ERα-Dependent Enhancer and Coding Gene Activation by Modulating the Recruitment of the CARM1/MED12 Co-activator Complex

“…Several studies reported recently that enhancer RNAs (eRNAs) are involved in transcriptional regulation of nearby coding genes (Lam et al, 2013, Kim et al, 2010, Melo et al, Lai et al, 2013, Mousavi et al, 2013, Hsieh et al, 2014, Schaukowitch et al, 2014, Pnueli et al, 2015, Zhao et al, 2016, Li et al, 2013). For instance, estrogen-induced eRNAs from ERα-bound active enhancers were critical for the transcriptional activation of cognate estrogen-induced coding genes (Li et al, 2013).…”

“…eRNAs have been defined as short transcripts (50–2000 nucleotides) that are transcribed bi-directionally, or sometimes uni-directionally, from enhancer regions (Kim et al, 2010). Although whether eRNAs themselves are functional remains to be unequivocally proven, many studies have clearly demonstrated that enhancer transcription occurs before coding gene activation and may help to create an open chromatin environment, facilitate promoter and enhancer looping, and contribute to coding gene transcriptional regulation (Hsieh et al, 2014, Lai et al, 2013, Lam et al, 2013, Melo et al, 2013, Mousavi et al, 2013, Schaukowitch et al, 2014, Pnueli et al, 2015, Zhao et al, 2016, Li et al, 2013). In addition, enhancer transcription has been suggested to play an essential role in enhancer marker (H3K4me1/2) deposition at de novo enhancers (Kaikkonen et al, 2013).…”

Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers Is Suppressed by a MicroRNA

“…SEs are thought to signal to proximal promoters to stabilize BRD4-containing coactivator complexes near TSSs, thereby facilitating p-TEFb-mediated Pol II phosphorylation and transcription elongation (Arner et al, 2015; Brown et al, 2014; Pnueli et al, 2015). ChIP-Seq data were further analyzed to assess whether PE and/or miR-9 alter BRD4 binding to cardiomyocyte gene promoters.…”

Epigenetic regulation of cardiac fibrosis

“…Enhancer RNAs are expressed in a signal-dependent manner [80], and regulate gene expression via decondensing chromatin at target promoters, facilitating Pol II recruitment to TSSs of target genes, and promoting direct enhancer/promoter interaction through chromatin looping [81–85]. In keeping with this model, genes that are acted upon by multiple eRNAs have significantly higher expression than eRNA-independent genes [84].…”