A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation

Nat Commun. 2019 Feb 11;10(1):691. doi: 10.1038/s41467-019-08487-5.


Most metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT). However, a set of genes escapes global repression and gets activated before MBT. Here we describe the formation and the spatio-temporal dynamics of a pair of distinct transcription compartments, which encompasses the earliest gene expression in zebrafish. 4D imaging of pri-miR430 and zinc-finger-gene activities by a novel, native transcription imaging approach reveals transcriptional sharing of nuclear compartments, which are regulated by homologous chromosome organisation. These compartments carry the majority of nascent-RNAs and active Polymerase II, are chromatin-depleted and represent the main sites of detectable transcription before MBT. Transcription occurs during the S-phase of increasingly permissive cleavage cycles. It is proposed, that the transcription compartment is part of the regulatory architecture of embryonic nuclei and offers a transcriptionally competent environment to facilitate early escape from repression before global genome activation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blastocyst / physiology
  • Blastula / diagnostic imaging
  • Blastula / physiology
  • Cell Cycle / genetics*
  • Cell Cycle / physiology
  • Cell Division
  • Cell Nucleus / physiology
  • Chromatin
  • Chromosomes
  • Four-Dimensional Computed Tomography
  • Gene Expression Regulation, Developmental / genetics*
  • Gene Expression Regulation, Developmental / physiology
  • Genome / genetics*
  • Genome / physiology
  • MicroRNAs
  • Models, Animal
  • S Phase / physiology
  • Spatio-Temporal Analysis
  • Transcription, Genetic / genetics*
  • Transcription, Genetic / physiology
  • Transcriptome / genetics
  • Zebrafish / genetics
  • Zygote / physiology


  • Chromatin
  • MicroRNAs