Structural and Functional Analysis of CMV Satellite RNAs in RNA Silencing

Viroids and satellite RNAs, which are the smallest infectious agents in plants, have noncoding RNA genomes and characteristic secondary structures. Some satellite RNAs (satRNAs) cause disease symptoms that are different from those induced by their helper virus. This phenomenon has been implicated in RNA silencing of host gene(s) as a result of sequence identity or complementarity between satRNAs and host RNAs. To investigate the effects of satRNA sequence on direct coincident interference with host gene expression, we developed a transient RNA silencing assay using protoplasts. With this protoplast system, we can induce various forms and lengths of silencing inducers at various concentrations to uniform cells without viral infection, and then we can use the satRNA-treated protoplasts in further analyses such as real-time RT-
PCR
and northern blot hybridization analyses to investigate whether the satRNA-induced symptoms are due to down-regulation of the target gene expression.