Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants
Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants
复制标题
选择同义位点以提高植物中 miRNA 结合位点的可及性
DOI：
10.1093/molbev/mss109
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发表时间：
2012-10-01
影响因子：
10.7
通讯作者：
Zhou, Tong
中科院分区：
文献类型：
--
作者：
Gu, Wanjun;Wang, Xiaofei;Zhou, Tong
在原核生物和真核生物中，同义密码子被广泛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靶点附近同义密码子的选择。为了更好地理解这一点，我们对四个植物基因组中miRNA靶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靶点周围的位置可及性增加的总体趋势。鸟嘌呤-胞嘧啶(GC)-贫乏密码子在miRNA靶点的侧翼区域是首选的。基因组内分析表明，不同物种的miRNA靶标之间存在显著差异。目的基因的GC含量可以部分解释miRNA靶标之间位点可及性的差异。富含GC的基因中的miRNA靶标显示出比缺乏GC的基因中更强的选择信号。基因的密码子使用偏好性和miRNA及其靶标的保守水平也对位点可及性有一定影响，但miRNA或其靶标的表达水平和miRNA活性机制并不影响不同miRNA靶标之间的位点可及性差异。我们建议选择靠近miRNA靶标的同义密码子，以实现有效的miRNA结合和适当的miRNA功能。我们的结果为植物miRNA靶点附近同义密码子的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。
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.