Non-coding RNA controls long-range enhancer-promoter interactions

Transcription regulation depends on interactions between enhancers and gene promoters, which often occur over large genomic distances. The molecular drivers of long-range enhancer-promoter interactions remain poorly understood. Enhancers themselves are known to be transcribed into non-coding RNAs, but the function of these transcripts is unclear. Here, we use acute genetic and chemical perturbations of transcription elongation and termination to study the role of non-coding RNA in enhancer-promoter interactions. By integrating high-resolution 3D genome mapping, transcriptomics, proteomics, biochemistry and live-cell super-resolution imaging in these perturbation contexts, we demonstrate that a strong increase in RNA molecules at enhancers disrupts their long-range interactions with gene promoters, whereas decreased RNA levels lead to stabilization of these interactions. Using separation-of-function perturbations, we show that this regulatory function of RNA is independent from the process of transcription and the proteins recruited to initiate transcription. Functionally, we show that RNA-mediated disruption of enhancer-promoter interactions is associated with reduced transcription of target genes, indicating a regulatory feedback mechanism. Together, our results uncover an additional regulatory principle of enhancer-promoter interactions mediated by non-coding RNA.