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Identification of microRNA targets in Arabidopsis by transcriptome profiling of wild-type and ago1-27 mutant plants

ABSTRACT: The goal of this study is to establish the global gene expression profiles of Arabidopsis wild type and ago1-27 mutant plants, and identify novel potential miRNA targets.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE77211 | GEO | 2016/01/30

SECONDARY ACCESSION(S): PRJNA309714

REPOSITORIES: GEO

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Degradome sequencing of Arabidopsis ago1-27 mutant

Project description:The goal of this study is to globally identify miRNA/siRNA cleavage sites on mRNAs in Arabidopsis wild type and ago1-27 mutant.

2017-10-23 | GSE84728 | GEO

Identification of microRNA targets in Arabidopsis by transcriptome profiling of wild-type and ago1-36 mutant plants

Project description:The goal of this study is to establish the global gene expression profiles of Arabidopsis wild type and ago1-36 mutant plants, and identify novel potential miRNA targets.

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Effect of submergence on wild-type (Col-0) and ago1-27 mutant

Project description:Hypoxia exerts major effects on gene expression, which is reconfigured to meet the needs of the stressed plant. In the recent years the mechanisms of oxygen sensing and transcriptional regulation of a cluster of anaerobic genes was described. We utilized a hypomorphic, post-transcriptional gene silencing defective ARGONAUTE1 (AGO1) mutant, ago1-27, to evaluate the contribution of AGO1 to plant tolerance to submergence and its effects on gene expression.

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Transcriptome comparison of Col-0, se-1, ago1-27 and se-1 35S::MIR156 in Arabidopsis thaliana.

Project description:Microarray analysis of wild type plants and plants with reduced (ago1-27 and se-1) or increased miR156 levels (se-1 p35S:MIR156). Shoot apices were dissected from 20-day-old, short-day grown plants.

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Total and AGO1 immunoprecipitated small RNA from Arabidopsis thaliana wild-type and ago1-57 mutant

Project description:In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role[AQ1] in microRNA (miRNA) and small interfering RNA (siRNA)- mediated silencing and is a key component in antiviral responses. The polerovirus F-box P0 protein triggers AGO1 degradation as a viral counterdefense. Here, we identified a motif in AGO1 that is required for its interaction with the S phase kinase-associated protein1-cullin 1-F-box protein (SCF) P0 (SCFP0) complex and subsequent degradation. The AGO1 P0 degron is conserved and confers P0-mediated degradation to other AGO[AQ2] proteins. Interestingly, the degron motif is localized in the DUF1785 domain of AGO1, in which a single point mutation (ago1-57, obtained by forward genetic screening) compromises recognition by SCFP0. Recapitulating formation of the RNA-induced silencing complex in a cell-free system revealed that this mutation impairs RNA unwinding, leading to stalled forms of AGO1 still bound to double-stranded RNAs. In vivo, the DUF1785 is required for unwinding perfectly matched siRNA duplexes, but is mostly dispensable for unwinding imperfectly matched miRNA duplexes. Consequently, its mutation nearly abolishes phased siRNA production and sense transgene posttranscriptional gene silencing. Overall, our work sheds new light on the mode of AGO1 recognition by P0 and the in vivo function of DUF1785 in RNA silencing.

2018-06-22 | GSE104015 | GEO

Effect of submergence on wild-type (Col-0) and ago1-27 mutant

Project description:Effect of submergence on wild-type (Col-0) and ago1-27 mutant

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Arabidopsis thaliana AGO1 immunoprecipitated small RNA from Col0 plants transformed with a transgene expressing wild-type or a nuclear localized form of AGO1 fused to GFP.

