Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat

Juan M Crescente,Leonardo S Vanzetti,Diego Zavallo,Sebastián Asurmendi,Elmer Fernandez,Mariana Del Vas,Marcelo Helguera

doi:10.1186/s12864-022-08364-4

Abstract

BackgroundPlant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs).ResultsWe used public small RNA and degradome libraries from Triticum aestivum to screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts.ConclusionsOur results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression.

Highlights

Plant microRNA produced by a Miniature Inverted-repeat Transposable Element (MITE)-related region (miRNA) are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression
Identification and annotation of MITEs in the wheat genome To identify and annotate MITEs in the wheat genome, we started by creating a comprehensive MITE wheat database using 569 sequences from the TREP database [13] and 6,013 sequences obtained from the wheat genome using the software MITE Tracker [12]
After clustering all sequences using VSEARCH [14], a FASTA file containing 2,002 unique MITEs was obtained, where 223 elements (11%) showed high homology with elements already described in the TREP database and 1.779 (89%) displayed high homology to new elements discovered by MITE Tracker (Additional file 1)

Summary

Introduction

Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs). Each miRNA gene in a specific location gives rise to only one functional RNA. Several hypotheses have been proposed to explain the origin of miRNA genes. The more accepted ones are miRNA genes originated by inverted duplication of target genes [6] or by fortuitous foldbacks in the genomes [7]. There is increasing evidence that some miRNAs can derive from certain transposable elements (TEs) [2, 8]

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Discussion

Conclusion