Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA profiling in an Arabidopsis transgenic line overexpressing AtmiR472

ABSTRACT: Virus resistance relies in some plant-viral interactions on the RNA-DEPENDANT RNA POLYMERASE 6 (RDR6), a major actor of RNA silencing that acts at the post-transcriptional level. Here, we demonstrate that RDR6 also plays a role in basal defense and race-specific resistance. RDR6 and the microRNA miR472, which target the mRNAs of disease resistance genes of coiled-coil nucleotide-binding leucine-rich-repeats family (e.g. RPS5), act in cooperation to control post-transcriptionally these immune receptors. Induction of these resistance genes is primed in rdr6- and miR472-elicited mutants and this effect is associated with an enhanced basal and race-specific immunity in these backgrounds. Comparison of Col0 WT sRNA with miR472 over-expressor mutant.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Alexis Sarazin

PROVIDER: E-GEOD-53484 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Small RNA profiling in an Arabidopsis transgenic line overexpressing AtmiR472

Project description:Virus resistance relies in some plant-viral interactions on the RNA-DEPENDANT RNA POLYMERASE 6 (RDR6), a major actor of RNA silencing that acts at the post-transcriptional level. Here, we demonstrate that RDR6 also plays a role in basal defense and race-specific resistance. RDR6 and the microRNA miR472, which target the mRNAs of disease resistance genes of coiled-coil nucleotide-binding leucine-rich-repeats family (e.g. RPS5), act in cooperation to control post-transcriptionally these immune receptors. Induction of these resistance genes is primed in rdr6- and miR472-elicited mutants and this effect is associated with an enhanced basal and race-specific immunity in these backgrounds.

2013-12-19 | GSE53484 | GEO

smRNAs in wildtype and RDR6-15 knockout Arabidopsis thaliana Col-0 leaf

Project description:This set consists of small RNAs sequenced from two replicates of wildtype and two replicates of RDR6-15 knockout Arabidopsis thaliana Col-0 leaf samples. RDR6 is required for the production of tasRNAs (trans-acting small RNAS) and so tags associated with the tasRNA loci should be severely down-regulated or absent in the knockout compared to wildtype. The set can thus be used as containing known true positives for testing differential expression detection methods. Examination of smRNA in 2 replicates wildtype and 2 replicates RDR6-15 knockout

2010-11-22 | E-GEOD-16959 | biostudies-arrayexpress

Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation

Project description:Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. To define the function of this new pathway, we have focused on the RDR6 protein, which plays a central role in the pathway we refer to as RDR6-dependent RNA-directed DNA Methylation (RDR6-RdDM). Methods: We have sequenced total small RNAs from wild-type and three mutant genotypes: ddm1, ddm1/rdr6, and rdr6. Conclusions: We demonstrate that RDR6-RdDM utilizes 21 and 22 nucleotide siRNAs to de novo methylate actively transcribing TEs. In addition, we find that the RDR6-RdDM pathway functions in the efficient initiation and re-establishment of TE transcriptional silencing, while it is not necessary to maintain trans-generational epigenetic silencing. Examination of flower bud small RNAs from wild-type and 3 mutant genotypes

2013-04-11 | E-GEOD-41755 | biostudies-arrayexpress

Reconstructing de novo silencing of an active plant retrotransposon: dynamics, mechanisms, biological implications

Project description:In plants, maintenance-methylation mediated by METHYLTRANSFERASE-1 (MET1), siRNA-directed de-novo methylation, and chromatin remodeling by DECREASE IN DNA METHYLATION -1 (DDM1) promote transcriptional gene-silencing of transposable elements (TEs). This process is mostly investigated at steady states reflecting how long-established silent conditions are maintained, faithfully re-iterated or temporarily modified during growth, stress and over generations. How invasive TEs are detected and silenced de novo, however, remains largely unknown. Using inbred lineages of hybrid Arabidopsis epigenomes combining wild-type and met1 or ddm1 chromosomes, we have deciphered the timing, spatial distribution and mechanisms underpinning the proliferation and eventual demise of the endogenous retrotransposon évadé (EVD). Both developmental and molecular features of EVD biology, including a remarkable ability to evade RNA interference, ultimately contribute to its silencing over multiple generations. The underlying processes are accompanied by widespread diversification of the Arabidopsis genome and de-novo epiallelism creating an extensive reservoir of selectable and potentially adaptive traits. Differential expression of EVADE small RNAs between three generations of one specific Col0 met1 derived EpiRIL.

2013-07-02 | E-GEOD-43412 | biostudies-arrayexpress

In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

Project description:Background: Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5' cap structure and their subsequent 5M-bM-^@M-^Y to 3M-bM-^@M-^Y degradation. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to double-stranded RNAs by the cellular RNA DEPENDENT RNA POLYMERASE 6 (RDR6). PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. Results: We show that that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of siRNAs, a subset of which depends on RDR6 for their production. Conclusions: Our results suggest that the decapping of aberrant endogenous RNA in P-bodies limits their entry into the PTGS pathway and prevents the subsequent deleterious consequences arising from this entry. We anticipate that the siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs that we coin rqc-siRNAs because they accumulate when RQC processes are impaired. Small RNA-seq experiments performed in duplicates for each condition.

