Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.

ABSTRACT: The initiation of gene expression during development, known as zygotic genome activation (ZGA), is accompanied by massive changes in chromosome organization. However, the earliest events of chromosome folding and their functional roles remain unclear. Using Hi-C on zebrafish embryos, we discovered that chromosome folding begins early in development with the formation of "fountains", a novel element of chromosome organization. Emerging preferentially at enhancers, fountains exhibit an initial accumulation of cohesin, which later redistributes to CTCF sites at TAD borders. Knockouts of pioneer transcription factors driving ZGA enhancers result in the specific loss of fountains, establishing a causal link between enhancer activation and fountain formation. Polymer simulations demonstrate that

SUBMITTER: Galitsyna A 

PROVIDER: S-EPMC10370019 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature