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Title: Analysis of RDR1 / RDR2 / RDR6 ‐independent small RNA s in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci

Plant smallRNAs (sRNAs) modulate key physiological mechanisms through post‐transcriptional and transcriptional silencing of gene expression. SmallRNAs fall into two major categories: those are reliant onRNA‐dependentRNApolymerases (RDRs) for biogenesis and those that are not. KnownRDR1/2/6‐dependentsRNAs include phased and repeat‐associated short interferingRNAs, while knownRDR1/2/6‐independentsRNAs are primarily microRNAs (miRNA) and other hairpin‐derivedsRNAs. In this study we produced and analyzedsRNA‐seq libraries fromrdr1/rdr2/rdr6triple mutant plants. We found 58 previously annotated miRNAloci that were reliant onRDR1, ‐2, or ‐6function, casting doubt on their classification. We also found 38RDR1/2/6‐independentsRNAloci that are notMIRNAs or otherwise hairpin‐derived, and did not fit into other known paradigms forsRNAbiogenesis. These 38sRNA‐producing loci have as‐yet‐undescribed biogenesis mechanisms, and are frequently located in the vicinity of protein‐coding genes. Altogether, our analysis suggests that these 38 loci represent one or more undescribed types ofsRNAinArabidopsis thaliana.

Publication Date:
Journal Name:
The Plant Journal
Page Range or eLocation-ID:
p. 1051-1063
Sponsoring Org:
National Science Foundation
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