Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor

Abstract

SUMMARY The function of enhancer RNAs (eRNAs) in transcriptional regulation remains obscure. By analyzing the genome-wide nascent transcript profiles in breast cancer cells, we identify a special group of eRNAs that are essential for estrogen-induced transcriptional repression. Using eRNAs of TM4SF1 and EFEMP1 as the paradigms, we find that these RNA molecules not only stabilize promoter-enhancer interactions but also recruit liganded estrogen receptor α (ERα) to particular enhancer regions, facilitate the formation of a functional transcriptional complex, and cause gene silencing. Interestingly, ERα is shown to directly bind with eRNAs by its DNA-binding domain. These eRNAs help with the formation of a specific ERα-centered transcriptional complex and promote the association of the histone demethylase KDM2A, which dismisses RNA polymerase II from designated enhancers and suppresses the transcription of target genes. Our work demonstrates a complete mechanism underlying the action of eRNAs in modulating and refining the locus-specific transcriptional program.

Regulation of telomere homeostasis and genomic stability in cancer by N 6 -adenosine methylation (m 6 A)

“…Lentivirus-mediated establishment of stable clones was performed as previously described ( 55 ). Briefly, lentiviral vectors for gene overexpression or shRNA knockdown were cotransfected into HEK293T cells together with packaging plasmid (pCMV delta R8.9 or psPAX2) and envelope-expressing plasmid (VSV-G).…”

“…RNA isolation and reverse transcription qPCR (RT-qPCR) assays were performed as previously described ( 55 ). Briefly, total RNAs were extracted using the TRIzol Reagent (Thermo Fisher Scientific) and quantified by Cytation5 (BioTek).…”

“…Co-IP was performed as previously described ( 55 ). Briefly, cells were collected and lysed in the lysis buffer [0.5% IGEPAL CA-630, 0.5% Triton X-100, 150 mM NaCl, 2 mM EDTA (pH 8.0), 50 mM tris-HCl (pH 7.5), 10 mM sodium fluoride, 2 mM sodium orthovanadate, 1 mM phenylmethanesulfonylfluoride, and 1× protease inhibitor (Roche)].…”

“…ChIP was performed as previously described with some modifications ( 55 ). Briefly, cells were double cross-linked by 6 mM disuccinimidyl glutarate (CovaChem) for 30 min and then 1% formaldehyde (Sigma-Aldrich) for 10 min at room temperature.…”

Circulating Long Non-Coding RNAs as Novel Potential Biomarkers for Osteogenic Sarcoma

“…The investigations on this small cohort of lncRNAs have demonstrated that these noncoding transcripts can serve as scaffolds or guides to regulate protein-protein or protein-DNA interactions [28][29][30][31] or can modulate post-translational modification of nonhistone proteins [32]. Moreover, lncRNAs are capable of controlling microRNAs (miRNAs) [33][34][35], and function as enhancers to influence gene transcription, when transcribed from the enhancer regions (enhancer RNA) [36][37][38] or their neighboring loci (noncoding RNA activator) [39,40].…”