GSE105262
Comprehensive Analysis of RDR1/2/6-independent Small RNAs in Arabidopsis thaliana
Plant small RNAs (sRNAs) regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren't. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs (miRNAs) and other hairpin-derived sRNAs. In this study, we produced and analyzed sRNA-seq libraries produced from rdr1/rdr2/rdr6 triple mutant plants.  We found 58 previously annotated MIRNA loci that were dependent on RDR function, casting doubt on their classification as MIRNAs.  We also found 38 RDR-independent sRNA clusters that were not MIRNAs or otherwise hairpin-derived. These 38 sRNA loci have novel biogenesis mechanisms, and frequently arise from protein-coding genes.  Altogether, our analysis suggests that these 38 sRNA loci represent one or more new types of sRNA loci in Arabidopsis thaliana. Overall design: Small RNA sequencing from Arabidopsis thaliana wild-type (Col-0 ecotype) and rdr1-1/rdr2-1/rdr6-15 triple mutant inflorescences