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circular code motifs in genomes of eukaryotes

JOURNAL OF THEORETICAL BIOLOGY 2016年第0期408卷 198-212页

作者： El Soufi, Karim Michel, Christian J. Univ Strasbourg ICube Theoret Bioinformat CNRS 300 Blvd Sebastien Brant F-67400 Illkirch Graffenstaden France

A set X of 20 trinucleotides was identified in genes of bacteria, eukaryotes, plasmids and viruses, which has in average the highest occurrence in reading frame compared to its two shifted frames (Michel, 2015;Argues and Michel, 1996). This set X has an interesting mathematical property as X is a circular code (Argues and Michel, 1996). Thus, the motifs from this circular code X, called X motifs, have the property to always retrieve, synchronize and maintain the reading frame in genes. In this paper, we develop several statistical analyzes of X motifs in 138 available complete genomes of eukaryotes in which genes as well as non-gene regions are examined. Large X motifs (with lengths of at least 15 consecutive trinucleotides of X and compositions of at least 10 different trinucleotides of X among 20) have the highest occurrence in genomes of eukaryotes compared to its 23 large bijective motifs, its two large permuted motifs and large random motifs. The largest X motifs identified in eukaryotic genomes are presented, e.g. an X motif in a non-gene region of the genome Solarium pennellii with a length of 155 trinucleotides (465 nucleotides) and an expectation E = 10(-71). In the human genome, the largest X motif occurs in a non gene region of the chromosome 13 with a length of 36 trinucleotides and an expectation E = 10(-11). X motifs in non-gene regions of genomes could be evolutionary relics of primitive genes using the circular code for translation. However, the proportion of X motifs (with lengths of at least 10 consecutive trinucleotides of X and compositions of at least 5 different trinucleotides of X among 20) in genes/non-genes of the 138 complete eukaryotic genomes is about 8. Thus, the X motifs occur preferentially in genes, as expected from the previous works of 20 years. (C) 2016 Elsevier Ltd. All rights reserved.

关键词： circular code motifs circular code Bijective transformation circular code permuted circular code Genomes of eukaryotes

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