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

ABSTRACT: 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(S): Arabidopsis thaliana

PROVIDER: GSE4684 | GEO | 2006/05/17

SECONDARY ACCESSION(S): PRJNA96795

REPOSITORIES: GEO

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Transcription profiling of Arabidopsis wild-type, ago1-10, ago1-11, and dcl1-9 ec. Landsberg erecta seedling at 9, 21, and 35 days after germination reveals miRNA-Targeted and siRNA-Mediated mRNA Degradation Regulated by Argonaute, Dicer and RdRP

Project description: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. Experiment Overall Design: Reference design, wild-type vs mutants, multiple biological replicates

2008-06-13 | E-GEOD-4684 | biostudies-arrayexpress

Expression analysis of TRANSPOSABLE ELEMENT KILLER (TEK) knockdown lines

Project description:Investigation of the effect of the knockdown of AT-hook motif DNA binding nuclear matrix protein TRANSPOSABLE ELEMENT KILLER (TEK) in the Arabidopsis Landsberg erecta (Ler) background Transposable elements (TEs) are silenced by epigenetic mechanisms of DNA and histone methylation. The repressive histone modification H3 lysine 9 dimethylation (H3K9me2) is TE-associated epigenetic hallmark, and is necessary for DNA methylation. However the mechanism to direct the repressive epigenetic modification in TEs has remained elusive. Here we show that knockdown of the AT-hook motif DNA binding nuclear matrix protein TRANSPOSABLE ELEMENT KILLER (TEK) in the Arabidopsis Landsberg erecta (Ler) background results in robust activation of various TEs, the repeat-containing floral repressor gene FWA and the TE-containing floral repressor FLOWERING LOCUS C (FLC). A four chip study using two separate wild-type seedling mRNA samples and two separate TEKi seedling mRNA samples

2012-09-12 | E-GEOD-39158 | biostudies-arrayexpress

Global and local perturbation of the tomato microRNA pathway by a trans-activated DICER-LIKE 1 mutant

Project description:DICER-like 1 (DCL1) is a major player in micro RNA (miRNA) biogenesis and accordingly, its few known loss-of-function mutants are either lethal or display arrested seedling development. Consequently, generation of dcl1 mutants by reverse genetics and functional analysis of DCL1 in late-developing organs are challenging. Here, these challenges were resolved through the unique use of trans-activated RNA interference. Global, as well as organ-specific tomato DCL1 (SlDCL1) silencing was induced by crossing the generated responder line (OP:SlDCL1IR) with the appropriate driver line. Constitutive trans-activation knocked down SlDCL1 levels by ~95%, resulting in severe abnormalities including post-germination growth arrest accompanied by decreased miRNA and 21-nucleotide small RNA levels, but prominently elevated levels of 22- nucleotide small RNAs. The elevation in the 22- nucleotide small RNAs was correlated with specific upregulation of SlDCL2b and SlDCL2d, which are likely involved in their biogenesis. Leaf- and flower-specific OP:SlDCL1IR trans-activation inhibited blade outgrowth, induced premature bud senescence and produced pale petals, respectively, emphasizing the importance of SlDCL1-dependent small RNAs in these processes. Together, our results establish OP:SlDCL1IR as an efficient tool for analyzing processes regulated by SlDCL1-mediated gene regulation in tomato.

2013-11-01 | GSE51959 | GEO

Global and local perturbation of the tomato microRNA pathway by a trans-activated DICER-LIKE 1 mutant

2013-11-01 | E-GEOD-51959 | biostudies-arrayexpress

Transcription profiling of Arabidopsis ecotypes Landsberg erecta (Ler) and Landsberg to assess the effect of ERECTA on gene expression

Project description:To assess the effect of ERECTA on gene expression in Arabidopsis, genome wide transcript abundance was measured in Landsberg erecta (Ler) compared to Landsberg. For the differentially expressed genes, genetic variation in gene expression in the Ler/Cvi recombinant inbred line (RIL) population, resulted in the construction of a putative genetic regulatory network downstream of ERECTA.

2010-01-20 | E-TABM-627 | biostudies-arrayexpress

Argonaute Surveillance and Dicer-Independent priRNAs TriggerRNAi and Heterochromatin Formation

Project description:The assembly of fission yeast pericentromeric heterochromatin and generation of small interfering RNAs (siRNAs) from noncoding centromeric transcripts are mutually dependent processes. How this interdependent positive feedback loop is first triggered is a fundamental unanswered question. Here we show that two distinct Argonaute (Ago1)-dependent pathways mediate small RNA generation. RNA-dependent RNA polymerase complex (RDRC) and Dicer act on specific noncoding RNAs to generate siRNAs by a mechanism that requires the slicer activity of Ago1 but is independent of pre-existing heterochromatin. In the absence of RDRC or Dicer, a distinct class of small RNAs, called primal small RNAs (priRNAs), associate with Ago1. priRNAs are degradation products of abundant transcripts, which bind to Ago1 and target antisense transcripts that result from bidirectional transcription of DNA repeats. Our results suggest that a transcriptome surveillance mechanism based on the random association of RNA degradation products with Argonaute triggers siRNA amplification and heterochromatin assembly within DNA repeats.

2010-02-23 | GSE19734 | GEO

Argonaute Surveillance and Dicer-Independent priRNAs TriggerRNAi and Heterochromatin Formation

2010-02-23 | E-GEOD-19734 | biostudies-arrayexpress

Identification of differentially expressed genes in brm-101 and syd-2 mutants

Project description:Global analysis of gene expression in 10 day old brm-101 and syd-2 mutant seedlings compared to wild type Landsberg erecta seedlings. Keywords: mutant analysis

2007-09-10 | GSE5806 | GEO

Identification of LEAFY targets during reproductive transition

Project description:Global analysis of gene expression in 9 day old LEAFY-GR, 35S::LFY or Landsberg erecta seedlings treated with the steroid dexamethasone and/or the protein synthesis inhibitor cycloheximide. Keywords: other

2003-12-18 | GSE911 | GEO

The identification of novel genes involved in seed dormancy and after-ripening in Arabidopsis thaliana

Project description:We analysed the transcriptome of dormant and after-ripened imbibed seeds of different genotypes (Landsberg erecta and the different NILs) to identify dormancy and after-ripening genes that are absolutely required for these traits.

2017-08-21 | GSE90162 | GEO

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