The human genome: a multifractal analysis

BMC Genomics

Research Article

Ember Martínez¹  Néstor Díaz¹  Siler Amador¹  Felipe García²  Fabián Tobar²  Irene Tischer³  Luis E Garreta³  Pedro A Moreno³  José M Gutiérrez⁴  Patricia E Vélez⁵  Ashwinikumar K Naik⁶ 

[1] Departamento de Sistemas, Universidad del Cauca, Popayán, Colombia;Escuela de Ciencias Básicas. Facultad de Salud, Universidad del Valle, Santiago de Cali, Colombia;Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Santiago de Cali, Colombia;Instituto de Física de Cantabria, Universidad de Cantabria-CSIC, Santander, España;Profesora del Departamento de Biología, FACNED, Universidad del Cauca, Popayán, Colombia;Escuela de Ciencias Básicas. Facultad de Salud, Universidad del Valle, Santiago de Cali, Colombia;Vaatsalya HealthCare Solutions Pvt Ltd, Bangalore, India;

关键词: Down Syndrome;    Chromosome Fragment;    Multifractal Analysis;    Multifractal Spectrum;    Chaos Game Representation;   

DOI  :  10.1186/1471-2164-12-506

 received in 2011-04-13, accepted in 2011-10-14,  发布年份 2011

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Moreno et al; licensee BioMed Central Ltd. 2011