Similar studies for GEO DataSets (Select 200023027) - GEO DataSets

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Items: 20

Select item 2000230271.

Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories.

(Submitter supplied) One of the major players controlling RNA decay is the cytoplasmic 5'-to-3' exoribonuclease, which is conserved among eukaryotic organisms. In Arabidopsis, the 5'-to-3' exoribonuclease XRN4 is involved in disease resistance, the response to ethylene, RNAi, and miRNA-mediated RNA decay. Curiously, XRN4 appears to display selectivity among its substrates because certain 3' cleavage products formed by miRNA-mediated decay, such as from ARF10 mRNA, accumulate in the xrn4 mutant, whereas others, such as from AGO1, do not. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL198
4 Samples

Download data: CEL, TXT

Series

Accession:: GSE23027

ID:: 200023027

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000719132.

Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear messenger RNA cap-binding complex in plant co-translational RNA decay

(Submitter supplied) RNA turnover is necessary for controlling proper mRNA levels post-transcriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5’ end to the 3’ end, such as XRN4, or in the opposite direction by the multi-subunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of co-translational mRNA decay in the Arabidopsis thaliana transcriptome. more...

Organism:: Arabidopsis thaliana

Type:: Other

Platform:: GPL13222
4 Samples

Download data: TXT

Series

Accession:: GSE71913

ID:: 200071913

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001197063.

RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

(Submitter supplied) Application of Parallel Analysis of RNA Ends (PARE), an RNA degradome approach to identify substrates of Arabidopsis XRN4. The xrn4 mutants overaccumulate decay intermediates from multiple mRNA turnover pathways. This material is based on work supported by the National Science Foundation [under Grant Numbers MCB1021636 and MCB1817764 to P.J.G.]

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL17639
22 Samples

Download data: FPKM_TRACKING, TXT

Series

Accession:: GSE119706

ID:: 200119706

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000110704.

A link between RNA metabolism and silencing affecting Arabidopsis development

(Submitter supplied) Whole genome small RNA sequencing (wild-type Col-0, abh1-1, ein5-6, ein5-6 abh1-1) and 5'-RACE (GMUCT) (wild-type Col-0 and ein5-6) sequencing of parenthetically indicated genotypes of Arabidopsis using the Illumina Genetic Analyzer. Whole-genome oligonucleotide tiling microarrays were used for gene expression studies of the entire transcriptome for wildtype Col-0, abh1-1, ein5-6, and ein5-6 abh1-1 plants. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by genome tiling array

Platforms:: GPL9062 GPL10977 GPL1979
22 Samples

Download data: CEL, TXT

Series

Accession:: GSE11070

ID:: 200011070

Select item 2000682685.

Seed transcriptome of xrn4-5 and vcs-8 mutants

(Submitter supplied) au14-08_xrn_vcs - seed transcriptome of xrn4-5 and vcs-8 mutants. - Role of RNA degradation in seed dormancy. - Study of the seeds regulation by the RNA-decay. Comparison between Col0 total RNA and mutants xrn4-5 and vcs-8 RNA, affected in the dormancy and in RNA metabolism.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL18904
12 Samples

Download data: GPR

Series

Accession:: GSE68268

ID:: 200068268

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Select item 2000053876.

Ethylene-insensitive5 encodes a 5'->3' exoribonuclease required for regulation of EIN3-targeting F-box proteins EBF1/2

(Submitter supplied) thylene is a gaseous plant growth regulator that controls a multitude of developmental and stress responses. Recently, the levels of Arabidopsis EIN3 protein, a key transcription factor mediating ethylene-regulated gene expression, have been demonstrated to increase in response to the presence of ethylene gas. Furthermore, in the absence ethylene, EIN3 is quickly degraded through a ubiquitin/proteasome pathway mediated by two F box proteins, EBF1 and EBF2 (1-3). more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by genome tiling array

12 related Platforms
24 Samples

Download data

Series

Accession:: GSE5387

ID:: 200005387

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Select item 2000051747.

ETHYLENE-INSENSITIVE5 encodes a 5' to 3' exoribonuclease required for posttranscriptional regulation

(Submitter supplied) Ethylene is a gaseous plant growth regulator that controls a multitude of developmental and stress responses. Recently, the levels of Arabidopsis EIN3 protein, a key transcription factor mediating ethylene-regulated gene expression, have been demonstrated to increase in response to the presence of ethylene gas. Furthermore, in the absence ethylene, EIN3 is quickly degraded through a ubiquitin/proteasome pathway mediated by two F box proteins, EBF1 and EBF2 (1-3). more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL198
12 Samples

Download data

Series

Accession:: GSE5174

ID:: 200005174

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Select item 2000518798.

