Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA136877 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptome analysis of two mutants rdr6/sgs2 and sgs3 impaired in post-transcriptional gene silencing (PTGS)
| PRJNA100103 | ENA
Project description:Identification of new genes regulated by RDR6 and SGS3 (two genes involved in PTGS) by analysis of the transcriptome of rdr6-1 and sgs3-1 mutants compared to wild-type plants in different tissues (flower and leaves). The comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS would allowed identification of genes involved in the developmental default (zip phenotype) of the null alleles (rdr6-1 and sgs3-1 mutants).
2006-08-01 | E-MEXP-531 | biostudies-arrayexpress
Project description:RNA quality control (RQC) and post-transcriptional gene silencing (PTGS) target and degrade aberrant endogenous RNAs and foreign RNAs, contributing to homeostasis of cellular RNAs. In plants, RQC and PTGS compete for foreign and selected endogenous RNAs; however, little is known about the mechanism interconnecting the two pathways. Using a reporter system designed for monitoring PTGS, we revealed that the 26S proteasome subunit RPT2a enhances transgene PTGS by promoting the accumulation of transgene-derived short interfering RNAs without affecting their biogenesis. RPT2a physically associated with a subset of RQC components and downregulated the protein level. Overexpression of the RQC components interfered with transgene silencing, and impairment of the RQC machinery reinforced transgene PTGS attenuated by rpt2a. Overall, we demonstrate that the 26S proteasome subunit RPT2a promotes PTGS by repressing the RQC machinery to control foreign RNAs.
2019-08-29 | GSE131009 | GEO
Project description:Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. A second, longer DCL4 transcript isoform encodes a nuclear-localization signal and its expression is repressed by DNA methylation. Consequently this isoform is induced when promoter methylation decreases due to infection with a bacterial pathogen or during silique development. Nuclear DCL4 produces unique populations of small RNAs, called DCL4NLS isoform-dependent siRNAs (disiRNAs), which function via a post-transcriptional silencing effector, but whose precursors are generated by the RdDM pathway. Arabidopsis cells can thus respond to genome methylation changes by modulating DCL4 localization, which in turn recruits PTGS factors to reinforce RNA silencing.
2016-11-14 | GSE74731 | GEO
Project description: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
| PRJNA133631 | ENA
Project description: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
| PRJNA136325 | ENA
Project description:Analysis of polyploidy-associated transcriptional gene silencing (paTGS) mutants
| PRJNA118693 | ENA
Project description:Next-generation Illumina sequencing technology was used to analyze small RNA associated with post-transcriptional gene silencing induced by intron-spliced hairpin RNA (ihpRNA) in Arabidopsis. The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine the specificity of the inhibition of gene expression. Despite its broad utility as a research tool, IR-PTGS is only a partially understood mechanism of RNA silencing in plants. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (CHS) gene fragments. The levels of PTGS were dependent on the orientation and position of the fragment in the IR construct. To investigate these differences, we characterized the sRNA profiles by Illumina sequencing of seven libraries generated from transgenic families showing different levels of IR-PTGS. Mapping of sRNA sequences to their corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation. Analyses of these patterns and peaks revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. Our observations provide new guidelines for designing constructs to increase the efficiency of IR-PTGS. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.
2012-06-26 | GSE38922 | GEO
Project description:Arginine/R methylation (R-met) of proteins is a widespread post-translational modification (PTM), deposited by a family of protein arginine/R methyl transferase enzymes (PRMT). Regulations by R-met are involved in key biological processes deeply studied in metazoan. Among those, post-transcriptional gene silencing (PTGS) can be regulated by R-met in animals and in plants. It mainly contributes to safeguard processes as protection of genome integrity in germlines through the regulation of piRNA pathway in metazoan, or response to bacterial infection through the control of AGO2 in plants. So far, only PRMT5 has been identified as the AGO/PIWI R-met writer in higher eukaryotes. We uncovered that AGO1, the main PTGS effector regulating plant development, contains unique R-met features among the AGO/PIWI superfamily. We pinpointed that AGO1 contains both symmetric and asymmetric R-dimethylations (sDMA and aDMA respectively) and is dually targeted by PRMT5 and by another type I PRMT in Arabidopsis thaliana. We showed that loss of sDMA didn’t compromise AtAGO1 subcellular trafficking in planta. Interestingly, we underscored that AtPRMT5 specifically promotes phasiRNA loading in AtAGO1. All our observations bring to consider this dual regulation of AtAGO1 in plant development and response to environment, and pinpoint the complexity of its post-translational regulation.
2024-01-18 | PXD043460 | Pride
Project description:ra09-03_sgs - mutants versus wt - Identification of new genes regulated by SGS1 and SGS6/UBP5 (two genes involved in PTGS) by analysis of the transcriptomes of sgs1 and sgs6 mutants compared to wild-type plants in the shoots of seedlings. The comparison between the transcriptomes of sgs3, chr11, chr17 simple mutants impaired differently in PTGS and development (juvenile-to-adult transition and bolting), and the transcriptomes of the sgs3 chr11, sgs3 chr17 double mutants showed additive effects on development (juvenile-to-adult transition and bolting), which allows a better understanding of the genetic link existing between SGS3 and its potential partners, CHR11 (which interacts with SGS3 in a two-hybrid assay and BiFC) and CHR17, 2 homologous proteins of the SWI/SNF2 family. Transcriptome comparison between mutants and wild-type plants L1 in the shoots of seedlings.
2011-01-08 | GSE26413 | GEO