title: Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.
abstract: The codon adaptation index (CAI) values of all protein-coding sequences of the full-length cDNA libraries of Mus musculus were computed based on the RIKEN mouse full-length cDNA library. We have also computed the extent of consensus in flanking sequences of the initiator ATG codon based on the 'relative entropy' values of respective nucleotide positions (from -20 to +12 bp relative to the initiator ATG codon) for each group of genes classified by CAI values. With regard to the two nucleotides positions (-3 and +4) known to be highly conserved in Kozak's consensus sequence, a clear correlation between CAI values and relative entropy values was observed at position -3 but this was not significant at position +4, although a significant correlation was found at position -1 of the consensus sequence. Further, although no correlation was observed at any additional positions, relative entropy values were very high at positions -4, -6, and -8 in genes with high CAI values. These findings suggest that the extent of conservation in the flanking sequence of the initiator ATG codon including Kozak's consensus sequence was an important factor in modulation of the translation efficiency as well as synonymous codon usage bias particularly in highly expressed genes.
authors.affiliation: Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252-8520, Kanagawa, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Sakai
authors.forename: T
authors.initials: T
authors.lastname: Washio
authors.forename: R
authors.initials: R
authors.lastname: Saito
authors.forename: A
authors.initials: A
authors.lastname: Shinagawa
authors.forename: M
authors.initials: M
authors.lastname: Itoh
authors.forename: K
authors.initials: K
authors.lastname: Shibata
authors.forename: P
authors.initials: P
authors.lastname: Carninci
authors.forename: H
authors.initials: H
authors.lastname: Konno
authors.forename: J
authors.initials: J
authors.lastname: Kawai
authors.forename: Y
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: M
authors.initials: M
authors.lastname: Tomita
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D000818:Animals; D001482:Base Composition; D003062:Codon / Q000235:genetics*; D017124:Conserved Sequence; D018076:DNA, Complementary / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D005796:Genes / Q000235:genetics; D006360:Heat-Shock Proteins / Q000235:genetics; D051379:Mice; D010445:Peptide Elongation Factors / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D003062:Codon; D018076:DNA, Complementary; D006360:Heat-Shock Proteins; D010445:Peptide Elongation Factors; D012269:Ribosomal Proteins; D012321:DNA-Directed RNA Polymerases