Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities
Publisher VersionDOI: 10.7554/eLife.06967.001
Lambert, Samuel A.
Yang, Ally W. H.
Najafabadi, Hamed S.
Reece-Hoyes, John S.
Fuxman Bass, Juan I.
Walhout, Albertha J. M.
Weirauch, Matthew T.
Hughes, Timothy R.
MetadataShow full item record
Citation (published version)K Narasimhan, SA Lambert, AWH Yang, J Riddell, S Mnaimneh, H Zheng, M Albu, HS Najafabadi, JS Reece-Hoyes, JIF Bass. 2015. "Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities." eLIFE, Volume 4, pp. e06967 - e06967. DOI: 10.7554/eLife.06967.001
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 sequencespecific 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.
RightsAttribution 4.0 International