The Caenorhabditis elegans genome: a multifractal analysis

Abstract

ABSTRACT. The Caenorhabditis elegans genome has several regular and irregular characteristics in its nucleotide composition; these are observed within and between chromosomes. To study these particularities, we carried out a multifractal analysis, which requires a large number of exponents to characterize scaling properties. We looked for a relationship between the genetic information content of the chromosomes and multifractal parameters and found less multifractality compared to the human genome. Differences in multifractality among chromosomes and in regions of chromosomes, and two group averages of chromosome regions were observed. All these differences were mainly dependent on differences in the contents of repetitive DNA. Based on these properties, we propose a nonlinear model for the structure of the C. elegans genome, with some biological implications. These results suggest that examining differences in multifractality is a viable approach for measuring local variations of genomic information contents along chromosomes. This approach could be extended to other genomes in order to characterize structural and functional regions of chromosomes.

The human genome: a multifractal analysis

“…Thus, the high contents of Alu account for the high aperiodicity and genetic variability of many chromosome sections. A similar result in C. elegans reported changes in multifractality related to a specific type of repetitive DNA [24]. Additionally, the correlations for CGI are lower but significant.…”

“…On the contrary, the 8p region in which a vast section of ~15 Mb has a strikingly high mutation rate lay on a medium multifractality region [36]. Similar behavior can be inferred in the C. elegans chromosome arms, rich in mutation rates [24]. …”

“…In fact, an in silico comparative genomics study between public and Celera versions of human genome sequences identifies several hundred new Alu insertion polymorphisms, showing that these elements are highly polymorphics [31]. A similar behavior is found in C. elegans where the TTAGGC repeat is abundant in number and combinations within the flanking sequences [24]. …”

“…Hence, a great number of mutations fall into the flanking regions of the coding sequences [37] and Alu elements become effectors of gene transcription by providing new enhancers, promoters and polyadenylation signals to many genes [38]. Based on these findings and those found in C. elegans [24], it seems that the non-linearity might be located on highly polymorphic genetic units that are distributed in many combinations through the genome. If so, we inquired on how these sequences have come to exist.…”

Sistema de Soporte a la Toma de Decisiones para el Análisis Multifractal del Genoma Humano

“…En este proyecto (AMGH) se aplicaron diferentes técnicas y herramientas de Bioinformática y de Geometría Fractal para la construcción de un modelo teórico, no lineal e "integrativo" que explica cómo se estructura y funciona el genoma humano (ver principales resultados del proyecto en [6] y [7]). Este estudio se adelantó a partir de la información del genoma humano publicada en el GenBank [2,5] y la gestión de datos también se basó en archivos planos, heredando de esta forma los problemas mencionados previamente.…”