Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.
Identifieur interne : 001D07 ( PubMed/Corpus ); précédent : 001D06; suivant : 001D08Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.
Auteurs : Heejoon Chae ; Jinwoo Park ; Seong-Whan Lee ; Kenneth P. Nephew ; Sun KimSource :
- Nucleic acids research [ 1362-4962 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
- classification : Mammals.
- genetics : Mammals.
- methods : Genomics.
- Algorithms, Animals, Artificial Intelligence, CpG Islands, Evolution, Molecular, Humans, Phylogeny, Sequence Analysis, DNA.
Abstract
CpG islands are GC-rich regions often located in the 5' end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.
DOI: 10.1093/nar/gkt144
PubMed: 23519616
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pubmed:23519616Le document en format XML
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Nephew</name></author><author><name sortKey="Kim, Sun" sort="Kim, Sun" uniqKey="Kim S" first="Sun" last="Kim">Sun Kim</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23519616</idno><idno type="pmid">23519616</idno><idno type="doi">10.1093/nar/gkt144</idno><idno type="wicri:Area/PubMed/Corpus">001D07</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001D07</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.</title><author><name sortKey="Chae, Heejoon" sort="Chae, Heejoon" uniqKey="Chae H" first="Heejoon" last="Chae">Heejoon Chae</name><affiliation><nlm:affiliation>Department of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Park, Jinwoo" sort="Park, Jinwoo" uniqKey="Park J" first="Jinwoo" last="Park">Jinwoo Park</name></author><author><name sortKey="Lee, Seong Whan" sort="Lee, Seong Whan" uniqKey="Lee S" first="Seong-Whan" last="Lee">Seong-Whan Lee</name></author><author><name sortKey="Nephew, Kenneth P" sort="Nephew, Kenneth P" uniqKey="Nephew K" first="Kenneth P" last="Nephew">Kenneth P. Nephew</name></author><author><name sortKey="Kim, Sun" sort="Kim, Sun" uniqKey="Kim S" first="Sun" last="Kim">Sun Kim</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Artificial Intelligence</term><term>CpG Islands</term><term>Evolution, Molecular</term><term>Genomics (methods)</term><term>Humans</term><term>Mammals (classification)</term><term>Mammals (genetics)</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Mammals</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mammals</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Artificial Intelligence</term><term>CpG Islands</term><term>Evolution, Molecular</term><term>Humans</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">CpG islands are GC-rich regions often located in the 5' end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23519616</PMID><DateCompleted><Year>2013</Year><Month>07</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>41</Volume><Issue>9</Issue><PubDate><Year>2013</Year><Month>May</Month></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation></Journal><ArticleTitle>Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.</ArticleTitle><Pagination><MedlinePgn>4783-91</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkt144</ELocationID><Abstract><AbstractText>CpG islands are GC-rich regions often located in the 5' end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chae</LastName><ForeName>Heejoon</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Jinwoo</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Seong-Whan</ForeName><Initials>SW</Initials></Author><Author ValidYN="Y"><LastName>Nephew</LastName><ForeName>Kenneth P</ForeName><Initials>KP</Initials></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Sun</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>CA113001</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>03</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001185" 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