Abstract
With respect to upstream regions of microRNA (miRNA) target sites located in protein coding sequences, experimental studies have suggested rare codons, rather than frequent codons, are important for miRNA function, because they slow down the local translational process. But, whether there is a trend of reduced translation efficiency near miRNA targets is still unknown. Using Arabidopsis thaliana, we perform genome-wide analysis of synonymous codon usage in upstream regions of miRNA target sites. At the whole genome level, we find no significant selection signals for decreased translational efficiency. However, the same genome analyses do show substantial variations of translation efficiency reduction among miRNA targets. We find that miRNA conservation level, gene codon usage bias, and the mechanism of miRNA action can account for the differences in translation efficiency. But gene's GC content, gene expression level, and miRNA target's conservation level have no effect on local translation efficiency of miRNA targets. Although local translation efficiency in the upstream region of miRNA targets is related to miRNA function in A. thaliana, the selection signal of rare codon usage in that region is weak. We propose some other biological factors are more important than local translation efficiency in miRNA action when miRNA targets are located in protein coding sequences.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 565-574 |
| Number of pages | 10 |
| Journal | Evolutionary Bioinformatics |
| Volume | 2012 |
| Issue number | 8 |
| DOIs | |
| State | Published - 2012 |
| Externally published | Yes |
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Keywords
- miRNA binding
- Synonymous codons
- Translation efficiency
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Computer Science Applications
- Genetics
Cite this
Translation efficiency in upstream region of microRNA targets in Arabidopsis thaliana. / Gu, Wanjun; Zhai, Chuanying; Wang, Xiaofei; Xie, Xueying; Parinandi, Gurunadh; Zhou, Tong.
In: Evolutionary Bioinformatics, Vol. 2012, No. 8, 2012, p. 565-574.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Translation efficiency in upstream region of microRNA targets in Arabidopsis thaliana
AU - Gu, Wanjun
AU - Zhai, Chuanying
AU - Wang, Xiaofei
AU - Xie, Xueying
AU - Parinandi, Gurunadh
AU - Zhou, Tong
PY - 2012
Y1 - 2012
N2 - With respect to upstream regions of microRNA (miRNA) target sites located in protein coding sequences, experimental studies have suggested rare codons, rather than frequent codons, are important for miRNA function, because they slow down the local translational process. But, whether there is a trend of reduced translation efficiency near miRNA targets is still unknown. Using Arabidopsis thaliana, we perform genome-wide analysis of synonymous codon usage in upstream regions of miRNA target sites. At the whole genome level, we find no significant selection signals for decreased translational efficiency. However, the same genome analyses do show substantial variations of translation efficiency reduction among miRNA targets. We find that miRNA conservation level, gene codon usage bias, and the mechanism of miRNA action can account for the differences in translation efficiency. But gene's GC content, gene expression level, and miRNA target's conservation level have no effect on local translation efficiency of miRNA targets. Although local translation efficiency in the upstream region of miRNA targets is related to miRNA function in A. thaliana, the selection signal of rare codon usage in that region is weak. We propose some other biological factors are more important than local translation efficiency in miRNA action when miRNA targets are located in protein coding sequences.
AB - With respect to upstream regions of microRNA (miRNA) target sites located in protein coding sequences, experimental studies have suggested rare codons, rather than frequent codons, are important for miRNA function, because they slow down the local translational process. But, whether there is a trend of reduced translation efficiency near miRNA targets is still unknown. Using Arabidopsis thaliana, we perform genome-wide analysis of synonymous codon usage in upstream regions of miRNA target sites. At the whole genome level, we find no significant selection signals for decreased translational efficiency. However, the same genome analyses do show substantial variations of translation efficiency reduction among miRNA targets. We find that miRNA conservation level, gene codon usage bias, and the mechanism of miRNA action can account for the differences in translation efficiency. But gene's GC content, gene expression level, and miRNA target's conservation level have no effect on local translation efficiency of miRNA targets. Although local translation efficiency in the upstream region of miRNA targets is related to miRNA function in A. thaliana, the selection signal of rare codon usage in that region is weak. We propose some other biological factors are more important than local translation efficiency in miRNA action when miRNA targets are located in protein coding sequences.
KW - miRNA binding
KW - Synonymous codons
KW - Translation efficiency
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UR - http://www.scopus.com/inward/citedby.url?scp=84867113248&partnerID=8YFLogxK
U2 - 10.4137/EBO.S10362
DO - 10.4137/EBO.S10362
M3 - Article
C2 - 23071387
AN - SCOPUS:84867113248
VL - 2012
SP - 565
EP - 574
JO - Evolutionary Bioinformatics
JF - Evolutionary Bioinformatics
SN - 1176-9343
IS - 8
ER -