Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities
Narasimhan, Kamesh ; Lambert, Samuel A. ; Yang, Ally ; Riddell, Jeremy ; Mnaimneh, Sanie ; Zheng, Hong ; Albu, Mihai ; Najafabadi, Hamed S. ; Reece-Hoyes, John S. ; Fuxman Bass, Juan ... show 3 more
Citations
Student Authors
Faculty Advisor
Academic Program
UMass Chan Affiliations
Document Type
Publication Date
Keywords
DM
T-Box
binding specificities
computational biology
evolutionary biology
genomics
nuclear hormone receptors
protein binding microarray
systems biology
transcription factors
Computational Biology
Ecology and Evolutionary Biology
Genomics
Molecular Biology
Molecular Genetics
Systems Biology
Subject Area
Embargo Expiration Date
Link to Full Text
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.
Source
Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. Elife. 2015 Apr 23;4. doi: 10.7554/eLife.06967. [Epub ahead of print] PubMed PMID: 25905672. Link to article on publisher's site
Year of Medical School at Time of Visit
Sponsors
Dates of Travel
DOI
Permanent Link to this Item
PubMed ID
Other Identifiers
Notes
This PDF is the version of the article that was accepted for publication after peer review.