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Article: Comparative Genomic Study Reveals a Transition from TA Richness in Invertebrates to GC Richness in Vertebrates at CpG Flanking Sites: An Indication for Context-Dependent Mutagenicity of Methylated CpG Sites

TitleComparative Genomic Study Reveals a Transition from TA Richness in Invertebrates to GC Richness in Vertebrates at CpG Flanking Sites: An Indication for Context-Dependent Mutagenicity of Methylated CpG Sites
Authors
KeywordsCpG deficiency
DNA methylation
GC content
invertebrate genomes
Issue Date2008
PublisherKexue Chubanshe.
Citation
Genomics, Proteomics And Bioinformatics, 2008, v. 6 n. 3-4, p. 144-154 How to Cite?
AbstractVertebrate genomes are characterized with CpG deficiency, particularly for GC-poor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5′ T to 5′ A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5′ Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected (obs/exp) values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes (except sea urchin) but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5′ T and 5′ A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions. © 2008 Beijing Genomics Institute.
Persistent Identifierhttp://hdl.handle.net/10722/60136
ISSN
2015 SCImago Journal Rankings: 1.058
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_HK
dc.contributor.authorLeung, FCCen_HK
dc.date.accessioned2010-05-31T04:04:21Z-
dc.date.available2010-05-31T04:04:21Z-
dc.date.issued2008en_HK
dc.identifier.citationGenomics, Proteomics And Bioinformatics, 2008, v. 6 n. 3-4, p. 144-154en_HK
dc.identifier.issn1672-0229en_HK
dc.identifier.urihttp://hdl.handle.net/10722/60136-
dc.description.abstractVertebrate genomes are characterized with CpG deficiency, particularly for GC-poor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5′ T to 5′ A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5′ Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected (obs/exp) values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes (except sea urchin) but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5′ T and 5′ A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions. © 2008 Beijing Genomics Institute.en_HK
dc.languageengen_HK
dc.publisherKexue Chubanshe.-
dc.relation.ispartofGenomics, Proteomics and Bioinformaticsen_HK
dc.subjectCpG deficiencyen_HK
dc.subjectDNA methylationen_HK
dc.subjectGC contenten_HK
dc.subjectinvertebrate genomesen_HK
dc.subject.meshAT Rich Sequence-
dc.subject.meshCpG Islands - genetics-
dc.subject.meshGenomics - methods-
dc.subject.meshInvertebrates - genetics-
dc.subject.meshVertebrates - genetics-
dc.titleComparative Genomic Study Reveals a Transition from TA Richness in Invertebrates to GC Richness in Vertebrates at CpG Flanking Sites: An Indication for Context-Dependent Mutagenicity of Methylated CpG Sitesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1672-0229&volume=6 &issue=3-4&spage=144&epage=154&date=2008&atitle=Comparative+Genomic+Study+Reveals+A+Transition+From+Ta+Richness+In+Invertebrates+To+Gc+Richness+In+Vertebrates+At+Cpg+Flanking+Sites:+An+Indication+For+Context-dependent+Mutagenicity+Of+Methylated+Cpg+Sites-
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/S1672-0229(09)60002-4en_HK
dc.identifier.pmid19329065-
dc.identifier.scopuseid_2-s2.0-62949240195en_HK
dc.identifier.hkuros166168en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-62949240195&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume6en_HK
dc.identifier.issue3-4en_HK
dc.identifier.spage144en_HK
dc.identifier.epage154en_HK
dc.publisher.placeChinaen_HK
dc.identifier.scopusauthoridWang, Y=8710320600en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK

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