Suboptimization of developmental enhancers

Science. 2015 Oct 16;350(6258):325-8. doi: 10.1126/science.aac6948.

Abstract

Transcriptional enhancers direct precise on-off patterns of gene expression during development. To explore the basis for this precision, we conducted a high-throughput analysis of the Otx-a enhancer, which mediates expression in the neural plate of Ciona embryos in response to fibroblast growth factor (FGF) signaling and a localized GATA determinant. We provide evidence that enhancer specificity depends on submaximal recognition motifs having reduced binding affinities ("suboptimization"). Native GATA and ETS (FGF) binding sites contain imperfect matches to consensus motifs. Perfect matches mediate robust but ectopic patterns of gene expression. The native sites are not arranged at optimal intervals, and subtle changes in their spacing alter enhancer activity. Multiple tiers of enhancer suboptimization produce specific, but weak, patterns of expression, and we suggest that clusters of weak enhancers, including certain "superenhancers," circumvent this trade-off in specificity and activity.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Ciona intestinalis / genetics
  • Ciona intestinalis / growth & development*
  • Consensus Sequence
  • Enhancer Elements, Genetic / genetics
  • Enhancer Elements, Genetic / physiology*
  • Fas-Associated Death Domain Protein / metabolism
  • Fibroblast Growth Factors / metabolism*
  • GATA Transcription Factors / metabolism*
  • Gene Expression Regulation, Developmental*
  • Molecular Sequence Data
  • Organ Specificity / genetics
  • Organ Specificity / physiology
  • Otx Transcription Factors / metabolism*

Substances

  • Fas-Associated Death Domain Protein
  • GATA Transcription Factors
  • Otx Transcription Factors
  • Fibroblast Growth Factors

Associated data

  • SRA/PRJNA294804