PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation

Abstract

Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.

Predicting symptom severity in PSTVd‐infected tomato plants using the PSTVd genome sequence

“…However, it should be noted that the algorithm is based on the hypothesis that vd‐sRNA affects the host genome and transcripts through RNA silencing, although no study to date provides conclusive evidence that vd‐sRNA can directly induce host transcript cleavage. Additionally, recent studies have reported that PSTVd may disrupt global alternative splicing of host transcripts (Zheng et al., 2017 ), alter global host genome methylation patterns (Tselika et al., 2023 ), and interfere with the host's endogenous factors involved in replication and transport (Ma et al., 2023 ). Thus, viroid pathogenicity extends beyond simple disruptions of gene regulations via RNA silencing.…”