Program in Systems Biology
Computational Biology | Ecology and Evolutionary Biology | Genomics | Molecular Biology | Molecular Genetics | Systems Biology
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.
C. elegans, DM, T-Box, binding specificities, computational biology, evolutionary biology, genomics, nuclear hormone receptors, protein binding microarray, systems biology, transcription factors
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© 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.
DOI of Published Version
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
Narasimhan K, Lambert SA, Yang A, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass J, Walhout AJ, Weirauch MT, Hughes TR. (2015). Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. Program in Systems Biology Publications. https://doi.org/10.7554/eLife.06967. Retrieved from https://escholarship.umassmed.edu/sysbio_pubs/57
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