GSE123455
Protein-RNA-Chromatin Interactions Reveal Nuclear RNA Architecture Functions in Transcriptional Condensation and Chromatin Folding
It has been proposed that nucleome organization and genome function involve interplays between protein, RNA and chromatin architectures. However, how chromatin interactions are cooperatively mediated by nuclear proteins and RNAs have not been fully explored. Here, we report the multivalent interplays in Drosophila cells involving RNA Polymerase II (RNAPII), nuclear RNAs and chromatin interactions. Using a novel genomic approach (pRChIA-PET) for protein-RNA-chromatin interactions, we discovered that extensive combination of nuclear RNAs cooperatively act in trans and co-localize with RNAPII and associated protein cofactors at chromatin interaction loci of active promoters and enhancers. Nuclear perturbation by aliphatic alcohol and RNase-A revealed that chromatin associated nuclear RNAs (canRNAs) are likely integral components in phase-separation for transcriptional condensation, and may act to maintain open chromatin accessibility and long-range chromatin interactions. These findings suggest a significant architectural role for combinatorial canRNAs as potential scaffolding elements in 3D genome organization and transcriptional regulation. Overall design: Investigation of protein-RNA-chromatin interactions by pRChIA-PET.