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Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

  1. Kamesh Narasimhan
  2. Samuel A Lambert
  3. Ally W H Yang
  4. Jeremy Riddell
  5. Sanie Mnaimneh
  6. Hong Zheng
  7. Mihai Albu
  8. Hamed S Najafabadi
  9. John S Reece-Hoyes
  10. Juan I Fuxman Bass
  11. Albertha J M Walhout
  12. Matthew T Weirauch
  13. Timothy R Hughes  Is a corresponding author
  1. University of Toronto, Canada
  2. University of Cincinnati, United States
  3. University of Massachusetts Medical School, United States
  4. Cincinnati Children's Hospital Medical Center, United States
Research Article
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Cite this article as: eLife 2015;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.

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Author details

  1. Kamesh Narasimhan

    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  2. Samuel A Lambert

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  3. Ally W H Yang

    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  4. Jeremy Riddell

    Department of Molecular and Cellular Physiology, Systems Biology and Physiology Program, University of Cincinnati, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Sanie Mnaimneh

    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  6. Hong Zheng

    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  7. Mihai Albu

    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  8. Hamed S Najafabadi

    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.

  9. John S Reece-Hoyes

    Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Juan I Fuxman Bass

    Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  11. Albertha J M Walhout

    Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  12. Matthew T Weirauch

    Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
    Competing interests
    The authors declare that no competing interests exist.

  13. Timothy R Hughes

    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    For correspondence
    t.hughes@utoronto.ca
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Nir Friedman, The Hebrew University of Jerusalem, Israel

Publication history

  1. Received: February 13, 2015
  2. Accepted: April 22, 2015
  3. Accepted Manuscript published: April 23, 2015 (version 1)
  4. Version of Record published: May 18, 2015 (version 2)

Copyright

© 2015, Narasimhan et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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