Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

Elife. 2020 Jul 23:9:e59610. doi: 10.7554/eLife.59610.


Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa's role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.

Keywords: ATAC-seq; ChIP-seq; D. melanogaster; RNA-seq; Zelda; developmental biology; genetics; genomics; maternal-to-zygotic transition (MZT); odd-paired.

Publication types

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

MeSH terms

  • Animals
  • Drosophila Proteins*
  • Drosophila melanogaster / genetics
  • Drosophila*
  • Gene Expression Regulation, Developmental
  • Homeodomain Proteins
  • Nuclear Proteins
  • Transcription Factors


  • Drosophila Proteins
  • Homeodomain Proteins
  • Nuclear Proteins
  • Opa protein, Drosophila
  • Transcription Factors
  • zld protein, Drosophila

Associated data

  • GEO/GSE140722
  • GEO/GSE153328
  • GEO/GSM763061
  • GEO/GSM763062