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Article: Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq

TitleQuantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq
Authors
Issue Date2017
Citation
Nucleic Acids Research, 2017, v. 45, n. 2, p. 832-845 How to Cite?
Abstract© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes.
Persistent Identifierhttp://hdl.handle.net/10722/253128
ISSN
2020 Impact Factor: 16.971
2020 SCImago Journal Rankings: 9.008
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorChang, Yiming K.-
dc.contributor.authorSrivastava, Yogesh-
dc.contributor.authorHu, Caizhen-
dc.contributor.authorJoyce, Adam-
dc.contributor.authorYang, Xiaoxiao-
dc.contributor.authorZuo, Zheng-
dc.contributor.authorHavranek, James J.-
dc.contributor.authorStormo, Gary D.-
dc.contributor.authorJauch, Ralf-
dc.date.accessioned2018-05-11T05:38:41Z-
dc.date.available2018-05-11T05:38:41Z-
dc.date.issued2017-
dc.identifier.citationNucleic Acids Research, 2017, v. 45, n. 2, p. 832-845-
dc.identifier.issn0305-1048-
dc.identifier.urihttp://hdl.handle.net/10722/253128-
dc.description.abstract© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes.-
dc.languageeng-
dc.relation.ispartofNucleic Acids Research-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleQuantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq-
dc.typeArticle-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/nar/gkw1198-
dc.identifier.pmid27915232-
dc.identifier.scopuseid_2-s2.0-85014017375-
dc.identifier.volume45-
dc.identifier.issue2-
dc.identifier.spage832-
dc.identifier.epage845-
dc.identifier.eissn1362-4962-
dc.identifier.isiWOS:000396576300031-
dc.identifier.issnl0305-1048-

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