Organizational Heterogeneity of Vertebrate Genomes

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...

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Autores principales: Frenkel, Svetlana, Kirzhner, Valery, Korol, Abraham
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288070/
https://www.ncbi.nlm.nih.gov/pubmed/22384143
http://dx.doi.org/10.1371/journal.pone.0032076
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author Frenkel, Svetlana
Kirzhner, Valery
Korol, Abraham
author_facet Frenkel, Svetlana
Kirzhner, Valery
Korol, Abraham
author_sort Frenkel, Svetlana
collection PubMed
description 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.
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spelling pubmed-32880702012-03-01 Organizational Heterogeneity of Vertebrate Genomes Frenkel, Svetlana Kirzhner, Valery Korol, Abraham PLoS One Research Article 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. Public Library of Science 2012-02-27 /pmc/articles/PMC3288070/ /pubmed/22384143 http://dx.doi.org/10.1371/journal.pone.0032076 Text en Frenkel et al. http://creativecommons.org/licenses/by/4.0/ 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.
spellingShingle Research Article
Frenkel, Svetlana
Kirzhner, Valery
Korol, Abraham
Organizational Heterogeneity of Vertebrate Genomes
title Organizational Heterogeneity of Vertebrate Genomes
title_full Organizational Heterogeneity of Vertebrate Genomes
title_fullStr Organizational Heterogeneity of Vertebrate Genomes
title_full_unstemmed Organizational Heterogeneity of Vertebrate Genomes
title_short Organizational Heterogeneity of Vertebrate Genomes
title_sort organizational heterogeneity of vertebrate genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288070/
https://www.ncbi.nlm.nih.gov/pubmed/22384143
http://dx.doi.org/10.1371/journal.pone.0032076
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