MicroRNAs (miRNAs) control the abundance of the majority of the vertebrate transcriptome. The recognition sequences, or target sites, for bilaterian miRNAs are found predominantly in the 3' untranslated regions (3'UTRs) of mRNAs, and are amongst the most highly conserved motifs within 3'UTRs. However, little is known regarding the evolutionary pressures that lead to loss and gain of such target sites. Here, we quantify the selective pressures that act upon miRNA target sites. Notably, selective pressure extends beyond deeply conserved binding sites to those that have undergone recent substitutions. Our approach reveals that even amongst ancient animal miRNAs, which exert the strongest selective pressures on 3'UTR sequences, there are striking differences in patterns of target site evolution between miRNAs. Considering only ancient animal miRNAs, we find three distinct miRNA groups, each exhibiting characteristic rates of target site gain and loss during mammalian evolution. The first group both loses and gains sites rarely. The second group shows selection only against site loss, with site gains occurring at a neutral rate, whereas the third loses and gains sites at neutral or above expected rates. Furthermore, mutations that alter the strength of existing target sites are disfavored. Applying our approach to individual transcripts reveals variation in the distribution of selective pressure across the transcriptome and between miRNAs, ranging from strong selection acting on a small subset of targets of some miRNAs, to weak selection on many targets for other miRNAs. miR-20 and miR-30, and many other miRNAs, exhibit broad, deeply conserved targeting, while several other comparably ancient miRNAs show a lack of selective constraint, and a small number, including mir-146, exhibit evidence of rapidly evolving target sites. Our approach adds valuable perspective on the evolution of miRNAs and their targets, and can also be applied to characterize other 3'UTR regulatory motifs.

中文翻译：

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整个脊椎动物进化过程中microRNA靶位的进化动力学。

MicroRNA（miRNA）控制着大多数脊椎动物转录组的丰度。双向miRNA的识别序列或目标位点主要在mRNA的3'非翻译区（3'UTR）中发现，并且是3'UTR中最保守的基序。然而，关于导致这种靶位点丢失和增加的进化压力知之甚少。在这里，我们量化了作用于miRNA靶位点的选择性压力。值得注意的是，选择性压力超出了深度保守的结合位点，延伸至最近被取代的结合位点。我们的方法表明，即使在古老的动物miRNA中，它们对3'UTR序列施加最强的选择压力，miRNA之间的靶位点进化模式也存在显着差异。仅考虑古代动物的miRNA，我们发现三个不同的miRNA组，每个组在哺乳动物进化过程中均表现出特征性的靶位点得失率。第一组很少失去和获得站点。第二组显示仅针对站点丢失的选择，站点获得以中性速率发生，而第三组丢失并获得站点以中性或高于预期速率。此外，不利于改变现有靶位点强度的突变。将我们的方法应用于单个转录本揭示了跨转录组以及miRNA之间选择性压力分布的变化，从对某些miRNA的一小部分靶标进行强选择到对其他miRNA的许多标靶进行弱选择。miR-20和miR-30以及许多其他miRNA表现出广泛的，深度保守的靶向，而其他几个相对较古老的miRNA则表现出缺乏选择性的约束，而包括mir-146在内的少数miRNA则显示出快速进化的靶位的证据。我们的方法为miRNA及其靶标的进化增添了宝贵的见解，也可用于表征其他3'UTR调控基序。