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Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

dc.contributor.authorNarasimhan, Kamesh
dc.contributor.authorLambert, Samuel A.
dc.contributor.authorYang, Ally
dc.contributor.authorRiddell, Jeremy
dc.contributor.authorMnaimneh, Sanie
dc.contributor.authorZheng, Hong
dc.contributor.authorAlbu, Mihai
dc.contributor.authorNajafabadi, Hamed S.
dc.contributor.authorReece-Hoyes, John S.
dc.contributor.authorFuxman Bass, Juan
dc.contributor.authorWalhout, Albertha J M
dc.contributor.authorWeirauch, Matthew T.
dc.contributor.authorHughes, Timothy R.
dc.date2022-08-11T08:11:00.000
dc.date.accessioned2022-08-23T17:27:46Z
dc.date.available2022-08-23T17:27:46Z
dc.date.issued2015-04-23
dc.date.submitted2015-04-24
dc.identifier.citationNarasimhan 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. <a href="http://dx.doi.org/10.7554/eLife.06967">Link to article on publisher's site</a></p>
dc.identifier.issn2050-084X
dc.identifier.doi10.7554/eLife.06967
dc.identifier.pmid25905672
dc.identifier.urihttp://hdl.handle.net/20.500.14038/49936
dc.description<p>This PDF is the version of the article that was accepted for publication after peer review.</p>
dc.description.abstractCaenorhabditis 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.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=25905672&dopt=Abstract">Link to article in PubMed</a>
dc.rights<p id="x-x-x-x-p-1">© 2015, Narasimhan et al.This article is distributed under the terms of the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</a> permitting unrestricted use and redistribution provided that the original author and source are credited.</p>
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectC. elegans
dc.subjectDM
dc.subjectT-Box
dc.subjectbinding specificities
dc.subjectcomputational biology
dc.subjectevolutionary biology
dc.subjectgenomics
dc.subjectnuclear hormone receptors
dc.subjectprotein binding microarray
dc.subjectsystems biology
dc.subjecttranscription factors
dc.subjectComputational Biology
dc.subjectEcology and Evolutionary Biology
dc.subjectGenomics
dc.subjectMolecular Biology
dc.subjectMolecular Genetics
dc.subjectSystems Biology
dc.titleMapping and analysis of Caenorhabditis elegans transcription factor sequence specificities
dc.typeAccepted Manuscript
dc.source.journaltitleElife
dc.source.volume4
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1056&amp;context=sysbio_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/sysbio_pubs/57
dc.identifier.contextkey7031484
refterms.dateFOA2022-08-23T17:27:46Z
html.description.abstract<p>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.</p>
dc.identifier.submissionpathsysbio_pubs/57
dc.contributor.departmentProgram in Systems Biology


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<p id="x-x-x-x-p-1">© 2015, Narasimhan et al.This article is distributed under the terms of the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</a> permitting unrestricted use and redistribution provided that the original author and source are credited.</p>
Except where otherwise noted, this item's license is described as <p id="x-x-x-x-p-1">© 2015, Narasimhan et al.This article is distributed under the terms of the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</a> permitting unrestricted use and redistribution provided that the original author and source are credited.</p>