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Selection on synonymous sites for increased accessibility around miRNA binding sites in plants.

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journal contribution
posted on 26.11.2013, 00:00 by Wanjun Gu, Xiaofei Wang, Chuanying Zhai, Xueying Xie, Tong Zhou
Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on synonymous codon usage around miRNA target sites in four plant genomes. We observed a general trend of increased site accessibility around miRNA target sites in plants. Guanine-cytosine (GC)-poor codons are preferred in the flank region of miRNA target sites. Within-genome analyses show significant variation among miRNA targets in species. GC content of the target gene can partly explain the variation of site accessibility among miRNA targets. miRNA targets in GC-rich genes show stronger selection signals than those in GC-poor genes. Gene's codon usage bias and the conservation level of miRNA and its target also have some effects on site accessibility, but the expression level of miRNA or its target and the mechanism of miRNA activity do not contribute to site accessibility differences among miRNA targets. We suggest that synonymous codons near miRNA targets are selected for efficient miRNA binding and proper miRNA function. Our results present a new dimension of natural selection on synonymous codons near miRNA target sites in plants, which will have important implications of coding sequence evolution.


This work was supported by grants from the National Basic Research Program of China [2012CB316501 to WG and XX], the National High Technology Research and Development Program of China (863 Project)[2012AA020401 to WG], National Natural Science Foundation of China [30900836 and 61171143 to WG, and 61001175 to XX], and a SRF for ROCS, SEM, China


Publisher Statement

This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Molecular Biology and Evolution following peer review. The definitive publisher-authenticated version Gu WJ, Wang XF, Zhai CY, Xie XY, Zhou T. Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants. Molecular Biology and Evolution. Oct 2012;29(10):3037-3044. is available online at:


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