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Article: GC content increased at CpG flanking positions of fish genes compared with sea squirt orthologs as a mechanism for reducing impact of DNA methylation

TitleGC content increased at CpG flanking positions of fish genes compared with sea squirt orthologs as a mechanism for reducing impact of DNA methylation
Authors
Issue Date2008
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
Citation
Plos One, 2008, v. 3 n. 11 How to Cite?
AbstractBackground: Fractional DNA methylation in sea squirts evolved to global DNA methylation in fish. The impact of global DNA methylation is reflected by more CpG depletions and/or more A/T to G/C changes at CpG flanking positions due to context-dependent mutations of methylated CpG sites. Methods and Findings: In this report, we demonstrate that the sea squirt genes have undergone more CpG to TpG/CpA substitutions than the fish orthologs using homologous fragments from orthologous genes among Ciona intestinalis, Ciona savignyi, fugufish and zebrafish. To avoid premature transcription, the TGA sites derived from CGA were largely converted to TGG in sea squirt genes. By contrast, a significant increment of GC content at CpG flanking positions was shown in fish genes. The positively selected A/T to G/C substitutions, in combination with the CpG to TpG/CpA substitutions, are the sources of the extremely low CpG observed/expected ratios in vertebrates. The nonsynonymous substitutions caused by the GC content increase have resulted in frequent amino acid replacements in the directions that were not noticed previously. Conclusion: The increased GC content at CpG flanking positions can reduce CpG loss in fish genes and attenuate the impact of DNA methylation on CpG-containing codons, probably accounting for evolution towards vertebrates. © 2008 Wang, Leung.
Persistent Identifierhttp://hdl.handle.net/10722/60133
ISSN
2015 Impact Factor: 3.057
2015 SCImago Journal Rankings: 1.395
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_HK
dc.contributor.authorLeung, FCCen_HK
dc.date.accessioned2010-05-31T04:04:18Z-
dc.date.available2010-05-31T04:04:18Z-
dc.date.issued2008en_HK
dc.identifier.citationPlos One, 2008, v. 3 n. 11en_HK
dc.identifier.issn1932-6203en_HK
dc.identifier.urihttp://hdl.handle.net/10722/60133-
dc.description.abstractBackground: Fractional DNA methylation in sea squirts evolved to global DNA methylation in fish. The impact of global DNA methylation is reflected by more CpG depletions and/or more A/T to G/C changes at CpG flanking positions due to context-dependent mutations of methylated CpG sites. Methods and Findings: In this report, we demonstrate that the sea squirt genes have undergone more CpG to TpG/CpA substitutions than the fish orthologs using homologous fragments from orthologous genes among Ciona intestinalis, Ciona savignyi, fugufish and zebrafish. To avoid premature transcription, the TGA sites derived from CGA were largely converted to TGG in sea squirt genes. By contrast, a significant increment of GC content at CpG flanking positions was shown in fish genes. The positively selected A/T to G/C substitutions, in combination with the CpG to TpG/CpA substitutions, are the sources of the extremely low CpG observed/expected ratios in vertebrates. The nonsynonymous substitutions caused by the GC content increase have resulted in frequent amino acid replacements in the directions that were not noticed previously. Conclusion: The increased GC content at CpG flanking positions can reduce CpG loss in fish genes and attenuate the impact of DNA methylation on CpG-containing codons, probably accounting for evolution towards vertebrates. © 2008 Wang, Leung.en_HK
dc.languageengen_HK
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.actionen_HK
dc.relation.ispartofPLoS ONEen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshDNA Methylation-
dc.subject.meshEvolution, Molecular-
dc.subject.meshTakifugu - genetics-
dc.subject.meshUrochordata - genetics-
dc.subject.meshZebrafish - genetics-
dc.titleGC content increased at CpG flanking positions of fish genes compared with sea squirt orthologs as a mechanism for reducing impact of DNA methylationen_HK
dc.typeArticleen_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1371/journal.pone.0003612en_HK
dc.identifier.pmid19005573-
dc.identifier.pmcidPMC2580031-
dc.identifier.scopuseid_2-s2.0-56649124554en_HK
dc.identifier.hkuros167648en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-56649124554&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume3en_HK
dc.identifier.issue11en_HK
dc.identifier.spagee3612-
dc.identifier.epagee3612-
dc.identifier.isiWOS:000265166200001-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWang, Y=12240680100en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK
dc.identifier.citeulike3582388-

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