Organizational Heterogeneity of Vertebrate Genomes
Identifieur interne : 001065 ( Pmc/Curation ); précédent : 001064; suivant : 001066Organizational Heterogeneity of Vertebrate Genomes
Auteurs : Svetlana Frenkel ; Valery Kirzhner ; Abraham KorolSource :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as “texts” using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter - GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.
Url:
DOI: 10.1371/journal.pone.0032076
PubMed: 22384143
PubMed Central: 3288070
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Organizational Heterogeneity of Vertebrate Genomes</title><author><name sortKey="Frenkel, Svetlana" sort="Frenkel, Svetlana" uniqKey="Frenkel S" first="Svetlana" last="Frenkel">Svetlana Frenkel</name></author><author><name sortKey="Kirzhner, Valery" sort="Kirzhner, Valery" uniqKey="Kirzhner V" first="Valery" last="Kirzhner">Valery Kirzhner</name></author><author><name sortKey="Korol, Abraham" sort="Korol, Abraham" uniqKey="Korol A" first="Abraham" last="Korol">Abraham Korol</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22384143</idno><idno type="pmc">3288070</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288070</idno><idno type="RBID">PMC:3288070</idno><idno type="doi">10.1371/journal.pone.0032076</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">001065</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001065</idno><idno type="wicri:Area/Pmc/Curation">001065</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001065</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Organizational Heterogeneity of Vertebrate Genomes</title><author><name sortKey="Frenkel, Svetlana" sort="Frenkel, Svetlana" uniqKey="Frenkel S" first="Svetlana" last="Frenkel">Svetlana Frenkel</name></author><author><name sortKey="Kirzhner, Valery" sort="Kirzhner, Valery" uniqKey="Kirzhner V" first="Valery" last="Kirzhner">Valery Kirzhner</name></author><author><name sortKey="Korol, Abraham" sort="Korol, Abraham" uniqKey="Korol A" first="Abraham" last="Korol">Abraham Korol</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as “texts” using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter - GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name></author><author><name sortKey="Ladunga, I" uniqKey="Ladunga I">I Ladunga</name></author><author><name sortKey="Blaisdell, Be" uniqKey="Blaisdell B">BE Blaisdell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lercher, Mj" uniqKey="Lercher M">MJ Lercher</name></author><author><name sortKey="Urrutia, Ao" uniqKey="Urrutia A">AO Urrutia</name></author><author><name sortKey="Pavlicek, A" uniqKey="Pavlicek A">A Pavlícek</name></author><author><name sortKey="Hurst, Ld" uniqKey="Hurst L">LD Hurst</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weir, Bs" uniqKey="Weir B">BS Weir</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22384143</article-id><article-id pub-id-type="pmc">3288070</article-id><article-id pub-id-type="publisher-id">PONE-D-11-15938</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0032076</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Agriculture</subject><subj-group><subject>Animal Management</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genomics</subject></subj-group></subj-group><subj-group><subject>Evolutionary Biology</subject></subj-group><subj-group><subject>Genomics</subject></subj-group></subj-group></article-categories><title-group><article-title>Organizational Heterogeneity of Vertebrate Genomes</article-title><alt-title alt-title-type="running-head">Organizational Heterogeneity of Vertebrate Genomes</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Frenkel</surname><given-names>Svetlana</given-names></name></contrib><contrib contrib-type="author"><name><surname>Kirzhner</surname><given-names>Valery</given-names></name></contrib><contrib contrib-type="author"><name><surname>Korol</surname><given-names>Abraham</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><addr-line>Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Laudet</surname><given-names>Vincent</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">Ecole Normale Supérieure de Lyon, France</aff><author-notes><corresp id="cor1">* E-mail: <email>korol@research.haifa.ac.il</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: VK AK. Performed the experiments: SF. Analyzed the data: SF VK. Contributed reagents/materials/analysis tools: VK SF AK. Wrote the paper: SF AK. Designed the software used in analysis: SF VK.</p></fn></author-notes><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>27</day><month>2</month><year>2012</year></pub-date><volume>7</volume><issue>2</issue><elocation-id>e32076</elocation-id><history><date date-type="received"><day>15</day><month>8</month><year>2011</year></date><date date-type="accepted"><day>23</day><month>1</month><year>2012</year></date></history><permissions><copyright-statement>Frenkel et al.</copyright-statement><copyright-year>2012</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><abstract><p>Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as “texts” using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter - GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.</p></abstract><counts><page-count count="15"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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