RNA-Chromatin Interactome Reveals Enhancer-Promoter Connectivity in 3D Genome

High eukaryotic genomes are populated with enhancers, but it has been a major challenge in defining specific enhancer-promoter relationship. Enhancers can also be divided into typical and super-enhancers, yet their functional distinctions remain to be understood. Here, we report a strategy to capture in situ Global RNA Interactions with DNA by deep sequencing (GRID-seq). By deducing general RNA background on chromatin, we unexpectedly detect a highly selective set of RNAs (including both lncRNAs and protein-coding pre-mRNAs) decorated on enhancers, particularly super-enhancers. Based on the origins of those RNAs and functional perturbation of enhancer activities, we are able to infer global enhancer-promoter connectivity, which is significantly beyond the traditional framework. These findings provide a functional RNA-chromatin interactome in 3D genome. Overall design: Exploration of global RNA-chromatin interactions in 3 cell types of 3 species