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AGO1-dependent Small RNA in Arabidopsis Identified by High-Throughput Sequencing

ABSTRACT: The goal of this study was to identify AGO1-dependent miRNA and tasiRNA in Arabidopsis by sequencing small RNA from wild type (Col-0) and ago1-25 plants. Keywords: Small RNA

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE13605 | GEO | 2008/11/17

SECONDARY ACCESSION(S): PRJNA110625

REPOSITORIES: GEO

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AGO1-dependent Small RNA in Arabidopsis Identified by High-Throughput Sequencing

Project description:The goal of this study was to identify AGO1-dependent miRNA and tasiRNA in Arabidopsis by sequencing small RNA from wild type (Col-0) and ago1-25 plants. Keywords: Small RNA Sequencing-by-synthesis technology was used to sequence small RNA from flower tissue (stages 1-12) from wild-type (Col-0) and ago1-25 Arabidopsis thaliana plants. Three biological replicates were sequenced for both Col-0 and ago1-25.

2008-11-17 | E-GEOD-13605 | biostudies-arrayexpress

Incorporation of transposable element small RNAs into the Arabidopsis AGO1 protein

Project description:Background: Transposable element 24 nucleotide small RNAs are not efficiently incorporated into the AGO1 protein, which is involved in endogenous RNAi and gene regulation through the microRNA and tasiRNA pathways. Results: The AGO1 protein incorporates large quantities of transposable element siRNAs when transposable elements are epigenetically activated and transcribed. The incorporation of transposable element siRNAs is at the expense of the most abundant microRNAs. These transposable element siRNAs can act as tasiRNAs, regulating genes that they have partial complementarity to. Conclusion: Transposable element small RNAs are more dynamic than previously thought. They can be incorporated into AGO1 and regulate genes.

2014-04-07 | GSE45990 | GEO

Incorporation of transposable element small RNAs into the Arabidopsis AGO1 protein

2014-04-07 | E-GEOD-45990 | biostudies-arrayexpress

Profiling of total and AGO1-associated small RNAs in Col-0 wild type, rns2-2 and rns2-3 flowers

Project description:Sequencing of small RNA libraries prepared from total RNA or RNA extracted from immuno affinity purified AGO1 from Col-0, rns2-2 and rns2-3 flowers. The aim of this experiment was to compare profiles of small RNA expression between Col-0 (wild type) and mutants of the ribonuclease T2 rns2-2 rns2-3 genotypes and characterize AGO1-bound small RNAs in the same genotypes. Two biological replicates of each genotype were prepared and analyzed.

2020-01-01 | E-MTAB-8493 | biostudies-arrayexpress

Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

Project description:To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.

2007-02-01 | E-GEOD-6682 | biostudies-arrayexpress

Expression data in Arabidopsis ago1-25 and hyl1-2 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis ago1-25 and hyl1-2 mutants.

2009-12-02 | GSE15699 | 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 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

Genome-wide maps of AGO1-bound small RNA in Arabidopsis leaves

Project description:We report flg22 regulate the accumulation of AGO1-bound small RNA in arabidopsis. We find that a number of miRNAs are up- or down-regulated by flg22, a well-studied PAMP. Examination of AGO1-bound small RNAs with or without flg22 treatment.

2010-02-25 | E-GEOD-20448 | biostudies-arrayexpress

Arabidopsis thaliana small RNA from epidermis and vasculature tissues of Col-0 and ago1 mutants leaves

Project description:Arabidopsis thaliana small RNA from epidermis and vasculature tissues of Col-0 and ago1 mutants leaves

| PRJNA601474 | ENA