Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
Department of Biology, Elon University, Elon, North Carolina, United States of America.
PLoS Genet. 2020 Feb 3;16(2):e1008285. doi: 10.1371/journal.pgen.1008285. eCollection 2020 Feb.
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.
微小 RNA（miRNA）控制着大多数脊椎动物转录组的丰度。双边动物 miRNA 的识别序列或靶位点主要存在于 mRNA 的 3'非翻译区（3'UTR）中，并且是 3'UTR 中最高度保守的基序之一。然而，对于导致这些靶位点丢失和获得的进化压力知之甚少。在这里，我们量化了作用于 miRNA 靶位点的选择压力。值得注意的是，选择压力不仅延伸到深度保守的结合位点，还延伸到最近发生替换的那些结合位点。我们的方法揭示了即使在对 3'UTR 序列施加最强选择压力的古老动物 miRNA 中，miRNA 之间靶位点进化模式也存在显著差异。仅考虑古老的动物 miRNA，我们发现了三个不同的 miRNA 组，每个组在哺乳动物进化过程中都表现出明显不同的靶位点获得和丢失率。第一组很少丢失和获得靶位点。第二组仅表现出对靶位点丢失的选择，靶位点获得率呈中性，而第三组以中性或高于预期的速率丢失和获得靶位点。此外，改变现有靶位点强度的突变是不利的。将我们的方法应用于单个转录本揭示了选择性压力在转录组和 miRNA 之间的分布存在差异，从一些 miRNA 的一小部分靶位上的强选择到其他 miRNA 的许多靶位上的弱选择不等。miR-20 和 miR-30 以及许多其他 miRNA 表现出广泛而深度保守的靶向，而其他一些相对古老的 miRNA 则缺乏选择性约束，少数 miRNA，包括 mir-146，表现出快速进化的靶位点的证据。我们的方法为 miRNA 及其靶标的进化提供了有价值的视角，并且还可以应用于表征其他 3'UTR 调节基序。
