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Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana

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...

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Detalles Bibliográficos
Autores principales: Gu, Wanjun, Zhai, Chuanying, Wang, Xiaofei, Xie, Xueying, Parinandi, Gurunadh, Zhou, Tong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Libertas Academica 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3469488/
https://www.ncbi.nlm.nih.gov/pubmed/23071387
http://dx.doi.org/10.4137/EBO.S10362
Descripción
Sumario: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.