C. elegans Motif Data

Kamesh Narasimhan^1*, Samuel A. Lambert^2,*, Ally W.H. Wang^1*, Jeremy Riddell³, Sanie Mnaimneh¹, Hong Zheng¹, Mihai Albu¹, Hamed S. Najafabadi¹, John S. Reece-Hoyes⁴, Juan I. Fuxman Bass⁴, Albertha J.M. Walhout⁴, Matthew T. Weirauch^5#, Timothy R. Hughes^1,2,6#

¹ Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
² Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
³ Department of Molecular and Cellular Physiology, Systems Biology and Physiology Program, University of Cincinnati, Cincinnati, OH, USA
⁴ Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
⁵ Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
⁶ Canadian Institutes For Advanced Research, Toronto, Canada

^*these authors contributed equally

^#To whom correspondance should be addressed: or

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 ~10% 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 97 TFs that have DNA-binding domains similar to those already characterized, resulting in coverage of binding specificities for ~40% of all C. elegans TFs. 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.

All C. elegans data from Cis-BP (for reviewers). This includes motifs, logos, annotation information, and E-scores. Click to Download .zip file

Supplemental Files. Click to Download

Supplemental File 1 Comparison of C. elegans TF collection from CisBP and wTF2.0.
Supplemental File 2 C. elegans curated motif collection.
Supplemental File 3 Number of motifs required for complete coverage of worm, fly and human TF collections.

Figure Source Data. Click to Download

Figure 1-source data 1 (Related to Figure 1). List of DBDs referred to in this study. This table provides the full names and Pfam IDs of DBDs used to compile the C. elegans TF collection.
Figure 3-source data 1 Table showing 8-mers bound by at least one TF with an E-score >=0.45 for all the 129 C. elegans TFs analyzed by PBMs in this study.
Figure 4-source data 1 Table showing 8-mers bound by at least one NHR with an E-score >=0.45 for all the C. elegans NHRs that have been analyzed by PBMs.
Figure 6-source data 1 Table showing 8-mers bound by at least one DM or T-Box TF with an E-score >=0.45 for TFs that have been analyzed by PBMs .
Figure 8-source data 1 Composite motif enrichment analysis of C. elegans TF ChIP-seq.
Figure 9-source data 1 Table of motif enrichments in promoters of gene set categories identified from KEGG pathway modules, Gene Ontology processes and tissue/developmental stage specific expression lists.

Web Supplemental Files. Click to Download

Web Supplemental File 1. List of primers used to obtain TF clones in this study (.xlsx).
Web Supplemental File 2. PBM plasmid (pTH6838) backbone map (.doc).

Web supplement to
"Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities"

Abstract

All C. elegans data from Cis-BP (for reviewers). This includes motifs, logos, annotation information, and E-scores. Click to Download .zip file

Supplemental Files. Click to Download

Figure Source Data. Click to Download

Web Supplemental Files. Click to Download

PBM data are available in the Cis-BP database and Gene Expression Omnibus (GEO)

Web supplement to "Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities"

Abstract

All C. elegans data from Cis-BP (for reviewers). This includes motifs, logos, annotation information, and E-scores. Click to Download .zip file

Supplemental Files. Click to Download

Figure Source Data. Click to Download

Web Supplemental Files. Click to Download

PBM data are available in the Cis-BP database and Gene Expression Omnibus (GEO)

Web supplement to
"Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities"