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Article: DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria

TitleDNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria
Authors
Issue Date2004
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2004, v. 20 n. 18, p. 3336-3345 How to Cite?
AbstractMotivation: It has been speculated that CpG dinucleotide deficiency in genomes is a consequence of DNA methylation. However, this hypothesis does not adequately explain CpG deficiency in bacteria. The hypothesis based on DNA structure constraint as an alternative explanation was therefore examined. Results: By comparing real bacterial genomes and Markov artificial genomes in the second order, we found that the core structure of a restricted pattern, the TTCGAA pattern, was under represented in low GC content bacterial genomes regardless of CpG dinucleotide level. This is in contrast to the AACGTT pattern, indicating that the counterselection is context-dependent. Further study discovered nine under-represented patterns that were supposed to be capable of inducing DNA structure constraint. In summary, most of them are in TTCGNA and TTCGAN patterns in both DNA strands. An explanation is also proposed for the strong correlation between GC content and CpG deficiency. The result of random sequence simulation showed that the occurrences of these patterns were correlated with GC content, as well as the percentage of CpG dinucleotides being trapped in these patterns. Finally, we suggest that the degree of counter-selection against these restricted patterns could be influenced by global GC content of a genome. © Oxford University Press 2004; all rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/84624
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_HK
dc.contributor.authorLeung, FCCen_HK
dc.date.accessioned2010-09-06T08:55:13Z-
dc.date.available2010-09-06T08:55:13Z-
dc.date.issued2004en_HK
dc.identifier.citationBioinformatics, 2004, v. 20 n. 18, p. 3336-3345en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/84624-
dc.description.abstractMotivation: It has been speculated that CpG dinucleotide deficiency in genomes is a consequence of DNA methylation. However, this hypothesis does not adequately explain CpG deficiency in bacteria. The hypothesis based on DNA structure constraint as an alternative explanation was therefore examined. Results: By comparing real bacterial genomes and Markov artificial genomes in the second order, we found that the core structure of a restricted pattern, the TTCGAA pattern, was under represented in low GC content bacterial genomes regardless of CpG dinucleotide level. This is in contrast to the AACGTT pattern, indicating that the counterselection is context-dependent. Further study discovered nine under-represented patterns that were supposed to be capable of inducing DNA structure constraint. In summary, most of them are in TTCGNA and TTCGAN patterns in both DNA strands. An explanation is also proposed for the strong correlation between GC content and CpG deficiency. The result of random sequence simulation showed that the occurrences of these patterns were correlated with GC content, as well as the percentage of CpG dinucleotides being trapped in these patterns. Finally, we suggest that the degree of counter-selection against these restricted patterns could be influenced by global GC content of a genome. © Oxford University Press 2004; all rights reserved.en_HK
dc.languageengen_HK
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.rightsBioinformatics. Copyright © Oxford University Press.en_HK
dc.titleDNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteriaen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1367-4803&volume=20&spage=3336&epage=3345&date=2004&atitle=DNA+structure+constraint+is+probably+a+fundamental+factor+inducing+CpG+deficiency+in+bacteria+en_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/bioinformatics/bth393en_HK
dc.identifier.pmid15247101-
dc.identifier.scopuseid_2-s2.0-12344304270en_HK
dc.identifier.hkuros103445en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-12344304270&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume20en_HK
dc.identifier.issue18en_HK
dc.identifier.spage3336en_HK
dc.identifier.epage3345en_HK
dc.identifier.isiWOS:000225786600006-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWang, Y=8710320600en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK

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