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Article: Correlated evolution of transcription factors and their binding sites

TitleCorrelated evolution of transcription factors and their binding sites
Authors
Issue Date2011
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2011, v. 27 n. 21, p. 2972-2978 How to Cite?
AbstractMOTIVATION: The interaction between transcription factor (TF) and transcription factor binding site (TFBS) is essential for gene regulation. Mutation in either the TF or the TFBS may weaken their interaction and thus result in abnormalities. To maintain such vital interaction, a mutation in one of the interacting partners might be compensated by a corresponding mutation in its binding partner during the course of evolution. Confirming this co-evolutionary relationship will guide us in designing protein sequences to target a specific DNA sequence or in predicting TFBS for poorly studied proteins, or even correcting and rescuing disease mutations in clinical applications. RESULTS: Based on six, publicly available, experimentally validated TF-TFBS binding datasets for the basic Helix-Loop-Helix (bHLH) family, Homeo family, High-Mobility Group (HMG) family and Transient Receptor Potential channels (TRP) family, we showed that the evolutions of the TFs and their TFBSs are significantly correlated across eukaryotes. We further developed a mutual information-based method to identify co-evolved protein residues and DNA bases. This research sheds light on the dynamic relationship between TF and TFBS during their evolution. The same principle and strategy can be applied to co-evolutionary studies on protein-DNA interactions in other protein families. AVAILABILITY: All the datasets, scripts and other related files have been made freely available at: http://jjwanglab.org/co-evo. CONTACT: junwen@uw.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Persistent Identifierhttp://hdl.handle.net/10722/147648
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
ISI Accession Number ID
Funding AgencyGrant Number
Research Grants Council of Hong Kong781511M
778609M
N_HKU752/ 10
AoE M-04/04
Food and Health Bureau of Hong Kong10091262
National Science Foundation of China31061160497
Funding Information:

The Research Grants Council of Hong Kong (781511M, 778609M, N_HKU752/ 10, AoE M-04/04); Food and Health Bureau of Hong Kong (10091262); the National Science Foundation of China (31061160497).

References
Grants

 

DC FieldValueLanguage
dc.contributor.authorYang, Sen_HK
dc.contributor.authorYalamanchili, HKen_HK
dc.contributor.authorLi, Xen_HK
dc.contributor.authorYao, KMen_HK
dc.contributor.authorSham, PCen_HK
dc.contributor.authorZhang, MQen_HK
dc.contributor.authorWang, Jen_HK
dc.date.accessioned2012-05-29T06:05:12Z-
dc.date.available2012-05-29T06:05:12Z-
dc.date.issued2011en_HK
dc.identifier.citationBioinformatics, 2011, v. 27 n. 21, p. 2972-2978en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/147648-
dc.description.abstractMOTIVATION: The interaction between transcription factor (TF) and transcription factor binding site (TFBS) is essential for gene regulation. Mutation in either the TF or the TFBS may weaken their interaction and thus result in abnormalities. To maintain such vital interaction, a mutation in one of the interacting partners might be compensated by a corresponding mutation in its binding partner during the course of evolution. Confirming this co-evolutionary relationship will guide us in designing protein sequences to target a specific DNA sequence or in predicting TFBS for poorly studied proteins, or even correcting and rescuing disease mutations in clinical applications. RESULTS: Based on six, publicly available, experimentally validated TF-TFBS binding datasets for the basic Helix-Loop-Helix (bHLH) family, Homeo family, High-Mobility Group (HMG) family and Transient Receptor Potential channels (TRP) family, we showed that the evolutions of the TFs and their TFBSs are significantly correlated across eukaryotes. We further developed a mutual information-based method to identify co-evolved protein residues and DNA bases. This research sheds light on the dynamic relationship between TF and TFBS during their evolution. The same principle and strategy can be applied to co-evolutionary studies on protein-DNA interactions in other protein families. AVAILABILITY: All the datasets, scripts and other related files have been made freely available at: http://jjwanglab.org/co-evo. CONTACT: junwen@uw.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.en_HK
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.subject.meshBase Sequence-
dc.subject.meshDNA - chemistry - metabolism-
dc.subject.meshEvolution, Molecular-
dc.subject.meshRegulatory Elements, Transcriptional-
dc.subject.meshTranscription Factors - chemistry - genetics - metabolism-
dc.titleCorrelated evolution of transcription factors and their binding sitesen_HK
dc.typeArticleen_HK
dc.identifier.emailYao, KM: kmyao@hku.hken_HK
dc.identifier.emailSham, PC: pcsham@hku.hken_HK
dc.identifier.emailWang, J: junwen@hku.hken_HK
dc.identifier.authorityYao, KM=rp00344en_HK
dc.identifier.authoritySham, PC=rp00459en_HK
dc.identifier.authorityWang, J=rp00280en_HK
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1093/bioinformatics/btr503en_HK
dc.identifier.pmid21896508-
dc.identifier.scopuseid_2-s2.0-80054901781en_HK
dc.identifier.hkuros208293-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-80054901781&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume27en_HK
dc.identifier.issue21en_HK
dc.identifier.spage2972en_HK
dc.identifier.epage2978en_HK
dc.identifier.eissn1460-2059-
dc.identifier.isiWOS:000296099300007-
dc.publisher.placeUnited Kingdomen_HK
dc.relation.projectA Novel Hidden Markov Model to Predict microRNAs and their Targets Simultaneously and its Application to the Epstein-Barr virus-
dc.identifier.scopusauthoridWang, J=8950599500en_HK
dc.identifier.scopusauthoridZhang, MQ=7601558554en_HK
dc.identifier.scopusauthoridSham, PC=34573429300en_HK
dc.identifier.scopusauthoridYao, KM=7403234578en_HK
dc.identifier.scopusauthoridLi, X=53877702500en_HK
dc.identifier.scopusauthoridYalamanchili, HK=35182263500en_HK
dc.identifier.scopusauthoridYang, S=53878833500en_HK
dc.identifier.citeulike9757170-

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