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Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of ire1 mutants after treatment with or without tunicamycin in the presence of actinomycin D

ABSTRACT: Arabidopsis seedlings of wildtype or ire1a ire1b double mutant were treated with or without tunicamycine in the presence of actinomycin D (ActD). 12 samples

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Yukihisa Shimada

PROVIDER: E-GEOD-39690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Defects in IRE1 enhance cell death and fail to degrade mRNAs encoding secretory pathway proteins in the Arabidopsis unfolded protein response.

Mishiba Kei-ichiro K Nagashima Yukihiro Y Suzuki Eiji E Hayashi Noriko N Ogata Yoshiyuki Y Shimada Yukihisa Y Koizumi Nozomu N

Proceedings of the National Academy of Sciences of the United States of America 20130318 14

The unfolded protein response (UPR) is a cellular response highly conserved in eukaryotes to obviate accumulation of misfolded proteins in the endoplasmic reticulum (ER). Inositol-requiring enzyme 1 (IRE1) catalyzes the cytoplasmic splicing of mRNA encoding bZIP transcription factors to activate the UPR signaling pathway. Arabidopsis IRE1 was recently shown to be involved in the cytoplasmic splicing of bZIP60 mRNA. In the present study, we demonstrated that an Arabidopsis mutant with defects in ...[more]

PMID: 23509268

Similar Datasets

Transcriptome analysis of ire1 mutants after treatment with or without tunicamycin in the presence of actinomycin D

Project description:Arabidopsis seedlings of wildtype or ire1a ire1b double mutant were treated with or without tunicamycine in the presence of actinomycin D (ActD).

2013-03-19 | GSE39690 | GEO

ire1 double mutant vs wild-type in response to tunicamycin

Project description:Arabidopsis thaliana wild-type and ire1a/ire1b double mutant plants were treated with tunicamycin. RNA was extracted and subjected to microarray analysis.

2012-03-13 | E-MEXP-3186 | biostudies-arrayexpress

RNAseq of isolated mitotic HeLa cells treated with Actinomycin D

Project description:The goal of this experiment was to assess whether transcription happens during mitosis. For this, we isolated mitotic HeLa cells and treated them with a transcription inhibitor, ActD.

2018-08-28 | E-MTAB-6661 | biostudies-arrayexpress

Actinomycin targets NPM1c-primed mitochondria in AML

Project description:Acute myeloid leukemia (AML) pathogenesis often involves a mutation in the NPM1 nucleolar chaperone, but the bases for its transforming properties and association with favorable outcome remain incompletely understood. Here we demonstrate that an oncogenic mutant form of NPM1 (NPM1c) hampers formation of PML nuclear bodies (NBs), key senescence effectors, and impairs mitochondrial function to drive an integrated stress response. Actinomycin D (ActD), an antibiotic with unambiguous clinical efficacy in relapsed/refractory NPM1c-AMLs, preferentially targets these primed mitochondria, activating cGAS signaling and boosting ROS production. The later restores PML NB formation to drive senescence of NPM1c-AMLs cells. Dual targeting of mitochondria by Venetoclax and ActD synergized for AML elimination. Our studies reveal a central role of mitochondria downstream of NPM1c and implicate a mitochondrial/ROS/PML/TP53 senescence pathway as a key effector of ActD-based, and possibly others, chemotherapies.

2021-12-17 | PXD025507 | Pride

Genome-wide miRNA turnover profile in various cell types after transcription inhibition

Project description:We measured miRNA turnover rates in 8 mammalian cell types post transcription inhibitors ActinomycinD (ActD) or 5,6-Dichlorobenzimidazole 1-M-NM-2-D-ribofuranoside (DRB) treatment with miRNA expression profiling, generating 218 expression profiles on 528 endogenous miRNAs. Cells were plated in six-well plates at around 200,000 cells/well. A media change was performed one day after plating. ActD and DRB treatment were started after confluency (around two days after plating) for 0, 2, 4, 6, 12, and 24 hours post treatment with biological duplicate (ActD treatment) or biological triplicate (DRB treatment). The concentration of ActD and DRB for different cell lines were titrated to achieve rapid c-myc down-regulation after 2 hours of ActD and DRB treatment. After treatment at indicated time points, cells were washed with PBS once and lysed in TriZol reagent immediately (Invitrogen). RNA extraction was performed following the manufacturerM-bM-^@M-^Ys protocol. miRNA profiling was performed using a Luminex bead-based method.

2015-02-05 | E-GEOD-46877 | biostudies-arrayexpress

IRE1 inhibitor [RNA-seq]

Project description:The role of the unfolded protein response (UPR) in the cellular innate response to RSV infection is not fully understood. To better the genomic targets for the IRE1-XBP1 pathway, RNA seq was conducted on RSV-infected small airway cells in the absence or presence of RSV infection and in the absence or presence of a selective IRE1a RNAse inhibitor. We identified expression changes in ~3.2K genes; of these, 279 required IRE1 and were enriched in IL-10 signaling and cytokine signaling pathways. These data indicate that IRE1a-XBP1s regulates genes important in epithelial mesenchymal transition, hexosamine biosynthesis and anti-viral signaling.

2023-04-30 | GSE228327 | GEO

RNA-seq of Arabidopsis thaliana shoots and roots treated with tunicamycin: a comparison between double mutant (ire1a ire1b) and wild type genotypes.

Project description:The aim of this study is to identify genes whose expression is under the control of IRE1A and IRE1B during a chronic proteotoxic endoplasmic reticulum stress induced by tunicamycin. The transcriptional response has been measured in separated shoot and root tissues from Arabidopsis seedlings.

2024-02-29 | E-MTAB-12284 | biostudies-arrayexpress

Transcription profiling of yeast using samples prepared with actinomycin D to exclude antisense artifacts

Project description:Recent transcription profiling studies have revealed an unanticipatedly large proportion of antisense transcription across eukaryotic and bacterial genomes. However, the extent and significance of antisense transcripts is controversial partly because experimental artifacts are suspected. Here, we present a method to generate clean genome-wide transcriptome profiles, using actinomycin D (ActD) during reverse transcription. We show that antisense artifacts appear to be triggered by spurious synthesis of second-strand cDNA during reverse transcription reactions. Strand-specific hybridization signals obtained from Saccharomyces cerevisiae tiling arrays were compared between samples prepared with and without ActD. Use of ActD removed about half of the detectable antisense transcripts, consistent with their being artifacts, while sense expression levels and about 200 antisense transcripts were not affected. Our findings thus facilitate a more accurate assessment of the extent and position of antisense transcription, towards a better understanding of its role in cells.

2007-10-30 | E-TABM-361 | biostudies-arrayexpress

BioID-based IRE1 interac-tome reveals participants of the ERAD machinery in the human mast cell leukemia cell line HMC-1.2

Project description:Investigation of the interactome of IRE1a and its relation to ERAD machinery

2024-04-29 | PXD047343 | Pride

Genome-wide miRNA turnover profile after transcription inhibition in HDMYZ cells with biological triplicate

Project description:HDMYZ cells were treated with 4ug/ml ActD for 0, 1, 4 and 12 hours. Small RNAs of 15-40 bases were gel-purified from 5 ug total RNA, and subjected to multiplex Illumina small RNA library preparation. Small RNA libraries were sequenced on a HiSeq2000 (Illumina). Measure miRNA expression level at 0, 1, 4, 12 hours post ActinomycinD treatment to examine miRNA turnover pattern.

2015-02-05 | E-GEOD-60036 | biostudies-arrayexpress

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