Transcription factor redundancy and tissue-specific regulation: evidence from functional and physical network connectivity

Genome Res. 2012 Oct;22(10):1907-19. doi: 10.1101/gr.133306.111. Epub 2012 Jun 22.

Abstract

Two major transcriptional regulators of Caenorhabditis elegans bodywall muscle (BWM) differentiation, hlh-1 and unc-120, are expressed in muscle where they are known to bind and regulate several well-studied muscle-specific genes. Simultaneously mutating both factors profoundly inhibits formation of contractile BWM. These observations were consistent with a simple network model in which the muscle regulatory factors drive tissue-specific transcription by binding selectively near muscle-specific targets to activate them. We tested this model by measuring the number, identity, and tissue-specificity of functional regulatory targets for each factor. Some joint regulatory targets (218) are BWM-specific and enriched for nearby HLH-1 binding. However, contrary to the simple model, the majority of genes regulated by one or both muscle factors are also expressed significantly in non-BWM tissues. We also mapped global factor occupancy by HLH-1, and created a genetic interaction map that identifies hlh-1 collaborating transcription factors. HLH-1 binding did not predict proximate regulatory action overall, despite enrichment for binding among BWM-specific positive regulatory targets of hlh-1. We conclude that these tissue-specific factors contribute much more broadly to the transcriptional output of muscle tissue than previously thought, offering a partial explanation for widespread HLH-1 occupancy. We also identify a novel regulatory connection between the BWM-specific hlh-1 network and the hlh-8/twist nonstriated muscle network. Finally, our results suggest a molecular basis for synthetic lethality in which hlh-1 and unc-120 mutant phenotypes are mutually buffered by joint additive regulation of essential target genes, with additional buffering suggested via newly identified hlh-1 interacting factors.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / metabolism*
  • Caenorhabditis elegans Proteins / genetics
  • Caenorhabditis elegans Proteins / metabolism
  • Conserved Sequence
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Gene Regulatory Networks
  • MADS Domain Proteins / genetics
  • MADS Domain Proteins / metabolism
  • Muscle Proteins
  • Muscles / metabolism
  • Mutation
  • Myogenic Regulatory Factors / genetics
  • Myogenic Regulatory Factors / metabolism
  • Nuclear Proteins
  • Nucleotide Motifs
  • Organ Specificity / genetics*
  • Protein Binding
  • RNA Interference
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcriptome

Substances

  • Caenorhabditis elegans Proteins
  • MADS Domain Proteins
  • Muscle Proteins
  • Myogenic Regulatory Factors
  • Nuclear Proteins
  • Transcription Factors
  • UNC-120 protein, C elegans
  • HLH-1 protein, C elegans

Associated data

  • GEO/GSE28561
  • GEO/GSE28562
  • GEO/GSE28563
  • GEO/GSM707199
  • GEO/GSM707200
  • GEO/GSM707201
  • GEO/GSM707202
  • GEO/GSM707203
  • GEO/GSM707204
  • GEO/GSM707205
  • GEO/GSM707206
  • GEO/GSM707207
  • GEO/GSM707208
  • GEO/GSM707209
  • GEO/GSM707210
  • GEO/GSM707211
  • GEO/GSM707212
  • GEO/GSM707213