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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data in Arabidopsis axe1-5 and met1-3 mutants.

ABSTRACT: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants. Fifteen-day-old Arabidopsis plants grown on the agar plates were harvested. The total RNA was prepared from 15-day-old Arabidopsis plants (axe1-5 (hda6 mutant), DR5 (parental line of axe1-5), met1-3 and Col) and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Motoaki Seki

PROVIDER: E-GEOD-23950 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1.

To Taiko Kim TK Kim Jong-Myong JM Matsui Akihiro A Kurihara Yukio Y Morosawa Taeko T Ishida Junko J Tanaka Maho M Endo Takaho T Kakutani Tetsuji T Toyoda Tetsuro T Kimura Hiroshi H Yokoyama Shigeyuki S Shinozaki Kazuo K Seki Motoaki M

PLoS genetics 20110428 4

Heterochromatin silencing is pivotal for genome stability in eukaryotes. In Arabidopsis, a plant-specific mechanism called RNA-directed DNA methylation (RdDM) is involved in heterochromatin silencing. Histone deacetylase HDA6 has been identified as a component of such machineries; however, its endogenous targets and the silencing mechanisms have not been analyzed globally. In this study, we investigated the silencing mechanism mediated by HDA6. Genome-wide transcript profiling revealed that the ...[more]

PMID: 21552333

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Expression data in Arabidopsis axe1-5 and met1-3 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

2011-05-16 | GSE23950 | GEO

Expression data in Arabidopsis hda6 mutant axe1-5 and its parental line DR5 under cold and control conditions.

Project description:To understand the role of Arabidopsis histone deacetylase HDA6 in plant cold acclimation, we have employed transcriptional profiling of the hda6 mutant and its parental line under cold and control conditions to identify genes differentially expressed in the hda6 mutant under cold and control conditions. Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K) were used. Arabidopsis hda6 mutant axe1-5 and its parental line DR5 were grown in MS agar plates for 2 weeks (16 hours light / 8 hours dark). For cold treated sample, the plants were subjected for cold treatment at 2?C for 3 days (12 hours light / 12 hours dark). Then total RNA was prepared and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.

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Expression data in Arabidopsis fry1-6, xrn2-4, xrn3-3 and xrn4-6 mutants.

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Expression data in Arabidopsis hda6 mutant axe1-5 and its parental line DR5 under drought and control conditions

Project description:To understand the role of Arabidopsis histone deacetylase HDA6 in drought tolerance, we have employed transcriptional profiling of the hda6 mutant and its parental line under drought and control conditions to identify genes differentially expressed in the hda6 mutant under drought and control conditions. Aligent's Whole Arabidopsis Gene Expression Microarray (Agilent-015059, G2519F, V3, 4x44K) was used. Arabidopsis hda6 mutant axe1-5 and its parental line DR5 were grown in soil for 3 weeks (16 hours light / 8 hours dark). For drought-treated sample, the plants were subjected to drought by withhelding water supply for indicated days. Then total RNA was prepared from the above-ground tissue and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.

2017-04-29 | E-GEOD-46365 | biostudies-arrayexpress

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Expression data for the mom1-2 mutant of Arabidopsis

Project description:Heterochromatin is an inert region in the genome and composed of mainly remnants of transposons and repetitive elements. In Arabidopsis, the major heterchromatin regions are present at around centromeres (pericentromeric regions) and at a region on the short arm of chromosome 4 (heterochromatin knob). Histones and DNAs in heterochromatin have characteristic features with abundant H3H9me2 and cytosine methylation, respectively. Here, by using a genome tiling array, we showed that a subset of heterochromatin loci are silenced by the action of Morpheus' molecule 1 (MOM1) that is an epigeneic regulator for transcriptional gene silencing independent of global DNA and histone modification. Most of the up-regulated loci in the mom1 mutant carried sequences related to transposable elements but none of them was annotated as functional transposons. No specific subclass of transposons was targeted by MOM1 and loci that were unrelated to transposons but flanked by short tandem repeats were also shown to be under the control of MOM1. The results suggest the presence of an unknown level of regulatory network maintaining the silent state of heterochromain in the genome. Keywords: Epigenetic regulation of endogenous loci by Morpheus' Molecule 1 (MOM1) Three-week-old Arabidopsis plants (Col-0 and mom1-2) grown on soil were subjected to RNA extraction and the total RNA samples were used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

2010-09-26 | E-GEOD-13092 | biostudies-arrayexpress

Expression data in Arabidopsis hda6 mutant axe1-5 and its parental line DR5 under cold and control conditions.

2011-01-27 | GSE26873 | GEO

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2017-04-29 | GSE46365 | GEO

Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

Project description:We report the application of ChIP-Seq of H4ac and H3K27me3 histone modifications to jasmonate-treated wild type (DR5) and HDA6 mutant (axe1-5) whole A. thaliana seedlings

2022-04-11 | GSE197733 | GEO

Deubiquitinases that digest Met1 chains in Rice

Project description:Met1 type ubiquitination and deubiquitination are involved in the regulation of many fundamental processes such as inflammation and innate immunity, and their interference by pathogens can suppress immune responses in human cells. However, few plant-derived deubiquitinases (DUBs) against Met1 ubiquitin chains has been reported, and the selection mechanism for linkage-type of ubiquitin chains remains elusive, which greatly limits our understanding of the functions of plant-derived DUBs. Using a dehydroalanine (DHA)-bearing Met1 diubiquitin (Met1-diUb) suicide probe, synthesized in one-pot, we captured OTUB1 from Oryza sativa (OsOTUB1) and uncovered its ability to hydrolyze Met1 ubiquitin chains (Met1 activity). Further, by resolving the apo structure of OsOTUB1 and its complex with Met1-diUb, we found that Met1-specific motifs (N-handle motif and C-handle motif) in the S1’ pocket of OsOTUB1 confers its Met1 activity. Through large-scale sequence alignment and hydrolysis experiments, Met1-specific motifs in the S1' pocket of the OTUB subfamily (OTUBs) were found to determine the Met1 ability of OTUBs, regardless of species. Furthermore, by analyzing the species distribution of OTUBs capable of hydrolyzing Met1 ubiquitin chains, we found that whereas this activity does not exist in metazoans, it is conserved in green plants (Viridiplantae). This discovery may inform studies of the differentiation between primitive plants and animals.

2022-10-15 | PXD032822 | Pride

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