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The human genome: a multifractal analysis
BACKGROUND: Several studies have shown that genomes can be studied via a multifractal formalism. Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. Here we investigate the possibility that the human genome shows a similar behavior...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277318/ https://www.ncbi.nlm.nih.gov/pubmed/21999602 http://dx.doi.org/10.1186/1471-2164-12-506 |
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author | Moreno, Pedro A Vélez, Patricia E Martínez, Ember Garreta, Luis E Díaz, Néstor Amador, Siler Tischer, Irene Gutiérrez, José M Naik, Ashwinikumar K Tobar, Fabián García, Felipe |
author_facet | Moreno, Pedro A Vélez, Patricia E Martínez, Ember Garreta, Luis E Díaz, Néstor Amador, Siler Tischer, Irene Gutiérrez, José M Naik, Ashwinikumar K Tobar, Fabián García, Felipe |
author_sort | Moreno, Pedro A |
collection | PubMed |
description | BACKGROUND: Several studies have shown that genomes can be studied via a multifractal formalism. Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. Here we investigate the possibility that the human genome shows a similar behavior to that observed in the nematode. RESULTS: We report here multifractality in the human genome sequence. This behavior correlates strongly on the presence of Alu elements and to a lesser extent on CpG islands and (G+C) content. In contrast, no or low relationship was found for LINE, MIR, MER, LTRs elements and DNA regions poor in genetic information. Gene function, cluster of orthologous genes, metabolic pathways, and exons tended to increase their frequencies with ranges of multifractality and large gene families were located in genomic regions with varied multifractality. Additionally, a multifractal map and classification for human chromosomes are proposed. CONCLUSIONS: Based on these findings, we propose a descriptive non-linear model for the structure of the human genome, with some biological implications. This model reveals 1) a multifractal regionalization where many regions coexist that are far from equilibrium and 2) this non-linear organization has significant molecular and medical genetic implications for understanding the role of Alu elements in genome stability and structure of the human genome. Given the role of Alu sequences in gene regulation, genetic diseases, human genetic diversity, adaptation and phylogenetic analyses, these quantifications are especially useful. |
format | Online Article Text |
id | pubmed-3277318 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32773182012-02-13 The human genome: a multifractal analysis Moreno, Pedro A Vélez, Patricia E Martínez, Ember Garreta, Luis E Díaz, Néstor Amador, Siler Tischer, Irene Gutiérrez, José M Naik, Ashwinikumar K Tobar, Fabián García, Felipe BMC Genomics Research Article BACKGROUND: Several studies have shown that genomes can be studied via a multifractal formalism. Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. Here we investigate the possibility that the human genome shows a similar behavior to that observed in the nematode. RESULTS: We report here multifractality in the human genome sequence. This behavior correlates strongly on the presence of Alu elements and to a lesser extent on CpG islands and (G+C) content. In contrast, no or low relationship was found for LINE, MIR, MER, LTRs elements and DNA regions poor in genetic information. Gene function, cluster of orthologous genes, metabolic pathways, and exons tended to increase their frequencies with ranges of multifractality and large gene families were located in genomic regions with varied multifractality. Additionally, a multifractal map and classification for human chromosomes are proposed. CONCLUSIONS: Based on these findings, we propose a descriptive non-linear model for the structure of the human genome, with some biological implications. This model reveals 1) a multifractal regionalization where many regions coexist that are far from equilibrium and 2) this non-linear organization has significant molecular and medical genetic implications for understanding the role of Alu elements in genome stability and structure of the human genome. Given the role of Alu sequences in gene regulation, genetic diseases, human genetic diversity, adaptation and phylogenetic analyses, these quantifications are especially useful. BioMed Central 2011-10-14 /pmc/articles/PMC3277318/ /pubmed/21999602 http://dx.doi.org/10.1186/1471-2164-12-506 Text en Copyright ©2011 Moreno et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Moreno, Pedro A Vélez, Patricia E Martínez, Ember Garreta, Luis E Díaz, Néstor Amador, Siler Tischer, Irene Gutiérrez, José M Naik, Ashwinikumar K Tobar, Fabián García, Felipe The human genome: a multifractal analysis |
title | The human genome: a multifractal analysis |
title_full | The human genome: a multifractal analysis |
title_fullStr | The human genome: a multifractal analysis |
title_full_unstemmed | The human genome: a multifractal analysis |
title_short | The human genome: a multifractal analysis |
title_sort | human genome: a multifractal analysis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277318/ https://www.ncbi.nlm.nih.gov/pubmed/21999602 http://dx.doi.org/10.1186/1471-2164-12-506 |
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