Genome-Wide Identification of Reverse Complementary microRNA Genes in Plants

Chaogang Shao,Xiufang Xu,Xiaoxia Ma,Yijun Meng,Huizhong Wang,Baohong Zhang

doi:10.1371/journal.pone.0046991

Abstract

MicroRNAs (miRNAs) are ∼21-nucleotide small RNAs (sRNAs) with essential regulatory roles in plants. They are generated from stem-loop-structured precursors through two sequential Dicer-like 1 (DCL1)-mediated cleavages. To date, hundreds of plant miRNAs have been uncovered. However, the question, whether the sequences reverse complementary (RC) to the miRNA precursors could form hairpin-like structures and produce sRNA duplexes similar to the miRNA/miRNA* pairs has not been solved yet. Here, we interrogated this possibility in 16 plant species based on sRNA high-throughput sequencing data and secondary structure prediction. A total of 59 RC sequences with great potential to form stem-loop structures and generate miRNA/miRNA*-like duplexes were identified in ten plants, which were named as RC-miRNA precursors. Unlike the canonical miRNAs, only a few cleavage targets of the RC-miRNAs were identified in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), and none in Soybean (Glycine max) based on degradome data. Surprisingly, the genomic regions surrounding some of the RC-miRNA target recognition sites were observed to be specifically methylated in both Arabidopsis and rice. Taken together, we reported a new class of miRNAs, called RC-miRNAs, which were generated from the antisense strands of the miRNA precursors. Based on the results, we speculated that the mature RC-miRNAs might have subtle regulatory activity through target cleavages, but might possess short interfering RNA-like activity by guiding sequence-specific DNA methylation.

Highlights

MicroRNAs are small non-coding molecules discovered at the end of the last century, and their critical regulatory roles in numerous biological processes in organisms were widely recognized at the beginning of this century [1,2,3,4]
All the miRBase-registered miRNA precursors belonging to 16 different plant species (Arabidopsis lyrata, Arabidopsis thaliana, Carica papaya, Citrus sinensis, Glycine max, Gossypium arboretum, Gossypium hirsutum, Hordeum vulgare, Medicago truncatula, Oryza sativa, Populus trichocarpa, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Vitis vinifera and Zea mays) with publicly available small RNA (sRNA) high-throughput sequencing (HTS) data were included to generate reverse complementary (RC) sequences
By using accumulation- and secondary structurebased screening, 59 RC-miRNA precursor candidates were identified in ten plant species (Figure S1 and Table S3)

Summary

Introduction

MicroRNAs (miRNAs) are small non-coding molecules discovered at the end of the last century, and their critical regulatory roles in numerous biological processes in organisms were widely recognized at the beginning of this century [1,2,3,4]. The miRNA precursors should be able to form compelling stemloop structures, and the mature miRNAs should be detectable by HTS or other fine-scale experimental methods such as Northern blot. Both miRNA and the corresponding miRNA* should be cloned. MiRNAs are sorted into Argonaute 1 (AGO1)-associated miRNA-induced silencing complexes (miRISCs) in most cases. Based on these well-established notions, the structure- and accumulation-based approach was widely adopted for new miRNA gene identification

Methods

Results

Conclusion