Smith Lisa M, Burbano Hernán A, Wang Xi, Fitz Joffrey, Wang George, Ural-Blimke Yonca, Weigel Detlef
Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany.
Plant J. 2015 Feb;81(4):597-610. doi: 10.1111/tpj.12754. Epub 2015 Jan 21.
MicroRNAs (miRNAs) are short RNAs involved in gene regulation through translational inhibition and transcript cleavage. After processing from imperfect fold-back structures, miRNAs are incorporated into RNA-induced silencing complexes (RISCs) before targeting transcripts with varying degrees of complementarity. Some miRNAs are evolutionarily deep-rooted, and sequence complementarity with their targets is maintained through purifying selection. Both Arabidopsis and Capsella belong to the tribe Camelineae in the Brassicaceae, with Capsella rubella serving as an outgroup to the genus Arabidopsis. The genome sequence of C. rubella has recently been released, which allows characterization of its miRNA complement in comparison with Arabidopsis thaliana and Arabidopsis lyrata. Through next-generation sequencing, we identify high-confidence miRNA candidates specific to the C. rubella lineage. Only a few lineage-specific miRNAs have been studied for evolutionary constraints, and there have been no systematic studies of miRNA target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in miRNAs and their targets within A. thaliana, and between A. thaliana, A. lyrata and C. rubella. We document a surprising amount of small-scale variation in miRNA-target pairs, where many miRNAs are predicted to have species-specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many miRNA-target pairs can be observed even on a relatively short evolutionary time-scale, with non-random occurrences of differences in miRNAs and their complements in the miRNA precursors, the miRNA* sequences.
微小RNA（miRNA）是一类短RNA，通过翻译抑制和转录本切割参与基因调控。从不完全回折结构加工后，miRNA在靶向具有不同程度互补性的转录本之前被整合到RNA诱导沉默复合体（RISC）中。一些miRNA在进化上根深蒂固，并且通过纯化选择维持与其靶标的序列互补性。拟南芥和荠菜都属于十字花科的亚麻荠族，其中风疹荠菜是拟南芥属的外类群。风疹荠菜的基因组序列最近已公布，这使得可以将其miRNA互补序列与拟南芥和琴叶拟南芥进行比较分析。通过新一代测序，我们鉴定出了风疹荠菜谱系特有的高可信度miRNA候选物。目前仅对少数谱系特异性miRNA的进化限制进行了研究，尚未对近缘植物物种内miRNA靶标的多样性或它们之间的差异进行系统研究。因此，我们比较了拟南芥内以及拟南芥、琴叶拟南芥和风疹荠菜之间miRNA及其靶标的序列变异。我们记录了miRNA-靶标对中惊人数量的小规模变异，其中许多miRNA除了具有物种间共享的靶标外，还被预测具有物种特异性靶标。我们的结果强调，即使在相对较短的进化时间尺度上，也可以观察到许多miRNA-靶标对的传递性质，miRNA及其在miRNA前体中的互补序列（miRNA*序列）存在非随机差异。
