Differential contribution of steady‐state RNA and active transcription in chromatin organization

Nuclear RNA and the act of transcription have been implicated in nuclear organization. However, their global contribution to shaping fundamental features of higher‐order chromatin organization such as topologically associated domains ( TAD s) and genomic compartments remains unclear. To investigate these questions, we perform genome‐wide chromatin conformation capture (Hi‐C) analysis in the presence and absence of RN ase before and after crosslinking, or a transcriptional inhibitor. TAD boundaries are largely unaffected by RN ase treatment, although a subtle disruption of compartmental interactions is observed. In contrast, transcriptional inhibition leads to weaker TAD boundary scores. Collectively, our findings demonstrate differences in the relative contribution of RNA and transcription to the formation of TAD boundaries detected by the widely used Hi‐C methodology.