Discriminative identification of transcriptional responses of promoters and enhancers after stimulus

Handle URI:
http://hdl.handle.net/10754/622038
Title:
Discriminative identification of transcriptional responses of promoters and enhancers after stimulus
Authors:
Kleftogiannis, Dimitrios A. ( 0000-0003-1086-821X ) ; Kalnis, Panos ( 0000-0002-5060-1360 ) ; Arner, Erik; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Promoters and enhancers regulate the initiation of gene expression and maintenance of expression levels in spatial and temporal manner. Recent findings stemming from the Cap Analysis of Gene Expression (CAGE) demonstrate that promoters and enhancers, based on their expression profiles after stimulus, belong to different transcription response subclasses. One of the most promising biological features that might explain the difference in transcriptional response between subclasses is the local chromatin environment. We introduce a novel computational framework, PEDAL, for distinguishing effectively transcriptional profiles of promoters and enhancers using solely histone modification marks, chromatin accessibility and binding sites of transcription factors and co-activators. A case study on data from MCF-7 cell-line reveals that PEDAL can identify successfully the transcription response subclasses of promoters and enhancers from two different stimulations. Moreover, we report subsets of input markers that discriminate with minimized classification error MCF-7 promoter and enhancer transcription response subclasses. Our work provides a general computational approach for identifying effectively cell-specific and stimulation-specific promoter and enhancer transcriptional profiles, and thus, contributes to improve our understanding of transcriptional activation in human.
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Kleftogiannis D, Kalnis P, Arner E, Bajic VB (2016) Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Nucleic Acids Research: gkw1015. Available: http://dx.doi.org/10.1093/nar/gkw1015.
Publisher:
Oxford University Press (OUP)
Journal:
Nucleic Acids Research
Issue Date:
17-Oct-2016
DOI:
10.1093/nar/gkw1015
Type:
Article
ISSN:
0305-1048; 1362-4962
Sponsors:
King Abdullah University of Science and Technology (KAUST); Research Grant from MEXT [to the RIKEN Center for Life Science Technologies]. Funding for open access charge: King Abdullah University of Science and Technology (KAUST).
Additional Links:
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1015
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorKleftogiannis, Dimitrios A.en
dc.contributor.authorKalnis, Panosen
dc.contributor.authorArner, Eriken
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2016-12-20T05:52:11Z-
dc.date.available2016-12-20T05:52:11Z-
dc.date.issued2016-10-17en
dc.identifier.citationKleftogiannis D, Kalnis P, Arner E, Bajic VB (2016) Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Nucleic Acids Research: gkw1015. Available: http://dx.doi.org/10.1093/nar/gkw1015.en
dc.identifier.issn0305-1048en
dc.identifier.issn1362-4962en
dc.identifier.doi10.1093/nar/gkw1015en
dc.identifier.urihttp://hdl.handle.net/10754/622038-
dc.description.abstractPromoters and enhancers regulate the initiation of gene expression and maintenance of expression levels in spatial and temporal manner. Recent findings stemming from the Cap Analysis of Gene Expression (CAGE) demonstrate that promoters and enhancers, based on their expression profiles after stimulus, belong to different transcription response subclasses. One of the most promising biological features that might explain the difference in transcriptional response between subclasses is the local chromatin environment. We introduce a novel computational framework, PEDAL, for distinguishing effectively transcriptional profiles of promoters and enhancers using solely histone modification marks, chromatin accessibility and binding sites of transcription factors and co-activators. A case study on data from MCF-7 cell-line reveals that PEDAL can identify successfully the transcription response subclasses of promoters and enhancers from two different stimulations. Moreover, we report subsets of input markers that discriminate with minimized classification error MCF-7 promoter and enhancer transcription response subclasses. Our work provides a general computational approach for identifying effectively cell-specific and stimulation-specific promoter and enhancer transcriptional profiles, and thus, contributes to improve our understanding of transcriptional activation in human.en
dc.description.sponsorshipKing Abdullah University of Science and Technology (KAUST); Research Grant from MEXT [to the RIKEN Center for Life Science Technologies]. Funding for open access charge: King Abdullah University of Science and Technology (KAUST).en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttps://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1015en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/4.0/ ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.subjecttranscriptionen
dc.subjectgeneticen
dc.subjectchromatinen
dc.subjectoncogenesen
dc.subjectfooten
dc.subjectenhancer of transcriptionen
dc.subjectmcf-7 cellsen
dc.titleDiscriminative identification of transcriptional responses of promoters and enhancers after stimulusen
dc.typeArticleen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalNucleic Acids Researchen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionThe Institute of Cancer Research (ICR), London, SW7 3RP, UKen
dc.contributor.institutionRIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST (DGT)), Yokohama, Kanagawa 230-0045, Japanen
kaust.authorKleftogiannis, Dimitrios A.en
kaust.authorKalnis, Panosen
kaust.authorBajic, Vladimir B.en
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