TY - JOUR
T1 - Correlation between sequence conservation of the 5′ untranslated region and codon usage bias in Mus musculus genes
AU - Sakai, Hiroaki
AU - Washio, Takanori
AU - Saito, Rintaro
AU - Shinagawa, Akira
AU - Itoh, Masayoshi
AU - Shibata, Kazuhiro
AU - Carninci, Piero
AU - Konno, Hideaki
AU - Kawai, Jun
AU - Hayashizaki, Yoshihide
AU - Tomita, Masaru
N1 - Funding Information:
This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas ‘Genome Science’ from the Ministry of Education, Science, Sports and Culture in Japan. This study has also been supported by a Research Grant for the RIKEN Genome Exploration Research Project from the Science and Technology Agency of the Japanese Government, CREST(Core Research for Evolutional Science and Technology) and ACT-JST (Research and Development for Applying Advanced Computational Science and Technology) of the Japan Science and Technology Corporation (JST) to Y.H. This work was also supported by a Grant-in-Aid for Scientific Research on Priority Areas and the Human Genome Program from the Ministry of Education, Science and Culture to Y.H. We thank Yusuke Ohkuma and Chiaki Imamura for their help with computer programming.
PY - 2001/10/3
Y1 - 2001/10/3
N2 - 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.
AB - 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.
KW - Codon adaptation index
KW - Relative entropy
KW - Translation efficiency
KW - cDNA
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U2 - 10.1016/S0378-1119(01)00671-0
DO - 10.1016/S0378-1119(01)00671-0
M3 - Article
C2 - 11591476
AN - SCOPUS:0035802429
VL - 276
SP - 101
EP - 105
JO - Gene
JF - Gene
SN - 0378-1119
IS - 1-2
ER -