Bicoid-Dependent Activation of the Target Gene hunchback Requires a Two-Motif Sequence Code in a Specific Basal Promoter

Jia Ling, Kristaley Yui Umezawa, Theresa Scott, Stephen Small

Research output: Contribution to journalArticlepeer-review


In complex genetic loci, individual enhancers interact most often with specific basal promoters. Here we investigate the activation of the Bicoid target gene hunchback (hb), which contains two basal promoters (P1 and P2). Early in embryogenesis, P1 is silent, while P2 is strongly activated. In vivo deletion of P2 does not cause activation of P1, suggesting that P2 contains intrinsic sequence motifs required for activation. We show that a two-motif code (a Zelda binding site plus TATA) is required and sufficient for P2 activation. Zelda sites are present in the promoters of many embryonically expressed genes, but the combination of Zelda plus TATA does not seem to be a general code for early activation or Bicoid-specific activation per se. Because Zelda sites are also found in Bicoid-dependent enhancers, we propose that simultaneous binding to both enhancers and promoters independently synchronizes chromatin accessibility and facilitates correct enhancer-promoter interactions.

Original languageEnglish (US)
Pages (from-to)1178-1187.e4
JournalMolecular Cell
Issue number6
StatePublished - Sep 19 2019


  • enhancer
  • gene regulation
  • promoter
  • promoter choice
  • transcription
  • Response Elements
  • Trans-Activators/genetics
  • DNA-Binding Proteins/biosynthesis
  • Drosophila Proteins/biosynthesis
  • Animals
  • Nucleotide Motifs
  • Homeodomain Proteins/genetics
  • Nuclear Proteins/genetics
  • Drosophila melanogaster
  • Transcription Factors/biosynthesis

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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