A highly specific microRNA‐mediated mechanism silences LTR retrotransposons of strawberry

Abstract

SUMMARYSmall RNAs are involved in a plethora of functions in plant genomes. In general, transcriptional gene silencing is mediated by 24-nucleotide siRNAs and is required for maintaining transposable elements in a silenced state. However, microRNAs are not commonly associated with transposon silencing. In this study, we performed small RNA transcriptome and degradome analyses of the Rosaceae model plant Fragaria vesca (the woodland strawberry) at the genome-wide level, and identified miRNA families and their targets. We report a highly specific mechanism of LTR retrotransposon silencing mediated by an abundant, ubiquitously expressed miRNA (fve-miR1511) generated from a single locus. This miRNA specifically targets LTR retroelements, silencing them post-transcriptionally by perfectly pairing to the highly conserved primer binding site for methionyl initiator tRNA that is essential for reverse transcription. We investigated the possible origins of this miRNA, and present evidence that the pre-miR1511 hairpin structure probably derived from a locus coding for tRNA iMet through a single microinversion event. Our study shows that this miRNA targets retrotransposons specifically and constitutively, and contributes to features such as genome stability, size and architecture in a far more direct way than previously thought.

tRNA-derived small RNAs target transposable element transcripts

“…Mutations in a subunit of RNaseP (involved in the processing of the 5΄ trailer of tRNA precursors) in Drosophila leads to sterility due to activation of DNA damage checkpoint proteins and TE reactivation coupled with piRNA source collapse ( 43 ). Moreover, two miRNAs (miR1511 and miR845, known to target LTR retrotransposons) ( 44 ) have precursors that have an evolutionary origin in the tRNA MetCAT ( 45 ). Interestingly, here we found that the tRNA MetCAT by itself produces a 19 nt tRF-5 that directly targets the LTR retrotransposon Athila6A .…”

Identification of Conserved and Novel MicroRNAs in Blueberry

“…Recently, high-throughput sequencing technology resulted in a sharp increase in the magnitude of genome information and gene expression profiles. Many studies have shown that miRNAs possess important regulatory roles in the process of fruit development and ripening (Zeng et al, 2015; Šurbanovski et al, 2016). Firstly, several expression profile studies indicated that numerous miRNAs are exclusively or preferentially expressed in fruits (Liu et al, 2014).…”

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

“…For example, in the preprocessing of DGE datasets, filtering out singleton reads is frequently included [46–48]. For the sRNA module, screening out reads based on alignment with noncoding RNA databases (such as tRNA, rRNA, and snoRNA) [49, 50] is under development. Adding statistics such as per-read quality distribution and length distribution is also worth consideration.…”