Abstract
Chromatin-associated RNA (caRNA) is a vital component of the interphase nucleus; yet its distribution and role in the 3D genome organization remain poorly understood. Here, we map caRNA’s spatial distribution on the 3D genome in human embryonic stem cells, fibroblasts, and myelogenous leukemia cells. We find that the relative abundance of trans-acting caRNA on DNA reflects the 3D compartmentalization, and the caRNA’s sequence is predictive of its spatial localization. We observe localized caRNA-genome interactions that span several hundred kilobases to several megabases. These caRNA domains correlate with chromatin loops and enhancer-promoter interactions. Global reduction of caRNA abundance increases the number of chromatin loops and strengths, which could be reversed by suppression of caRNA’s electrostatic interactions. These results indicate that caRNA regulates chromatin looping, at least in part through RNA’s electrostatic interactions.
Competing Interest Statement
The authors have declared no competing interest.