Translation efficiency in upstream region of microRNA targets in Arabidopsis thaliana

Wanjun Gu, Chuanying Zhai, Xiaofei Wang, Xueying Xie, Gurunadh Parinandi, Tong Zhou

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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 languageEnglish (US)
Pages (from-to)565-574
Number of pages10
JournalEvolutionary Bioinformatics
Issue number8
StatePublished - 2012


  • Synonymous codons
  • Translation efficiency
  • miRNA binding

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications


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