Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

Mol Syst Biol. 2011 Oct 11;7:538. doi: 10.1038/msb.2011.73.

Abstract

Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors (TFs) comprising retinoic acid receptor (RARα, β, γ) and retinoid X receptor (RXRα, β, γ). How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model, we defined the temporal changes in the genome-wide binding patterns of RARγ and RXRα and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRα heterodimers targeting identical loci. Comparison of RARγ and RXRα co-binding at RA-regulated genes identified putative RXRα-RARγ target genes that were validated with subtype-selective agonists. Gene-regulatory decisions during differentiation were inferred from TF-target gene information and temporal gene expression. This analysis revealed six distinct co-expression paths of which RXRα-RARγ is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRα-RARγ regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RAR heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cell Differentiation / drug effects
  • Cell Differentiation / genetics*
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Early Growth Response Protein 1 / genetics
  • Early Growth Response Protein 1 / metabolism
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism*
  • Gene Expression Profiling
  • Gene Expression Regulation / drug effects*
  • Gene Regulatory Networks*
  • Genomics / methods*
  • Mice
  • Molecular Sequence Data
  • Protein Binding / genetics
  • Receptor Cross-Talk / drug effects
  • Receptors, Retinoic Acid / genetics
  • Receptors, Retinoic Acid / metabolism*
  • Retinoid X Receptor alpha / genetics
  • Retinoid X Receptor alpha / metabolism*
  • SOXB1 Transcription Factors / genetics
  • SOXB1 Transcription Factors / metabolism
  • Signal Transduction / drug effects*
  • Signal Transduction / genetics
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic
  • Tretinoin / pharmacology*

Substances

  • Chromatin
  • Early Growth Response Protein 1
  • Egr1 protein, mouse
  • Receptors, Retinoic Acid
  • Retinoid X Receptor alpha
  • SOXB1 Transcription Factors
  • Sox2 protein, mouse
  • Transcription Factors
  • retinoic acid receptor gamma
  • Tretinoin