Alterations in siRNA and miRNA expression profiles detected by deep sequencing of transgenic rice with siRNA-mediated viral resistance.

Cheng Guo,Xifeng Wang,Li Li,Chun Liang

doi:10.1371/journal.pone.0116175

Abstract

RNA-mediated gene silencing has been demonstrated to serve as a defensive mechanism against viral pathogens by plants. It is known that specifically expressed endogenous siRNAs and miRNAs are involved in the self-defense process during viral infection. However, research has been rarely devoted to the endogenous siRNA and miRNA expression changes under viral infection if the resistance has already been genetically engineered in plants. Aiming to gain a deeper understanding of the RNA-mediated gene silencing defense process in plants, the expression profiles of siRNAs and miRNAs before and after viral infection in both wild type and transgenic anti-Rice stripe virus (RSV) rice plants were examined by small RNA high-throughput sequencing. Our research confirms that the newly generated siRNAs, which are derived from the engineered inverted repeat construct, is the major contributor of the viral resistance in rice. Further analysis suggests the accuracy of siRNA biogenesis might be affected when siRNAs machinery is excessively used in the transgenic plants. In addition, the expression levels of many known miRNAs are dramatically changed due to RSV infection on both wild type and transgenic rice plants, indicating potential function of those miRNAs involved in plant-virus interacting process.

Highlights

MicroRNAs and small interfering RNAs are two major classes of small RNAs that play substantial roles in regulating gene expression transcriptionally and post-transcriptionally [1, 2]
The length distributions of small RNAs were shown in S1 Fig. It is clear that the majority of small RNA sequences for all 4 datasets were 20–25 nt in length
All small RNAs (sRNAs) reads that were mapped to the rice genome have been further annotated and categorized as or as a short fragment derived from miRNAs, siRNAs, rRNAs, tRNAs, and other un-annotated RNAs

Summary

Introduction

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two major classes of small RNAs (sRNAs) that play substantial roles in regulating gene expression transcriptionally and post-transcriptionally [1, 2]. They are often discussed and compared together in many studies because of sharing many common features. They are both small non-coding RNAs that target mRNAs by recognizing and binding their complementary sequences [3,4,5].

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Discussion

Conclusion