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dc.contributor.authorRye, Morten Beck
dc.contributor.authorSætrom, Pål
dc.contributor.authorHåndstad, Tony
dc.contributor.authorDrabløs, Finn
dc.date.accessioned2019-10-08T10:58:31Z
dc.date.available2019-10-08T10:58:31Z
dc.date.created2012-01-12T22:01:30Z
dc.date.issued2011
dc.identifier.issn1741-7007
dc.identifier.urihttp://hdl.handle.net/11250/2620875
dc.description.abstractBackground Transcription factor binding to DNA requires both an appropriate binding element and suitably open chromatin, which together help to define regulatory elements within the genome. Current methods of identifying regulatory elements, such as promoters or enhancers, typically rely on sequence conservation, existing gene annotations or specific marks, such as histone modifications and p300 binding methods, each of which has its own biases. Results Herein we show that an approach based on clustering of transcription factor peaks from high-throughput sequencing coupled with chromatin immunoprecipitation (Chip-Seq) can be used to evaluate markers for regulatory elements. We used 67 data sets for 54 unique transcription factors distributed over two cell lines to create regulatory element clusters. By integrating the clusters from our approach with histone modifications and data for open chromatin, we identified general methylation of lysine 4 on histone H3 (H3K4me) as the most specific marker for transcription factor clusters. Clusters mapping to annotated genes showed distinct patterns in cluster composition related to gene expression and histone modifications. Clusters mapping to intergenic regions fall into two groups either directly involved in transcription, including miRNAs and long noncoding RNAs, or facilitating transcription by long-range interactions. The latter clusters were specifically enriched with H3K4me1, but less with acetylation of lysine 27 on histone 3 or p300 binding. Conclusion By integrating genomewide data of transcription factor binding and chromatin structure and using our data-driven approach, we pinpointed the chromatin marks that best explain transcription factor association with different regulatory elements. Our results also indicate that a modest selection of transcription factors may be sufficient to map most regulatory elements in the human genome.nb_NO
dc.language.isoengnb_NO
dc.publisherBMC (part of Springer Nature)nb_NO
dc.rightsNavngivelse 4.0 Internasjonal*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/deed.no*
dc.titleClustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elementsnb_NO
dc.typeJournal articlenb_NO
dc.typePeer reviewednb_NO
dc.description.versionpublishedVersionnb_NO
dc.source.volume9nb_NO
dc.source.journalBMC Biologynb_NO
dc.identifier.doi10.1186/1741-7007-9-80
dc.identifier.cristin884208
dc.description.localcode© 2011 Rye et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.nb_NO
cristin.unitcode194,65,15,0
cristin.unitcode194,63,10,0
cristin.unitnameInstitutt for klinisk og molekylær medisin
cristin.unitnameInstitutt for datateknologi og informatikk
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.qualitycode2


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