Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

Handle URI:
http://hdl.handle.net/10754/621494
Title:
Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells
Authors:
Wong, Ka-Chun; Li, Yue; Peng, Chengbin ( 0000-0002-7445-2638 )
Abstract:
Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
Wong K-C, Li Y, Peng C (2015) Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells. Bioinformatics 32: 321–324. Available: http://dx.doi.org/10.1093/bioinformatics/btv555.
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
Issue Date:
27-Sep-2015
DOI:
10.1093/bioinformatics/btv555
PubMed ID:
26411866
Type:
Article
ISSN:
1367-4803; 1460-2059
Sponsors:
The work described in this article was substantially supported by a grant from City University of Hong Kong (Project No 7200444/CS).
Appears in Collections:
Articles; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorWong, Ka-Chunen
dc.contributor.authorLi, Yueen
dc.contributor.authorPeng, Chengbinen
dc.date.accessioned2016-11-03T08:30:43Z-
dc.date.available2016-11-03T08:30:43Z-
dc.date.issued2015-09-27en
dc.identifier.citationWong K-C, Li Y, Peng C (2015) Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells. Bioinformatics 32: 321–324. Available: http://dx.doi.org/10.1093/bioinformatics/btv555.en
dc.identifier.issn1367-4803en
dc.identifier.issn1460-2059en
dc.identifier.pmid26411866en
dc.identifier.doi10.1093/bioinformatics/btv555en
dc.identifier.urihttp://hdl.handle.net/10754/621494-
dc.description.abstractMotivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.en
dc.description.sponsorshipThe work described in this article was substantially supported by a grant from City University of Hong Kong (Project No 7200444/CS).en
dc.publisherOxford University Press (OUP)en
dc.titleIdentification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cellsen
dc.typeArticleen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalBioinformaticsen
dc.contributor.institutionDepartment of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kongen
dc.contributor.institutionCSAIL, Massachusetts Institute of Technology, Cambridge, MA, United Statesen
kaust.authorPeng, Chengbinen
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