Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

Elife. 2015 Apr 23;4:e06967. doi: 10.7554/eLife.06967.

Abstract

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (∼40%). These data highlight the diversification of binding motifs for the nuclear hormone receptor and C2H2 zinc finger families and reveal unexpected diversity of motifs for T-box and DM families. Motif enrichment in promoters of functionally related genes is consistent with known biology and also identifies putative regulatory roles for unstudied TFs.

Keywords: C. elegans; DM; T-box; binding specificities; computational biology; evolutionary biology; genomics; nuclear hormone receptors; protein-binding microarray; systems biology; transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Binding Sites
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / metabolism
  • Caenorhabditis elegans Proteins / chemistry
  • Caenorhabditis elegans Proteins / genetics*
  • Caenorhabditis elegans Proteins / metabolism
  • DNA, Helminth / chemistry
  • DNA, Helminth / genetics*
  • DNA, Helminth / metabolism
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • Molecular Sequence Data
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Receptors, Cytoplasmic and Nuclear
  • Transcription Factors / chemistry
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Zinc Fingers / genetics*

Substances

  • Caenorhabditis elegans Proteins
  • DNA, Helminth
  • Receptors, Cytoplasmic and Nuclear
  • Transcription Factors