Microarray and Degradome Sequencing Reveal MicroRNA Differential Expression Profiles and Their Targets in Pinellia pedatisecta

Wei Zhou,Dongfeng Yang,Tao Xu,Ke Lan,Shaowei Xu,Miao Dong,Qiulei Lang

doi:10.1371/journal.pone.0075978

Wei Zhou, Dongfeng Yang + Show 5 more

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https://doi.org/10.1371/journal.pone.0075978

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Abstract

MicroRNAs (miRNAs) are endogenous small non-coding RNAs which play a critical role in gene regulation in plants. Pinellia pedatisecta is one of the most important herbs in traditional Chinese medicine, but there are no microRNAs of Pinellia pedatisecta were deposited in miRBase and the research of the related miRNA biological functions is still insufficient. To detect Pinellia pedatisecta miRNAs and discover their expression difference with Pinellia ternata , we carried out a microarray profiling. A total of 101 miRNAs belonging to 22 miRNA families were detected both in Pinellia pedatisecta and Pinellia ternata respectively, among them 21 miRNAs showed their differentially expression. GO (gene ontology) term enrichment analysis of the target genes of differential expression miRNAs reveal that these miRNAs mainly affect the reproduction, transcription factor activity and plant developmental process. To elucidate the target function of miRNAs, we constructed a degradome library from Pinellia pedatisecta leaf. The result showed that a total of 18 transcript were identified as targets of miRNAs and further analysis indicated that miR156 and miR529 may function together to repress SPL14.

Highlights

MicroRNAs are endogenous ~21-nucleotide non-coding RNAs derived from single-stranded stem-loop RNA precursors; these RNA molecules regulate gene expression by guiding targeted mRNA cleavage or translational inhibition at the transcriptional and post-transcriptional levels [1,2]
Mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), which regulates the expression of the complementary target mRNAs via the Argonaute (AGO) endoribonucleases [3]
101 unique plant miRNAs from 22 miRNA families were commonly identified from P. pedatisecta and P. ternata

Summary

Introduction

MicroRNAs (miRNAs) are endogenous ~21-nucleotide (nt) non-coding RNAs derived from single-stranded stem-loop RNA precursors; these RNA molecules regulate gene expression by guiding targeted mRNA cleavage or translational inhibition at the transcriptional and post-transcriptional levels [1,2]. Mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), which regulates the expression of the complementary target mRNAs via the Argonaute (AGO) endoribonucleases [3]. Given that plant miRNAs usually have near-perfect complementary to their target sites in the protein-coding regions of mRNAs, most plant miRNAs function like siRNAs that guide target mRNA cleavage [7]. Based on known miRNA sequences of a plant species, It may be used for plants with limited sequence information

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