skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


  • NSF Public Access
  • Search Results
  • Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis
Title: Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis
RNA silencing pathways control eukaryotic gene expression transcriptionally or posttranscriptionally in a sequence-specific manner. In RNA silencing, the production of double-stranded RNA (dsRNA) gives rise to various classes of 20–24 nucleotide (nt) small RNAs (smRNAs). In Arabidopsis thaliana, smRNAs are often derived from long dsRNA molecules synthesized by one of the six genomically encoded RNA-dependent RNA Polymerase (RDR) proteins. However, the full complement of the RDR-dependent smRNAs and functions that these proteins and their RNA-binding cofactors play in plant RNA silencing has not been fully uncovered. To address this gap, we performed a global genomic analysis of all six RDRs and two of their cofactors to find new substrates for RDRs and targets of the resulting RDR-derived siRNAs to uncover new functions for these proteins in plants. Based on these analyses, we identified substrates for the three RDRγ clade proteins (RDR3–5), which had not been well-characterized previously. We also identified new substrates for the other three RDRs (RDR1, RDR2, and RDR6) as well as the RDR2 cofactor RNA-directed DNA methylation 12 (RDM12) and the RDR6 cofactor suppressor of gene silencing 3 (SGS3). These findings revealed that the target substrates of SGS3 are not limited to those solely utilized by RDR6, but that this protein seems to be a more general cofactor for the RDR family of proteins. Additionally, we found that RDR6 and SGS3 are involved in the production of smRNAs that target transcripts related to abiotic stresses, including water deprivation, salt stress, and ABA response, and as expected the levels of these mRNAs are increased in rdr6 and sgs3 mutant plants. Correspondingly, plants that lack these proteins (rdr6 and sgs3 mutants) are hypersensitive to ABA treatment, tolerant to high levels of PEG8000, and have a higher survival rate under salt treatment in comparison to wild-type plants. In total, our analyses have provided an extremely data-rich resource for uncovering new functions of RDR-dependent RNA silencing in plants, while also revealing a previously unexplored link between the RDR6/SGS3-dependent pathway and plant abiotic stress responses.  more » « less
Award ID(s):
1849708 2023310
PAR ID:
10232791
Author(s) / Creator(s):
; ; ; ; ;
Date Published:
Journal Name:
Non-Coding RNA
Volume:
7
Issue:
2
ISSN:
2311-553X
Page Range / eLocation ID:
28
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. (, Molecular Plant)
    Abscisic acid (ABA) is an essential plant hormone that regulates multiple aspects of plant development and numerous abiotic stress responses (Cutler et al., 2010; Waadt et al., 2022). In fact, at the heart of plants’ responses to stresses such as salinity, drought, and hypertonic conditions, among others, is this phytohormone (Cutler et al., 2010; Waadt et al., 2022). Interestingly, stress-triggered and developmental responses to this hormone have been found to involve basic RNA metabolism components, including the two subunits of the nuclear cap-binding complex, ABA HYPERSENSITIVE1 (ABH1/CBP80) and CBP20 (Hugouvieux et al., 2001). Additionally, multiple lines of evidence have linked small RNA (smRNA)-mediated RNA silencing to ABA responses (Gregory et al., 2008; Laubinger et al., 2008). A new study by Yan et al. (2025) has provided new insights regarding how RNA degradation and silencing factors modulate smRNA biogenesis from NITRATE REDUCTASE1/2 transcripts to affect ABA-regulated abiotic stress responses. 
    more » « less
  2. ; ; ; ; ; (, bioRxiv)
    ABSTRACT RNAs in circulation carry sequence-specific regulatory information between cells in plant, animal, and host-pathogen systems. Such RNA can cross generational boundaries, as evidenced by somatic double-stranded RNA (dsRNA) in the nematodeC. eleganssilencing genes of matching sequence in progeny. Here we dissect the intergenerational path taken by dsRNA from parental circulation and discover that cytosolic import through the dsRNA importer SID-1 in the parental germline and/or developing progeny varies with developmental time and dsRNA substrates. Loss of SID-1 enhances initiation of heritable RNA silencing within the germline and causes changes in the expression of thesid-1-dependentgenesdg-1that last for more than 100 generations after restoration of SID-1. The SDG-1 protein is enriched in perinuclear Z granules required for heritable RNA silencing but is expressed from a retrotransposon targeted by such silencing. This auto-inhibitory loop reveals how retrotransposons could persist by hosting genes that regulate their own silencing. 
