De novo origination of MIRNAs through generation of short inverted repeats in target genes
De novo origination of MIRNAs through generation of short inverted repeats in target genes
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通过在目标基因中生成短反向重复序列从头起源 MIRNA
DOI：
10.1080/15476286.2019.1593744
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发表时间：
2019
期刊：
影响因子：
4.1
通讯作者：
Shanfa Lu
中科院分区：
文献类型：
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作者：
Shanfa Lu
摘要微小RNA（MIRNA，MIR）基因的起源和早期进化过程，如发夹前体序列的产生、启动子活性的获得以及这两个过程的先后顺序等，是一个基础性的、令人感兴趣的研究课题。发夹前体序列的从头起源有三种模型，即反向基因复制、自发进化和转座子转座。然而，这些模式仍有待讨论。此外，MIR基因启动子的从头起源尚未得到很好的研究。在这里，我系统地研究了进化上年轻的多酚氧化酶基因（PPO）靶向MIRs的起源，包括MIR 1444，MIR 058和MIR 12112，以及一个被称为AasPPO-as-hp的基因组区域，其中包含发夹形成序列。我发现MIR 058前体和AasPPO-as-hp的发夹形成序列通过形成短反向重复序列起源于古老的PPO基因。古PPO基因中的回文样序列和不完美的反向重复序列可能通过在DNA复制过程中引起错误而促进了短反向重复序列的产生。对MIR 058和AasPPO-as-hp启动子的分析表明，它们起源于古老PPO基因的3 ′侧翼区。通过在富含AT的TATA盒样序列上游插入CAAT盒和含多铜反应元件（CuRE）的微型反向重复转座元件（MITE）获得启动子活性。启动子活性的获得发生在发夹形成序列起源之前。MIR 1444、MIR 058和MIR 12112启动子的序列比较显示CuRE频繁的出生和死亡，表明铜可能对PPO靶向MIRs的起源和进化至关重要。在此基础上，提出了一个新的植物MIR起源和进化模型。
ABSTRACT MIRNA (MIR) gene origin and early evolutionary processes, such as hairpin precursor sequence origination, promoter activity acquirement and the sequence of these two processes, are fundamental and fascinating subjects. Three models, including inverted gene duplication, spontaneous evolution and transposon transposition, have been proposed for de novo origination of hairpin precursor sequence. However, these models still open to discussion. In addition, de novo origination of MIR gene promoters has not been well investigated. Here, I systematically investigated the origin of evolutionarily young polyphenol oxidase gene (PPO)-targeting MIRs, including MIR1444, MIR058 and MIR12112, and a genomic region termed AasPPO-as-hp, which contained a hairpin-forming sequence. I found that MIR058 precursors and the hairpin-forming sequence of AasPPO-as-hp originated in an ancient PPO gene through forming short inverted repeats. Palindromic-like sequences and imperfect inverted repeats in the ancient PPO gene contributed to initiate the generation of short inverted repeats probably by causing errors during DNA duplication. Analysis of MIR058 and AasPPO-as-hp promoters showed that they originated in the 3ʹ-flanking region of the ancient PPO gene. Promoter activities were gained by insertion of a CAAT-box and multiple-copper-response element (CuRE)-containing miniature inverted-repeat transposable element (MITE) in the upstream of AT-rich TATA-box-like sequence. Gain of promoter activities occurred before hairpin-forming sequence origination. Sequence comparison of MIR1444, MIR058 and MIR12112 promoters showed frequent birth and death of CuREs, indicating copper could be vital for the origination and evolution of PPO-targeting MIRs. Based on the evidence obtained, a novel model for plant MIR origination and evolution is proposed.