Alterations in SiRNA and MiRNA Expression Profiles Detected by Deep Sequencing of Transgenic Rice with SiRNA-Mediated Viral Resistance

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.

Analyses of RNA-Seq and sRNA-Seq data reveal a complex network of anti-viral defense in TCV-infected Arabidopsis thaliana

“…From our vsiRNAs size distribution results, 21 nt is the major size, which is different from previous result39, but in consistent with other sRNA-seq reports that performed in other types of viruses4041. This indicates the major size of vsiRNAs may vary among different viruses.…”

Differential mRNA Accumulation upon Early Arabidopsis thaliana Infection with ORMV and TMV-Cg Is Associated with Distinct Endogenous Small RNAs Level

“…Furthermore a study characterizing miRNAs promoters showed that several of them contains responsive boxes to hormones that implies that the hormones regulation is a plausible outcome in the incoherent regulation of miRNA/target pairs [ 62 ]. Finally the existence of an interference of the RISC functionality by competition with miRNAs and siRNAs pathways cannot be ruled out as suggested by Khan et al, [ 63 ] and in agreement to the recently demonstrated impact on the miRNAs level on transgenic rice plants expressing a harping construct RNAs to generate siRNAs against RSV [ 64 ]. AGO1 is proposed to be the first antiviral defense barrier while AGO2 is involved in limiting viral accumulation [ 65 ].…”

Identification and characterization of microRNAs from in vitro-grown pear shoots infected with Apple stem grooving virus in response to high temperature using small RNA sequencing

“…In plants, most miRNAs are processed specifically by the Dicer-Like 1 (DCL1) protein, and in contarst, siRNAs are cleaved by DCL2, DCL3 and DCL4. After excision, mature miRNAs or siRNAs are loaded onto the Argonaute (AGO) proteins, with other factors to assemble the RNA-induced silencing complex (RISC), guiding miRNA/siRNA to pair with specific RNA targets to implement the translational repression or silencing [ 5 – 11 ]. siRNA function is primarily to detect and eliminate invading viruses by targeting the virus-derived single strand RNA (ssRNA).…”