Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities
- University of Toronto, Canada
- University of Cincinnati, United States
- University of Massachusetts Medical School, United States
- Cincinnati Children's Hospital Medical Center, United States
- Cited 21
- Views 4,253
- Annotations
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.
Article and author information
Author details
Reviewing Editor
- Nir Friedman, The Hebrew University of Jerusalem, Israel
Publication history
- Received: February 13, 2015
- Accepted: April 22, 2015
- Accepted Manuscript published: April 23, 2015 (version 1)
- 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.
Metrics
-
- 4,253
- Page views
-
- 805
- Downloads
-
- 21
- Citations
Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, PubMed Central.
Download links
Downloads (link to download the article as PDF)
Download citations (links to download the citations from this article in formats compatible with various reference manager tools)
Open citations (links to open the citations from this article in various online reference manager services)
Further reading
-
- Computational and Systems Biology
- Developmental Biology
-
- Computational and Systems Biology
- Neuroscience
