Nanoscale dynamics of enhancer-promoter interactions during exit from pluripotency.

ABSTRACT: While compelling genetic evidence supports the role of enhancers in regulating promoter activity even over large genomic distances, it remains unclear to what extent physical proximity to promoters is required. To address this, we combined fluorescence in situ hybridization (FISH) with super-resolution microscopy and Tri-C to examine enhancer-promoter (E-P) distances and regulatory element clustering at regulated loci (Nanog, Dppa3, Dnmt3a, Sox2, Prdm14) during the transition from naive to primed pluripotency in mouse embryonic stem cells. Despite transcriptional changes of several orders of magnitude, most genes show no major alterations in median E-P distances or in the probability of multiway contacts across states. However, Tri-C reveals a weak enrichment of multiway contacts at Nanog

SUBMITTER: Stumberger G 

PROVIDER: S-EPMC12684394 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature