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BMC Genomics

, 12:506

Human and rodent genomics

Abstract

BackgroundSeveral 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.

ResultsWe 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.

ConclusionsBased 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.

AbbreviationsCGRChaos Game Representation

MD or ΔDqmultifractality degree

RMrange of multifractality

AMDaverage of multifractality degree

LMMlow and medium multifractality

GCICpG islands

XCIX chromosome inactivation

chr.chromosome.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-12-506 contains supplementary material, which is available to authorized users.

Pedro A Moreno, Patricia E Vélez contributed equally to this work.

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Autor: Pedro A Moreno - Patricia E Vélez - Ember Martínez - Luis E Garreta - Néstor Díaz - Siler Amador - Irene Tischer - J

Fuente: https://link.springer.com/article/10.1186/1471-2164-12-506



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