 The study generates genome-wide RNA-DNA and DNA-DNA contact maps in human cells to reveal the chromosomal domains defined by locally transcribed RNA and demonstrates that the spreading of chromatin-associated RNA is constrained by topologically associating domains. Additionally, the study shows that stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide, and activation or suppression of specific gene transcription suppresses or creates chromatin loops straddling those genes. The data suggests a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization. This article was authored by Riccardo Calandrelli, Shingya Wen, John Laliff, Charles Richard and others.