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Ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

ABSTRACT: au05-03_gaba - ler vs pop2-1: gaba over-accumulation effects - The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition. Designed experiment consisted in comparison of transcriptomes of Arabidopsis thaliana Landsberg erecta ecotype and its mutant pop2-1 (impaired in GABA transaminase activity) during a kinetic of endogenous GABA accumulation. For this purpose, 10-day-old plants grown on half strength Hoagland's agar medium were transferred to agar plates supplemented with 1 mM GABA. We isolated RNA from plants treated for 0, 1 and 4 days. Treatments were made in duplicate. Keywords: gene knock-out, time course

ORGANISM(S): Arabidopsis thaliana Populus x canadensis

PROVIDER: GSE11129 | GEO | 2009/04/11

SECONDARY ACCESSION(S): PRJNA106913

REPOSITORIES: GEO

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ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

Project description:au05-03_gaba - ler vs pop2-1: gaba over-accumulation effects - The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition. Designed experiment consisted in comparison of transcriptomes of Arabidopsis thaliana Landsberg erecta ecotype and its mutant pop2-1 (impaired in GABA transaminase activity) during a kinetic of endogenous GABA accumulation. For this purpose, 10-day-old plants grown on half strength Hoagland's agar medium were transferred to agar plates supplemented with 1 mM GABA. We isolated RNA from plants treated for 0, 1 and 4 days. Treatments were made in duplicate. Keywords: gene knock-out, time course 6 dye-swap - CATMA arrays

2009-04-11 | E-GEOD-11129 | biostudies-arrayexpress

ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

Project description:ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

| PRJNA106913 | ENA

Gene expression data from Arabidopsis wild-type and pop2-1 mutant flowers

Project description:Although two genes responsive to GABA were characterized previously in plants (Kathiresan et al 1997), a comprehensive study in reproductive and vegetative tissues has not been performed. Consequently, genes that mediate GABA response in plants remain unknown. We therefore used microarrays to survey the genome, identifying genes modulated in response to GABA in reproductive tissues. Flowers were collected as described in the protocols section for RNA extraction and hybridization on Affymetrix ATH1 Genechip microarrays. Gene expression in wild-type and pop2-1 mutant flowers containing high levels of endogenous GABA were compared.

2010-06-16 | E-GEOD-21945 | 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

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

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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. Keywords: mutant response

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Expression data from wt, pop2, pbp1, and mpt5-deletion yeast cells.

Project description:The S. cerevisiae Pop2 protein is an exonuclease in the Ccr4-Not complex that is a conserved regulator of gene expression. Pop2 regulates gene expression post-transcriptionally by shortening the poly(A) tail of mRNA. A previous study has shown that Pop2 is phosphorylated at threonine 97 (T97) by Yak1 protein kinase in response to glucose limitation. However, the physiological importance of Pop2 phosphorylation remains unknown. In this study, we found that Pop2 is phosphorylated at serine 39 (S39) under unstressed conditions. The dephosphorylation of S39 was occurred within 1 min after glucose depletion, and the addition of glucose to the glucose-deprived culture recovered this phosphorylation, suggesting that Pop2 phosphorylation at S39 is regulated by glucose. We previously reported that Pop2 takes a part in the cell wall integrity pathway by regulation of LRG1 mRNA; however, S39 phosphorylation of Pop2 is not involved in LRG1 expression. On the other hand, Pop2 phosphorylation at S39 is involved in the expression of HSP12 and HSP26, encoding small heat shock proteins. In medium supplemented with glucose, Pop2 might be phosphorylated at S39 by Pho85 kinase to repress the expression of HSP12 and HSP26. Glucose starvation inactivated Pho85, which resulted in the derepression of HSP12 and HSP26. Thus, Pop2 phosphorylation at S39 is important for Pop2 to repress the expression of stress response genes, HSP12 and HSP26, in the presence of glucose. Our results suggest that Pop2 phosphorylation by Pho85 kinase is a part of the glucose sensing system in yeast.

2019-03-01 | GSE124908 | GEO

Gene expression data from Arabidopsis wild-type and pop2-1 mutant flowers

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sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

Project description:We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents.

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rnadapt- Non-coding RNAs in the adaptation of root growth to phosphate starvation [miRNA-Seq]

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