A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

Handle URI:
http://hdl.handle.net/10754/561843
Title:
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
Authors:
Kulakovskiy, Ivan V.; Belostotsky, A. A.; Kasianov, Artem S.; Esipova, Natalia G.; Medvedeva, Yulia; Eliseeva, Irina A.; Makeev, Vsevolod J.
Abstract:
Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3'-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. © The Author 2011. Published by Oxford University Press. All rights reserved.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
Issue Date:
18-Aug-2011
DOI:
10.1093/bioinformatics/btr453
PubMed ID:
21852305
Type:
Article
ISSN:
13674803
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorKulakovskiy, Ivan V.en
dc.contributor.authorBelostotsky, A. A.en
dc.contributor.authorKasianov, Artem S.en
dc.contributor.authorEsipova, Natalia G.en
dc.contributor.authorMedvedeva, Yuliaen
dc.contributor.authorEliseeva, Irina A.en
dc.contributor.authorMakeev, Vsevolod J.en
dc.date.accessioned2015-08-03T09:32:15Zen
dc.date.available2015-08-03T09:32:15Zen
dc.date.issued2011-08-18en
dc.identifier.issn13674803en
dc.identifier.pmid21852305en
dc.identifier.doi10.1093/bioinformatics/btr453en
dc.identifier.urihttp://hdl.handle.net/10754/561843en
dc.description.abstractMotivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3'-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. © The Author 2011. Published by Oxford University Press. All rights reserved.en
dc.publisherOxford University Press (OUP)en
dc.titleA deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sitesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBioinformaticsen
dc.contributor.institutionLaboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federationen
dc.contributor.institutionLaboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russian Federationen
dc.contributor.institutionLaboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russian Federationen
dc.contributor.institutionGroup of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federationen
kaust.authorMedvedeva, Yuliaen

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