title: Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.
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.
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Kamesh
authors.initials: K
authors.lastname: Narasimhan
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, Canada.
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Lambert
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Ally W H
authors.initials: AW
authors.lastname: Yang
authors.affiliation: Department of Molecular and Cellular Physiology, Systems Biology and Physiology Program, University of Cincinnati, Cincinnati, United States.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Riddell
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Sanie
authors.initials: S
authors.lastname: Mnaimneh
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Hong
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Mihai
authors.initials: M
authors.lastname: Albu
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Hamed S
authors.initials: HS
authors.lastname: Najafabadi
authors.affiliation: Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: John S
authors.initials: JS
authors.lastname: Reece-Hoyes
authors.affiliation: Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Juan I
authors.initials: JI
authors.lastname: Fuxman Bass
authors.affiliation: Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.
authors.forename: Albertha J M
authors.initials: AJ
authors.lastname: Walhout
authors.affiliation: Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Weirauch
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D018509:DNA, Helminth / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D018160:Receptors, Cytoplasmic and Nuclear; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D029742:Caenorhabditis elegans Proteins; D018509:DNA, Helminth; D018160:Receptors, Cytoplasmic and Nuclear; D014157:Transcription Factors
keywords: C. elegans; DM; T-box; binding specificities; computational biology; evolutionary biology; genomics; nuclear hormone receptors; protein-binding microarray; systems biology; transcription factors