2015-01-21 | E-GEOD-65056 | biostudies-arrayexpress

Transcriptome profiling of Arabidopsis using strand-specific RNA-seq

Project description:We applied single-end strand-specific RNA-seq experiments to compare the abundance of natural antisense transcripts in Arabidopsis. Examination of 3 wild type (WT) organs, including leaves, inflorescences and siliques.

2013-12-23 | E-GEOD-49950 | biostudies-arrayexpress

RNA-seq analysis of the effect of kanamycin and the ABC transporter AtWBC19 on Arabidopsis thaliana seedlings reveals changes in metal content

Project description:Plants are exposed to antibiotics produced by soil microorganisms but little is known about their responses at the transcriptional level. Likewise, few endogenous mechanisms of antibiotic resistance have been reported. The Arabidopsis thaliana ATP Binding Cassette (ABC) transporter AtWBC19 (ABCG19) is known to confer kanamycin resistance, but the exact mechanism of resistance is not well understood. Here we examined the transcriptomes of control seedlings and wbc19 mutant seedlings using RNA-seq analysis. Exposure to kanamycin indicated changes in the organization of the photosynthetic apparatus, metabolic fluxes and metal uptake. Elemental analysis showed a 60% and 80% reduction of iron uptake in control and wbc19 mutant seedlings respectively, upon exposure to kanamycin. The drop in iron content was accompanied by the upregulation of the gene encoding for FERRIC REDUCTION OXIDASE 6 (FRO6) in mutant seedlings but not by the differential expression of other transport genes known to be induced by iron deficiency. In addition, wbc19 mutants displayed a distinct expression profile in the absence of kanamycin. Most notably, the expression of several zinc ion binding proteins, including ZINC TRANSPORTER 1 PRECURSOR (ZIP1), was increased, suggesting abnormal zinc uptake. Elemental analysis confirmed a 50% decrease of zinc content in wbc19 mutants. Thus, the antibiotic resistance gene WBC19 appears to also have a role in zinc uptake. Examination of transcriptome in control and wbc19 mutant seedlings with or without exposure to kanamycin.

2014-06-20 | E-GEOD-58662 | biostudies-arrayexpress

Acute effects of light on alternative splicing in light-grown plants

Project description:We report the results of a genome-wide analysis of AS in Arabidopsis thaliana plants exposed to a 2h light pulse given in the middle of the night, a treatment that simulates the effects of early dawn or late dusk signals. This light affects the plant transcriptome at multiple regulatory layers, and that light regulation of mRNA levels of splicing regulatory factors is likely to mediate light effects on AS contributing to adjust plant physiological processes to the prevailing light environment. Arabidopsis seedlings of the Columbia ecotype were grown under 12 hr light/12 hr dark cycles for 9 days. On the 10th day, half of the plants were exposed to a two-hour pulse of white light given in the middle of the night (ZT18), while the other half were kept in darkness as controls. Both groups of plants were harvested at ZT 20 and light effects on mRNA levels and AS were analyzed through RNA-seq.

2016-08-09 | E-GEOD-68560 | biostudies-arrayexpress

Identification of chromatin regulatory sites in conditions of basal and increased SF-1 dosage in the H295R adrenocortical tumor cell line

Project description:The goal of this study was to identify chromatin regulatory sites by FAIRE-seq under conditions of basal and increased dosage of transcription factor SF-1 in the H295R human adrenocortical tumor cell line. 4 samples: input DNA in basal SF-1 expression conditions - FAIRE-seq in basal SF-1 expression conditions - input DNA in SF-1 overexpression conditions - FAIRE-seq in SF-1 overexpression conditions

2013-08-01 | E-GEOD-44221 | biostudies-arrayexpress

A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [RNA-seq]

Project description:To understand how atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), and close homologue, IBH1-like1 (IBL1) (At4g30410), interact to regulate cell elongation, genome-wide RNA-Seq expression analyses of IBH1 and IBL1 gain-(IBH1OE, IBL1OE) and loss-of-function (ibh1 (SALK 049177), ibl1(SALK 119457)) mutants were conducted. For loss-of-function mutant, homozygous ibh1(SALK 049177) and ibl1(SALK 119457) were compared to wild type (Col). For gain-of-function mutant, homozygous 35Spro:IBH1-GFP and 35Spro:IBL1-GFP were compared to wild type (Col). Total RNAs were extracted from seedling of each genotypes. For each genotype two biological replicates were sequenced.

2014-03-05 | E-GEOD-51119 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data