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

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, distinct elements of chromosome organization. Emerging preferentially at enhancers, fountains show an initial accumulation of cohesin, which later redistributes to CTCF sites at TAD borders. Knockouts of pioneer transcription factors driving ZGA enhancers cause a specific loss of fountains, establishing a causal link between enhancer…

• DF
  Deutsche Forschungsgemeinschaft

  Awards: DFG-ON86/5-1, EXC2189, DFG-EXC2189
• RS
  Russian Science Foundation

  Awards: 21-64-00001, 21-64-00001-P, 23-14-00136
• NI
  National Institutes of Health

  Awards: GM114190, AI164728, R01 NS113929, 00001, 21-64-00001, NS113929