RNA binds to a CBP regulatory motif to stimulate histone acetylation and transcription

CBP/p300 are transcription co-activators whose binding is a signature of enhancers, cis-regulatory elements that control patterns of gene expression in multicellular organisms. Active enhancers produce bi-directional enhancer RNAs (eRNAs) and display CBP/p300 dependent histone acetylation. Here, we demonstrate that CBP binds directly to RNAs in vivo and in vitro. RNAs bound to CBP in vivo include a large number of eRNAs. Using steady-state histone acetyltransferase (HAT) assays we show that an RNA binding region in the HAT domain of CBP—a regulatory motif unique to CBP/p300—allows RNA to stimulate CBP’s HAT activity. At enhancers where CBP interacts with eRNAs, stimulation manifests in RNA-dependent changes in the histone acetylation mediated by CBP, such as H3K27ac, and by corresponding changes in gene expression. By interacting directly with CBP, eRNAs contribute to the unique chromatin structure at active enhancers, which in turn is required for regulation of target genes. MEFs were treated with 4-thiouridine for 16h, irradiated with 365nm UV and CBP immunopreciptated. RNA species cross-linked to CBP were purified and sequenced. The series contains 2 biological replicates for CBP PAR-CLIP seq, and negative controls for background PAR-CLIP binding: nuclear flag-tagged GFP (nGFP) and the DNA binding domain of yeast protein Gal4p (Gal4-DBD) (two replicates each)