Combinatorial action of NF-Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish

Dev Biol. 2020 Mar 15;459(2):161-180. doi: 10.1016/j.ydbio.2019.12.003. Epub 2019 Dec 17.


Animal embryogenesis is initiated by maternal factors, but zygotic genome activation (ZGA) shifts regulatory control to the embryo during blastula stages. ZGA is thought to be mediated by maternally provided transcription factors (TFs), but few such TFs have been identified in vertebrates. Here we report that NF-Y and TALE TFs bind zebrafish genomic elements associated with developmental control genes already at ZGA. In particular, co-regulation by NF-Y and TALE is associated with broadly acting genes involved in transcriptional control, while regulation by either NF-Y or TALE defines genes in specific developmental processes, such that NF-Y controls a cilia gene expression program while TALE controls expression of hox genes. We also demonstrate that NF-Y and TALE-occupied genomic elements function as enhancers during embryogenesis. We conclude that combinatorial use of NF-Y and TALE at developmental enhancers permits the establishment of distinct gene expression programs at zebrafish ZGA.

Keywords: Embryogenesis; Enhancer; Maternal; Nucleosome; Transcription; Zygotic.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CCAAT-Binding Factor / metabolism*
  • Cilia / genetics
  • Embryonic Development / genetics
  • Female
  • Gene Expression Regulation, Developmental
  • Gene Expression*
  • Genome*
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism*
  • Male
  • Transcriptional Activation*
  • Zebrafish / embryology*
  • Zebrafish Proteins
  • Zygote / metabolism*


  • CCAAT-Binding Factor
  • Homeodomain Proteins
  • Zebrafish Proteins