Organizational Heterogeneity of Vertebrate Genomes
Identifieur interne : 002253 ( Main/Merge ); précédent : 002252; suivant : 002254Organizational Heterogeneity of Vertebrate Genomes
Auteurs : Svetlana Frenkel ; Valery Kirzhner ; Abraham KorolSource :
- PLoS ONE [ 1932-6203 ] ; 2012.
Descripteurs français
- KwdFr :
- Algorithmes, Analyse de séquence d'ADN, Animaux, Biodiversité, Chromosomes (ultrastructure), Données de séquences moléculaires, Génome, Humains, Ilots CpG, Logiciel, Mammifères (métabolisme), Modèles génétiques, Modèles statistiques, Oligonucléotides (génétique), Poissons, Séquence nucléotidique, Variation génétique, Vertébrés.
- MESH :
- génétique : Oligonucléotides.
- métabolisme : Mammifères.
- ultrastructure : Algorithmes, Analyse de séquence d'ADN, Animaux, Biodiversité, Chromosomes, Données de séquences moléculaires, Génome, Humains, Ilots CpG, Logiciel, Modèles génétiques, Modèles statistiques, Poissons, Séquence nucléotidique, Variation génétique, Vertébrés.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Oligonucleotides.
- metabolism : Mammals.
- ultrastructure : Chromosomes.
- Algorithms, Animals, Base Sequence, Biodiversity, CpG Islands, Fishes, Genetic Variation, Genome, Humans, Models, Genetic, Models, Statistical, Molecular Sequence Data, Sequence Analysis, DNA, Software, Vertebrates.
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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PMC:3288070Le document en format XML
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xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Base Sequence</term><term>Biodiversity</term><term>Chromosomes (ultrastructure)</term><term>CpG Islands</term><term>Fishes</term><term>Genetic Variation</term><term>Genome</term><term>Humans</term><term>Mammals (metabolism)</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Molecular Sequence Data</term><term>Oligonucleotides (genetics)</term><term>Sequence Analysis, DNA</term><term>Software</term><term>Vertebrates</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Biodiversité</term><term>Chromosomes (ultrastructure)</term><term>Données de séquences moléculaires</term><term>Génome</term><term>Humains</term><term>Ilots CpG</term><term>Logiciel</term><term>Mammifères (métabolisme)</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Oligonucléotides (génétique)</term><term>Poissons</term><term>Séquence nucléotidique</term><term>Variation génétique</term><term>Vertébrés</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligonucleotides</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Oligonucléotides</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Mammals</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Mammifères</term></keywords><keywords scheme="MESH" qualifier="ultrastructure" xml:lang="en"><term>Chromosomes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Base Sequence</term><term>Biodiversity</term><term>CpG Islands</term><term>Fishes</term><term>Genetic Variation</term><term>Genome</term><term>Humans</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Molecular Sequence Data</term><term>Sequence Analysis, DNA</term><term>Software</term><term>Vertebrates</term></keywords><keywords scheme="MESH" qualifier="ultrastructure" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Biodiversité</term><term>Chromosomes</term><term>Données de séquences moléculaires</term><term>Génome</term><term>Humains</term><term>Ilots CpG</term><term>Logiciel</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Poissons</term><term>Séquence nucléotidique</term><term>Variation génétique</term><term>Vertébrés</term></keywords></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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Hiisila</name></author><author><name sortKey="Mannila, H" uniqKey="Mannila H">H Mannila</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lieberman Aiden, E" uniqKey="Lieberman Aiden E">E Lieberman-Aiden</name></author><author><name sortKey="Van, Berkumnl" uniqKey="Van B">BerkumNL van</name></author><author><name sortKey="Williams, L" uniqKey="Williams L">L Williams</name></author><author><name sortKey="Imakaev, M" uniqKey="Imakaev M">M Imakaev</name></author><author><name sortKey="Ragoczy, T" uniqKey="Ragoczy T">T Ragoczy</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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