Transcriptomic analysis of WT and larp1 mutant 21 days old seedling at 20°C or following a heat stress (15 min at 38°C)

(Submitter supplied) We report the identification of a heat-stress mediated mRNA decay in arabidopsis that is mediated by the XRN4 exonuclease and LARP1 RNA-binding protein.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13222
4 Samples

Download data: TXT, XLSX

Series

Accession:: GSE51879

ID:: 200051879

PubMed Similar studies SRA Run Selector

Select item 2000046849.

miRNA-Targeted and siRNA-Mediated mRNA Degradation Regulated by Argonaute, Dicer and RdRP

(Submitter supplied) Microarray expression profiles of wild-type, ago1-10, ago1-11, and dcl1-9 Arabidopsis thaliana ec. Landsberg erecta seedling at 9, 21, and 35 days after germination. Keywords: mutant response

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL71
37 Samples

Download data

Series

Accession:: GSE4684

ID:: 200004684

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Select item 20019324710.

RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis

(Submitter supplied) To gain insight into the functional role of DNE1 in cytoplasmic mRNA decay, we performed Parallel Analysis of RNA Ends (PARE) and Global Mapping of Uncapped and Cleaved Transcripts (GMUCT) analysis to identify DNE1-dependent cleavage sites based on their sensitivity to XRN4 within the Arabidopsis transcriptome

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL17639 GPL24270
24 Samples

Download data: BEDGRAPH, DIFF

Series

Accession:: GSE193247

ID:: 200193247

PubMed Full text in PMC Similar studies

Select item 20003556211.

Differentiated Truncation and Uridylation Patterns of miRNAs in Arabidopsis and Rice hen1 Mutants Suggest miRNAs May Re-program RISC

(Submitter supplied) miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. more...

Organism:: Oryza sativa; Zea mays; Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

4 related Platforms
33 Samples

Download data: TXT

Series

Accession:: GSE35562

ID:: 200035562

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010707012.

Degradation of unmethylated miRNA/miRNA*s by a DEDDy-type 3’ to 5’ exoribonuclease ATRIMMER2 in Arabidopsis

(Submitter supplied) 3’ end methylation catalyzed by HUA ENHANCER1 (HEN1) is a crucial step of small RNA stabilization in plants, yet how unmethylated small RNAs undergo degradation remains largely unknown. Using a reverse genetic approach, we here show that ATRIMMER2 (ATRM2), a DEDDy-type 3’ to 5’ exoribonuclease, acts in the degradation of unmethylated miRNAs and miRNA*s in Arabidopsis. A loss-of-function mutations in ATRM2 partially suppress the morphological defects caused by HEN1 malfunction, with restored levels of a subset of miRNAs and receded expression of corresponding miRNA targets. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL17639
16 Samples

Download data: TXT

Series

Accession:: GSE107070

ID:: 200107070

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20008636113.

The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL17639
140 Samples

Download data

Series

Accession:: GSE86361

ID:: 200086361

PubMed Full text in PMC Similar studies

Select item 20008636014.

The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings [small RNA-seq]

(Submitter supplied) Cytoplasmic mRNA decay occurs through several pathways, but the contributions of these decay pathways to the degradation of specific mRNAs, and interactions between the pathways, are not well understood. We carried out a genome-wide analysis of mRNA decay rates using wild-type Arabidopsis and mutants with defects in mRNA decapping and SOV/DIS3L2. Decay rates and contributions of decapping and SOV to decay were estimated for 18,674 mRNAs using maximum likelihood modeling. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL17639
12 Samples

Download data: CSV

Series

Accession:: GSE86360

ID:: 200086360

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20008635915.

The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings [RNA-seq]

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17639
128 Samples

Download data: XLSX

Series

Accession:: GSE86359

ID:: 200086359

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006636916.

Difference in gene expression between WT (Col-0) and atxrn4-3 mutant under non-stress and heat stress condition

(Submitter supplied) Arabidopsis 5’-3’ exoribonuclease, AtXRN4, a homolog of yeast Xrn1p, functions in degradation of uncapped RNAs after de-capping step. While Xrn1p-dependent on plant XRN4’s targets for degradation is still limited. For understanding biological function of AtXRN4, we tested survivability of atxrn4 mutants under heat stress. Our results showed that atxrn4 mutants increased survival rate under short-term degradation is a main mRNA decay in yeast, knowledge heat stress compared with WT plants. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL19830
12 Samples

Download data: TXT

Series

Accession:: GSE66369

ID:: 200066369

Select item 20004025917.

Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13222
11 Samples

Download data: GFF3

Series

Accession:: GSE40259

ID:: 200040259

PubMed Full text in PMC Similar studies

Select item 20004025818.

Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Small RNA immunoprecipitation

(Submitter supplied) The Arabidopsis ARGONAUTE (AGO) protein AGO1 associates with microRNA (miRNA) and specific classes of short-interfering RNA (siRNA). AGO1-small RNA complexes recognize target RNA transcripts through base-pairing interactions and inhibit translation of target RNAs through endonucleolytic cleavage (slicing) or non-degradative mechanisms. The PIWI domain of AGO1 contains a metal-coordinating triad [Asp-Asp-His] (DDH) that is required for slicer activity. more...