<i>De novo</i> origination of <i>MIRNAs</i> through generation of short inverted repeats in target genes

2019-03-14T18:05:49Z (GMT) by Shanfa Lu
<p><i>MIRNA</i> (<i>MIR</i>) 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 <i>de novo</i> origination of hairpin precursor sequence. However, these models still open to discussion. In addition, <i>de novo</i> origination of <i>MIR</i> gene promoters has not been well investigated. Here, I systematically investigated the origin of evolutionarily young polyphenol oxidase gene (<i>PPO</i>)-targeting <i>MIRs</i>, including <i>MIR1444, MIR058</i> and <i>MIR12112</i>, and a genomic region termed <i>AasPPO-as-hp</i>, which contained a hairpin-forming sequence. I found that <i>MIR058</i> precursors and the hairpin-forming sequence of <i>AasPPO-as-hp</i> originated in an ancient <i>PPO</i> gene through forming short inverted repeats. Palindromic-like sequences and imperfect inverted repeats in the ancient <i>PPO</i> gene contributed to initiate the generation of short inverted repeats by causing errors during DNA duplication. Analysis of <i>MIR058</i> and <i>AasPPO-as-hp</i> promoters showed that they originated in the 3ʹ-flanking region of the ancient <i>PPO</i> 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 <i>MIR1444, MIR058</i> and <i>MIR12112</i> promoters showed frequent birth and death of CuREs, indicating copper could be vital for the origination and evolution of <i>PPO</i>-targeting <i>MIRs</i>. Based on the evidence obtained, a novel model for plant <i>MIR</i> origination and evolution is proposed.</p>