title: Universal tight correlation of codon bias and pool of RNA codons (codonome): The genome is optimized to allow any distribution of gene expression values in the transcriptome from bacteria to humans.
abstract: Codon bias is the phenomenon in which distinct synonymous codons are used with different frequencies. We define here the "codonome value" as the total number of codons present across all the expressed mRNAs in a given biological condition. We have developed the "CODONOME" software, which calculates the codon bias and, following integration with a gene expression profile, estimates the actual frequency of each codon at the transcriptome level (codonome bias) of a given tissue. Systematic analysis across different human tissues and multiple species shows a surprisingly tight correlation between the codon bias and the codonome bias. An aneuploidy and cancer condition such as that of Down Syndrome-related acute megakaryoblastic leukemia (DS-AMKL), does not appear to alter this relationship. The law of correlation between codon bias and codonome emerges as a property of the distribution and range of the number, sequence and expression level of the genes in a genome.
authors: Department of Experimental, Diagnostic and Specialty Medicine, Activity of Histology, Embryology and Applied Biology, University of Bologna, via Belmeloro 8, 40126 Bologna (BO), Italy. allison.piovesan2@unibo.it
authors: Allison
authors: A
authors: Piovesan
authors: Lorenza
authors: L
authors: Vitale
authors: Maria Chiara
authors: MC
authors: Pelleri
authors: Pierluigi
authors: P
authors: Strippoli
mesh_terms: D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000378:metabolism; D017173:Caenorhabditis elegans / Q000235:genetics; D003062:Codon / Q000235:genetics*; D030561:Databases, Nucleic Acid; D004912:Erythrocytes / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation; D016680:Genome, Bacterial; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics
chemical_list: D003062:Codon; D000604:Amino Acyl-tRNA Synthetases