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.
Subject(s)
Caenorhabditis elegans/genetics , Genome , Animals , Chromosomes/genetics , Expressed Sequence Tags , Fractals , Genome, Human , Humans , Models, Genetic , Models, Statistical , Nonlinear Dynamics , Sequence Analysis, DNAABSTRACT
Regulation of human olfactory receptor (hOR) genes is a complex process of control and signalization with various structures and functions that are not clearly understood. To date, nearly 390 functional hOR genes and 462 pseudogenes have been discovered in the human genome. Enhancer models and trans-acting elements for the regulation of different hOR genes are among the few examples of our knowledge concerning regulation of these genes. We looked for upstream control elements that might help explain these complex control mechanisms. To analyze the human olfactory gene family, we looked for functional genes and pseudogenes common to all hOR genes obtained from public databases. Subsequently, we analyzed sequences upstream of the transcription start sites with data mining and bioinformatics tools. We found two highly conserved regions, which we called HCR I and HCR II, upstream of the transcription start sites in 77 hOR genes and 87 pseudogenes. These regions showed possible enhancer functions common to both genes and pseudogenes, an intriguing feature that may be associated with the expression of pseudogenes. Based on these HCRs, we propose a structural model of gene regulation for the olfactory gene family.
