Nascent RNA antagonises the interaction of a set of regulatory proteins with chromatin

A number of regulatory factors are recruited to chromatin by specialised RNAs. Whether RNA has a more general role in regulating the interaction of proteins with chromatin has not been determined. We used proteomics methods to measure the global impact of nascent RNA on chromatin in embryonic stem cells. Surprisingly, we found that nascent RNA primarily antagonised the interaction of chromatin modifiers and transcriptional regulators with chromatin. Transcriptional inhibition and RNA degradation induced recruitment of a set of transcriptional regulators, chromatin modifiers, nucleosome remodelers, and regulators of higher-order structure. RNA directly bound to factors including BAF, NuRD, EHMT1 and INO80 and inhibited their interaction with nucleosomes. The transcriptional elongation factor P-TEFb directly bound pre-mRNA and its recruitment to chromatin upon Pol II inhibition was regulated by the 7SK ribonucleoprotein complex. We postulate that by antagonising the interaction of regulatory proteins with chromatin, nascent RNA links transcriptional output with chromatin composition. iCLIP for P-TEFb, LARP7 and input in mESC treated with either DMSO or pla-B. Also RNA-seq from chromatin or whole cell extract from mESC treated with triptolide or flavopiridol for 0, 1, 3 or 9 hours and also from permeabilised mock or RNaseA-treated mESC. Total RNA and polyA+ RNA was sequenced from the chromatin fraction to measure mature polyA+ and nascent RNA associated with chromatin and polyA+ RNA was sequenced from the whole cell extract samples to measure mature polyA+ RNA.