Isolation and characterization of single-stranded and double-stranded RNAs in mitochondria

Detection of long and short double-stranded RNAs

In RNA interference (RNAi), long double-stranded RNAs (dsRNAs) of more than 100 nucleotides (nt) are diced into short dsRNAs (small interfering RNAs, siRNAs) of about 21-24 nt, the guide strand of which is incorporated into the RNA-induced silencing complex (RISC) that slices a specific mRNA. Consequently viral dsRNAs are known as potent inducers for RNAi, which probably originated from a defense mechanism against nucleic acid parasites. Therefore detection of long and short dsRNAs must be crucial techniques for RNAi or virus research. The methods for simple and sensitive detection of short dsRNAs (siRNAs) by northern hybridization, isolation of long dsRNAs by CF-11 cellulose chromatography, and detection of long dsRNAs by agarose gel electrophoresis and northern hybridization are described here.

RNA-dependent RNA polymerase activity associated with endogenous double-stranded RNA in rice

RNA-dependent RNA polymerase (RdRp) activity was detected in the crude microsomal fraction of rice cultured cells that contain a 14 kbp double-stranded RNA (dsRNA). RdRp activity is maximal in the presence of all four nucleotide triphosphates and Mg2+ ion and is resistant to inhibitors of DNA-dependent RNA polymerases (actinomycin D and alpha-amanitin). RdRp activity increases approximately 2.5-fold in the presence of 0.5% deoxycholate. Treatment of purified microsomal fraction with proteinase K plus deoxycholate suggests that the RdRp enzyme complex with its own 14 kb RNA template is located in vesicles. The RdRp enzyme complex was solubilized with Nonidet P-40 and purified by glycerol gradient centrifugation, then exogenous RNA templates were added. Results indicate that exogenous dsRNA reduces RNA synthesis from the endogenous 14 kb RNA template.

Enigmatic double-stranded RNA in Japonica rice

We have found a linear, 16 kb, double-stranded RNA (dsRNA) in symptomless Japonica rice (Oryza sativa L.) that is not found in Indica rice (Oryza sativa L.). The dsRNA was detected in every tissue and at every developmental stage, and its copy number was approximately constant (about 20 copies/cell). Double-stranded RNA was also detected in two strains of Oryza rufipogon (an ancestor of O. sativa). Hybridization experiments indicated that the dsRNA of O. rufipogon was homologous but not identical to that of O. sativa. The sequence of about 13.2 kb of the dsRNA was determined and two open reading frames (ORFs) were found. The larger ORF (ORF B) was more than 12,351 nucleotides long and encoded more than 4,117 amino acid residues.