Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci

Abstract

SummaryPlant small RNAs 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 and other hairpinderived sRNAs. In this study, we produced and analyzed small RNA-seq libraries from rdr1/rdr2/rdr6 triple mutant plants. Only a small fraction of all sRNA loci were RDR1/RDR2/RDR6-independent; most of these were microRNA loci or associated with 22, 2017; 2 predicted hairpin precursors. We found 58 previously annotated microRNA loci that were reliant on RDR1, -2, or -6 function, casting doubt on their classification. We also found 38 RDR1/2/6-independent small RNA loci that are not MIRNAs or otherwise hairpin-derived, and did not fit into other known paradigms for small RNA biogenesis. These 38 small RNA-producing loci have novel biogenesis mechanisms, and are frequently located in the vicinity of protein-coding genes. Altogether, our analysis suggest that these 38 loci represent one or more new types of small RNAs in Arabidopsis thaliana.International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/238691 doi: bioRxiv preprint first posted online Dec.Significance Statement: Small RNAs regulate gene expression in plants and are produced through a variety of previously-described mechanisms. Here, we examine a set of previously undiscovered small RNA-producing loci that are produced by novel mechanisms.

Genome-Wide Identification and Coexpression Network Analysis of DNA Methylation Pathway Genes and Their Differentiated Functions in Ginkgo biloba L.

“…The major function of AtRDR1 is an anti-virus function. Using the single-stranded RNA produced by the virus, AtRDR2 is related to the synthesis of endogenous siRNAs (hsiRNAs), and AtRDR6 is involved in the formation of ta-siRNAs and nat-siRNAs [60]. In the present study, the G. biloba genome encoded three types of RDR genes, including RDR1, RDR3 and RDR6.…”

“…The function of RDRs is to synthesize the precursor of double-stranded RNA with the single-stranded RNA template [18]. There are two types of RDRs in Arabidopsis thaliana, including RDRα (AtRDR1, AtRDR2 and AtRDR6), which has been well-studied, and RDRγ (AtRDR3, AtRDR4 and AtRDR5), which still has an unknown function [60,61]. The major function of AtRDR1 is an anti-virus function.…”

Root-to-Shoot Long-Distance Mobile miRNAs Identified from Nicotiana Rootstocks

“…The mechanisms of underlying scion or rootstock phenotypic changes could be very diverse and have been extensively explored, with the focus on what signals communicate between the scion and rootstock to have their impact on phenotypes [ 67 , 69 ]. Grafting experiments combined with next-generation sequencing technology and genetic studies have shown that many sRNAs, particularly the 23–24-nt siRNAs associated with epigenetic regulation in the scion, moved into the rootstock to induce DNA methylation in the target loci [ 20 , 70 , 71 ]. In terms of scion trait modification, one recent study showed that an enhanced growth vigor conferred by the msh1 rootstock in both Arabidopsis and tomato graft progenies was due to RdDM-dependent epigenetic changes in 1380 differentially methylated genes, including many auxin-related gene pathways [ 72 ].…”

“…On the contrary, the endogenous miRNAs are RDR-independent small RNAs (sRNAs) and tend to exert their functions locally [ 19 , 20 ]. However, many studies have shown a good number of miRNAs can perform long-distance movement from a scion to a rootstock [ 21 , 22 ].…”

Introduction to Non-coding RNAs and High Throughput Sequencing

“…Examples of valid and invalid microRNA loci. Small RNA-seq data were from GSE105262 (Polydore and Axtell, 2017).Left: Arabidopsis thaliana (ath) MIR399b, a locus judged valid under the new criteria. Right: ath-MIR405a, a locus judged invalid under the new criteria.…”