Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities
Date
2015-04-23
Authors
Narasimhan, Kamesh
Lambert, Samuel A.
Yang, Ally W. H.
Riddell, Jeremy
Mnaimneh, Sanie
Zheng, Hong
Albu, Mihai
Najafabadi, Hamed S.
Reece-Hoyes, John S.
Fuxman Bass, Juan I.
Version
Published version
OA Version
Citation
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
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 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.
Description
License
Attribution 4.0 International