TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains

The Transforming Growth Factor-beta (TGF beta) signaling pathway controls transcription by regulating enhancer activity. How TGF beta-regulated enhancers are selected and what chromatin changes are associated with TGF beta-dependent enhancers regulation are still unclear. Here we report that TGF beta treatment triggers fast and widespread increase in chromatin accessibility in about 80% of the enhancers of normal mouse mammary epithelial-gland cells, irrespective of whether they are activated, repressed or not regulated by TGF beta. This enhancer opening depends on both the canonical and non-canonical TGF beta pathways. Most TGF beta-regulated genes are located around enhancers regulated in the same way, often creating domains of several co-regulated genes that we term TGF beta regulatory domains (TRD). CRISPR-mediated inactivation of enhancers within TRDs impairs TGF beta-dependent regulation of all co-regulated genes, demonstrating that enhancer targeting is more promiscuous than previously anticipated. The area of TRD influence is restricted by topologically associating domains (TADs) borders, causing a bias towards co-regulation within TADs.