Abstract
Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.
| Original language | English |
|---|---|
| Pages (from-to) | 79-87 |
| Number of pages | 9 |
| Journal | Gene |
| Volume | 300 |
| Issue number | 1-2 |
| DOIs | |
| Publication status | Published - 2002 Oct 30 |
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Keywords
- CAI value
- CAI, Codon Adaptation Index
- Codon Adaptation Index
- Consensus sequence
- Gene expression
- Stop codon
- Translation termination efficiency
ASJC Scopus subject areas
- Genetics
Cite this
Comprehensive sequence analysis of translation termination sites in various eukaryotes. / Ozawa, Y.; Hanaoka, S.; Saito, R.; Washio, T.; Nakano, S.; Shinagawa, A.; Itoh, M.; Shibata, K.; Carninci, P.; Konno, H.; Kawai, J.; Hayashizaki, Y.; Tomita, Masaru.
In: Gene, Vol. 300, No. 1-2, 30.10.2002, p. 79-87.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Comprehensive sequence analysis of translation termination sites in various eukaryotes
AU - Ozawa, Y.
AU - Hanaoka, S.
AU - Saito, R.
AU - Washio, T.
AU - Nakano, S.
AU - Shinagawa, A.
AU - Itoh, M.
AU - Shibata, K.
AU - Carninci, P.
AU - Konno, H.
AU - Kawai, J.
AU - Hayashizaki, Y.
AU - Tomita, Masaru
PY - 2002/10/30
Y1 - 2002/10/30
N2 - Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.
AB - Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.
KW - CAI value
KW - CAI, Codon Adaptation Index
KW - Codon Adaptation Index
KW - Consensus sequence
KW - Gene expression
KW - Stop codon
KW - Translation termination efficiency
UR - http://www.scopus.com/inward/record.url?scp=0037202367&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0037202367&partnerID=8YFLogxK
U2 - 10.1016/S0378-1119(02)01042-9
DO - 10.1016/S0378-1119(02)01042-9
M3 - Article
VL - 300
SP - 79
EP - 87
JO - Gene
JF - Gene
SN - 0378-1119
IS - 1-2
ER -