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Expression profiling in silencing suppressor plants or in mirna mutants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

ABSTRACT: gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages. Keywords: gene knock in (transgenic),gene knock out

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE26739 | GEO | 2011/08/23

SECONDARY ACCESSION(S): PRJNA136325

REPOSITORIES: GEO

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gene profiling in silencing suppressor plants or in mirna mutants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

Project description:gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages. Keywords: gene knock in (transgenic),gene knock out

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gene profiling in silencing suppressor plants or in mirna mutants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

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Expression profiling in silencing suppressor plants or in mirna mutants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing

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silencing mutants-Transcriptome analysis of silencing mutants and endogenous hairpin KO insertion.

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NGS of sRNA reads in plants

Project description:Previous works had found correlation between the association of small RNAs (sRNAs) to Potyvirus HCPro variants in infected plants, and their abilities to suppress silencing. Moreover, we had shown a preference by HCPro for sRNAs of 21-22 nt with 5´-end adenines, and of viral sequence. Conformational properties can explain preferences for sRNAs by size and/or 5´-ends, but preference for sRNAs of viral over plant sequence would require their having different accessibilities to the suppressor, or chemical properties. To investigate this, we expressed suppressor-competent and –deficient HCPro variants by agro-infiltration or from potex- and potyviral vectors and characterized the sRNAs in infiltrated tissues and associated to the purified proteins. In input infiltrated or virus-infected tissues, methylation levels in selected sRNAs of either T-DNA or plant sequence were assessed, and the former were found significantly less methylated in the presence of suppression-competent HCPro. In purified preparations of suppression-competent HCPro, sRNAs of non-plant sequence of 21 ntwere selectively enriched in those having 5´-end adenines. Our data indicate that the ratio of sRNAs of plant vs. non-plant sequence associated to HCPro is influenced by the context in its expression, and suggest that also by a concurrent interference by HCPro on the methylation of newly generated sRNAs of non-plant sequence.

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silencing mutants-Transcriptome analysis of silencing mutants and endogenous hairpin KO insertion.

2010-09-14 | E-GEOD-23915 | biostudies-arrayexpress

Potato virus Y HCPro suppression of antiviral silencing in Nicotiana benthamiana plants correlates with its ability to bind in vivo to small RNAs of 21 and 22 nucleotides in length of viral sequence

Project description:We have investigated short and small RNAs (sRNAs) that were bound to a biologically active hexahistidine-tagged Potato virus Y (PVY) HCPro suppressor of silencing, expressed from a heterologous virus vector in Nicotiana benthamiana plants, and purified under non-denaturing conditions. We found that RNAs in purified preparations were differentially enriched in sRNAs of 21 and to a much lesser extent of 22 nucleotides (nt) in length and of viral sequence (vsRNAs) when compared to those found in a control plant protein background bound to the nickel resin in the absence of HCPro, or in a purified alanine substitution HCPro mutant (HCPro mutB) control that lacked suppressor of silencing activity. In both controls, sRNAs were composed almost entirely by molecules of plant sequence, indicating that the resin-bound protein background had no affinity for vsRNAs, and also that HCPro mutB failed to bind to vsRNAs. Therefore, PVY HCPro suppressor activity correlated with its ability to bind to 21 and 22 nt vsRNAs. HCPro constituted at least 54 % of the total protein content in purified preparations and we were able to calculate its contribution to the 21 and the 22 nt pool of sRNAs present in the purified samples and its binding strength relative to the background. We also found that in the 21 nt vsRNAs of the HCPro preparation 5´ terminal adenines were overrepresented relative to the controls, but not in vsRNAs of other sizes or of plant sequence.

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comparisons wt-mutants 1 et 3-Gene profiling upon biotic stress treatment. Gene profiling in microRNA mutants.

Project description:rs06-06_mirna - comparisons wt-mutants 1 et 3 - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - Col-0, dcl2-1, dcl3-1 and rdr2-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after. Keywords: gene knock out

2008-06-02 | GSE10352 | GEO

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Project description:rs06-06_mirna - comparisons wt-mutants 1 - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - What are the genes (including miRNA precursors) that are differentially regulated in a set of tasiRNA mutants? Col-0, dcl4-1, rdr6-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after. Keywords: gene knock out

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