Project description:Plant microRNAs undergo stepwise-nuclear maturation before engaging cytosolic sequence-complementary transcripts in association with the silencing-effector protein ARGONAUTE1(AGO1). How plant miRNAs translocate to the cytosol remains mysterious as does their cellular loading site(s) into AGO1. Here, we show that the N-termini of plant AGO1s contain a nuclear-localization (NLS) and nuclear-export signal (NES), which, in Arabidopsis thaliana (At) enables AtAGO1 nucleo-cytosolic shuttling in a Leptomycin-B-inhibited manner, diagnostic of CRM1(Expo1)/NES-dependent nuclear export. Nuclear-only AtAGO1 contains the same 2’O-methylated miRNA cohort as its nucleo-cytosolic counterpart, but specifically interacts with the miRNA loading-chaperone HSP90. AtAGO1 nucleo-cytosolic shuttling is required for mature miRNA translocation and for miRNA-mediated silencing. We propose that plant miRNAs are matured, methylated, loaded into AGO1 in the nucleus, and exported cytoplasmically as AGO1:miRNA complexes in a CRM1(Expo1)/NES-dependent manner.

2018-01-04 | GSE100395 | GEO

The Arabidopsis F-box protein FBW2 degrades AGO1 to avoid spurious loading of illegitimate small RNA

Project description:RNA silencing is a conserved mechanism in eukaryotes and is involved in development, heterochromatin maintenance and defense against viruses. In plants, ARGONAUTE1 (AGO1) protein plays a central role in both microRNA (miRNA) and small interfering RNA (siRNA)-directed silencing and its expression is regulated at multiple levels. Here, we report that the F-box protein FBW2 targets proteolysis of AGO1 by a CDC48-mediated mechanism. We found that FBW2 assembles an SCF complex that recognizes the MID-PIWI domain of AGO1 and requires its C-terminal domain containing a GW motif for AGO1 turnover. We showed that FBW2 has a preference for the unloaded and for some mutated forms of AGO1 protein. While FBW2 loss of function does not lead to strong growth or developmental defects, it significantly increases RNA silencing activity. Interestingly, under conditions in which small RNA production or accumulation is affected, the failure to degrade AGO1 in fbw2 mutants becomes more deleterious for the plant. Hence, we showed that the non-degradable AGO1 protein assembles high molecular complexes and binds illegitimate small RNA leading to the cleavage of new target genes that belong to stress responses and cellular metabolic processes. Therefore, the control of AGO1 homeostasis by ubiquitin ligases, plays an important quality control to avoid off-target cleavage.

2022-04-01 | PXD024840 | Pride

Total and AGO1 immuniprecipitated small RNA from Arabidopsis thaliana WT and ago1-57 mutant, mock and TuYV infected rosette leaves

Project description:In plants and some animal lineages, RNA silencing is an efficient and adaptable defense mechanism against viruses. To counter it, viruses encode suppressor proteins that interfere with RNA silencing. Phloem-restricted viruses are spreading at an alarming rate and cause substantial reduction of crop yield, but how they interact with their hosts at the molecular level is still insufficiently understood. Here, we investigate the antiviral response against phloem-restricted turnip yellows virus (TuYV) in the model plant Arabidopsis thaliana. Using a combination of genetics, deep sequencing, and mechanical vasculature enrichment, we show that the main axis of silencing active against TuYV involves 22-nt vsiRNA production by DCL2, and their preferential loading into AGO1. Moreover, we identify vascular secondary siRNA produced from plant transcripts and initiated by DCL2-processed AGO1-loaded vsiRNA Unexpectedly, and despite the viral encoded VSR P0 previously shown to mediate degradation of AGO proteins, vascular AGO1 undergoes specific post-translational stabilization during TuYV infection. Collectively, our work uncovers the complexity of antiviral RNA silencing against phloem-restricted TuYV and prompts a re-assessment of the role of its suppressor of silencing P0 during genuine infection.

2021-11-10 | GSE176378 | GEO

Root cell layer specific AGO1-bound sRNA and total sRNA from Arabidopsis ktn1 mutant

Project description:We profiled total sRNA and root cell layer specific AGO1-bound sRNA in ktn1 mutant to study the role of KTN1 in miRNA non-cell autonomous activiy in Arabidopsis.

2022-03-21 | GSE168805 | GEO

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