Key Laboratory of Child Development and Learning Science of Ministry of Education of China, Southeast University, Nanjing, Jiangsu 210096, China.
Mol Biol Evol. 2012 Oct;29(10):3037-44. doi: 10.1093/molbev/mss109. Epub 2012 Apr 4.
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.
同义密码子在原核生物和真核生物中都被广泛选择用于各种生物学机制。最近的证据表明，microRNA（miRNA）的功能可能会影响 miRNA 靶位点附近的同义密码子选择。为了更好地理解这一点，我们在四个植物基因组中对 miRNA 靶位点附近的同义密码子使用进行了全基因组分析。我们观察到植物中 miRNA 靶位点周围的靶位区可及性增加的一般趋势。miRNA 靶位点侧翼区域偏好使用 GC 含量低的密码子。在种内的基因组分析显示，miRNA 靶标之间存在显著的变化。靶基因的 GC 含量可以部分解释 miRNA 靶标之间靶位区可及性的变化。GC 丰富基因中的 miRNA 靶标比 GC 贫乏基因中的靶标显示出更强的选择信号。基因的密码子使用偏向性和 miRNA 及其靶标的保守水平也对靶位区可及性有一定的影响，但 miRNA 或其靶标的表达水平以及 miRNA 活性的机制并不能导致 miRNA 靶标之间靶位区可及性的差异。我们认为，miRNA 靶位附近的同义密码子是为了有效地结合 miRNA 并发挥适当的 miRNA 功能而被选择的。我们的研究结果为植物中 miRNA 靶位附近的同义密码子受到自然选择提供了一个新的维度，这将对编码序列进化具有重要意义。
