The relationship between genome-wide RNA-chromatin interactions and 3D genome organization

It remains unclear to what extent chromatin-associated RNAs can reflect the 3D organization of the genome. To this end, we used iMARGI to map genome-wide RNA-chromatin interactions in H1, HFFc6, and K562 cells and yielded on average 1.9 billion read pairs per sample. This project will compare these iMARGI data with genome interaction data including Hi-C and PLAC-seq on three different scales. At the compartment scale, we will test whether the A compartment chromatin is associated with large amounts of RNAs, involving both intrachromosomal and interchromosomal RNA-chromatin interactions. At the TAD scale, we will test whether the RNA ends of nearly all RNA-chromatin interactions are confined to within the boundaries of one or of a few consecutive TADs. At the loop scale, we will test whether RNA-chromatin interactions are enriched with PLAC-seq derived enhancer-promoter interactions.