    more » « less
  3. ; (, Annual Review of Entomology)
    The RNA interference (RNAi) triggered by short/small interfering RNA (siRNA) was discovered in nematodes and found to function in most living organisms. RNAi has been widely used as a research tool to study gene functions and has shown great potential for the development of novel pest management strategies. RNAi is highly efficient and systemic in coleopterans but highly variable or inefficient in many other insects. Differences in double-stranded RNA (dsRNA) degradation, cellular uptake, inter- and intracellular transports, processing of dsRNA to siRNA, and RNA-induced silencing complex formation influence RNAi efficiency. The basic dsRNA delivery methods include microinjection, feeding, and soaking. To improve dsRNA delivery, various new technologies, including cationic liposome–assisted, nanoparticle-enabled, symbiont-mediated, and plant-mediated deliveries, have been developed. Major challenges to widespread use of RNAi in insect pest management include variable RNAi efficiency among insects, lack of reliable dsRNA delivery methods, off-target and nontarget effects, and potential development of resistance in insect populations. 
    more » « less
  4. ; ; ; ; ; ; ; ; ; ; et al (, Journal of Integrative Plant Biology)
    ABSTRACT One of the most promising tools for the control of fungal plant diseases is spray‐induced gene silencing (SIGS). In SIGS, small interfering RNA (siRNA) or double‐stranded RNA (dsRNA) targeting essential or virulence‐related pathogen genes are exogenously applied to plants and postharvest products to trigger RNA interference (RNAi) of the targeted genes, inhibiting fungal growth and disease. However, SIGS is limited by the unstable nature of RNA under environmental conditions. The use of layered double hydroxide or clay particles as carriers to deliver biologically active dsRNA, a formulation termed BioClay™, can enhance RNA durability on plants, prolonging its activity against pathogens. Here, we demonstrate that dsRNA delivered as BioClay can prolong protection against Botrytis cinerea , a major plant fungal pathogen, on tomato leaves and fruit and on mature chickpea plants. BioClay increased the protection window from 1 to 3 weeks on tomato leaves and from 5 to 10 days on tomato fruits, when compared with naked dsRNA. In flowering chickpea plants, BioClay provided prolonged protection for up to 4 weeks, covering the critical period of poding, whereas naked dsRNA provided limited protection. This research represents a major step forward for the adoption of SIGS as an eco‐friendly alternative to traditional fungicides. 
    more » « less
  5. ; ; ; ; ; ; ; ; ; ; et al (, Plant Biotechnology Journal)
    Summary Recent discoveries show that fungi can take up environmental RNA, which can then silence fungal genes through environmental RNA interference. This discovery prompted the development of Spray‐Induced Gene Silencing (SIGS) for plant disease management. In this study, we aimed to determine the efficacy of SIGS across a variety of eukaryotic microbes. We first examined the efficiency of RNA uptake in multiple pathogenic and non‐pathogenic fungi, and an oomycete pathogen. We observed efficient double‐stranded RNA (dsRNA) uptake in the fungal plant pathogensBotrytis cinerea,Sclerotinia sclerotiorum,Rhizoctonia solani,Aspergillus nigerandVerticillium dahliae, but no uptake inColletotrichum gloeosporioides, and weak uptake in a beneficial fungus,Trichoderma virens. For the oomycete plant pathogen,Phytophthora infestans, RNA uptake was limited and varied across different cell types and developmental stages. Topical application of dsRNA targeting virulence‐related genes in pathogens with high RNA uptake efficiency significantly inhibited plant disease symptoms, whereas the application of dsRNA in pathogens with low RNA uptake efficiency did not suppress infection. Our results have revealed that dsRNA uptake efficiencies vary across eukaryotic microbe species and cell types. The success of SIGS for plant disease management can largely be determined by the pathogen’s RNA uptake efficiency. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email