Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks

PLoS One. 2015 Jul 23;10(7):e0133387. doi: 10.1371/journal.pone.0133387. eCollection 2015.

Abstract

Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Binding Sites
  • Body Patterning / genetics*
  • Chromosome Mapping*
  • Drosophila Proteins / genetics*
  • Drosophila melanogaster / genetics*
  • Embryo, Nonmammalian
  • Embryonic Development / genetics*
  • Gene Expression Regulation, Developmental*
  • Gene Regulatory Networks
  • Signal Transduction / genetics
  • Transcription Factors / genetics*

Substances

  • Drosophila Proteins
  • Transcription Factors
  • kn protein, Drosophila

Associated data

  • GEO/GSE67805

Grant support

This work was supported by Fondation de la Recherche Médicale (FRM) grant DEQ20090515429, http://www.frm.org/; Agence Nationale de la Recherche grant 13-BSVE2-0010-0, http://www.agence-nationale-recherche.fr/; and Association Française contre lesMyopathies, http://www.afm-telethon.fr/association. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.