International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

Table of Contents * Genes, Physical Mapping and Sequencing * Gene Identification * Bioinformatics * Common Resources * RIKEN Session * Functional Genomics * Complex Traits * Mutagenesis * Developmental Genetics and Differentiation * Verne Chapman Memorial Lecture I and II

C20. Correlation between codon usage bias and conservation of 5' untranslated region

Hiroaki Sakai¹², Yusuke Ohkuma¹³, Chiaki Imamura¹⁴ ,Akira Shinagawa⁵, Masayoshi Itoh⁵, Kazuhiro Shibata⁵, Piero Carninci⁵, Hideaki Konno⁵, Jun Kawai⁵, Yoshifumi Fukunishi⁵, Yoshihide Hayashizaki⁵ ,and Masaru Tomita¹³.
¹Laboratory for Bioinformatics,
²Graduate School of Media and Governance,
³Department of Policy Management and
⁴Department of Environmental Information, Keio University,
⁵Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute

The codon adaptation index (CAI) values of all protein coding sequences were calculated based on the full-length cDNA libraries of Mus musculus recently generated by RIKEN. We have also computed the extent of consensus in flanking sequence of the initiator ATG codon by conducting the `relative entropy' of respective nucleotide positions (-20bp to +12bp relative to the initiator ATG codon) in some sets of genes sorted by CAI values. As a result, of the two nucleotides positions (-3 and +4) as known to be highly conserved in Kozak's consensus sequence, clear correlation between CAI values and relative entropy was observed at the position (-3) but not significant at the position (+4). We have found the significant correlation at the position (-1) of the consensus sequence instead. Furthermore though no correlation was observed in other positions, relative entropy was very high at the position (-4, -6 and -8) in genes with high CAI values. These finding suggest that the extent of conservation in flanking sequence of the initiator ATG codon including Kozak's consensus sequence was important factor to modulate the translation efficiency as well as synonymous codon usage bias particularly in highly expressed genes.