International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)


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,
2
Graduate School of Media and Governance,
3
Department of Policy Management and
4
Department of Environmental Information, Keio University,
5
Laboratory 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.


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