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Genome-Wide Study Based On Abasic Site Revealed Selective RNA Oxidation In Neuro 2a Cells

ABSTRACT: To investigate selectivity of mRNA oxidation, total RNA and oxidized RNA isolated from Neuro 2a cells before and after H2O2 treatment were employed for microarray analysis. It was found that selective oxidation of mRNA already occurs under normal culture conditions but was increased by H2O2, especially in a subset of mRNAs related to certain functions. Moreover, mRNA oxidation level is also related to its abundance or stability (half-life time). This shows for the first time that mRNA oxidation is associated with RNA homeostasis including function, stability and abundance depending on cellular redox status in a genome-wide scale.

ORGANISM(S): Mus musculus

PROVIDER: GSE39641 | GEO | 2012/10/01

SECONDARY ACCESSION(S): PRJNA171312

REPOSITORIES: GEO

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Genome-Wide Study Based On Abasic Site Revealed Selective RNA Oxidation In Neuro 2a Cells

Project description:To investigate selectivity of mRNA oxidation, total RNA and oxidized RNA isolated from Neuro 2a cells before and after H2O2 treatment were employed for microarray analysis. It was found that selective oxidation of mRNA already occurs under normal culture conditions but was increased by H2O2, especially in a subset of mRNAs related to certain functions. Moreover, mRNA oxidation level is also related to its abundance or stability (half-life time). This shows for the first time that mRNA oxidation is associated with RNA homeostasis including function, stability and abundance depending on cellular redox status in a genome-wide scale. Neuro 2a cells received hydrogen peroxide treatment or no treatment as a control. Samples were applied for RNA extraction and ARP labeling, which could bind with apurinic/apyrimidinic sites, and then a pull-down process to isolate oxidized RNA. Total RNA and oxidized RNA were used for subsequent transcriptomic profiling. 4 types of samples were analyzed: Basal-total: untreated N2a cells labeled with ARP, but not processed for the pull-down assay. Ox-total: hydrogen peroxide-treated N2a cells labeled with ARP, but not processed for the pull-down assay. Basal-ARP: untreated N2a cells labeled with ARP, and processed for the pull-down assay. ARP-derivatized RNA, which is also oxidized RNA, was concentrated and used for the microarray analysis. Ox-ARP: hydrogen peroxide-treated N2a cells labeled with ARP, and processed for the pull-down assay. ARP-derivatized RNA, which is also oxidized RNA, was concentrated and used for the microarray analysis.

2012-10-01 | E-GEOD-39641 | biostudies-arrayexpress

Microarray analysis of RNA stability in mouse Neuro-2A cells

Project description:Microarray analysis of RNA stability in mouse Neuro-2A cells

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RNAseq of wild type and GDF11-/- Neuro-2a cells

Project description:Growth differentiation factor 11 (GDF11), is one of the members of transforming growth factor β (TGFβ) superfamily. We set out to unequivocally reveal the effect of endogenous GDF11 on biological process by adopting CRISPR/Cas9 gene knockout strategy to specifically delete GDF11 gene in Neuro-2a cells. We analyze mRNA profiles of differentially genes in wild type (WT) and GDF11 knockout (GDF11-/-) Neuro-2a cells by using RNA-seq technology. The RNA-seq data reported here provide a fundamental materials and evidence for investigations of biological function of GDF11.

2021-10-06 | GSE167538 | GEO

mRNA oxidation data from dry dormant and after-ripened wheat seeds

Project description:After-ripening induced seed dormancy release in wheat is associated with mRNA oxidation. We used Affymetrix GeneChip Wheat Genome Array to identify mRNAs differentially oxidized by after-ripening Dormant and after-ripened seeds in dry state were used for isolating oxidized mRNAs and hybridization on Affymetrix GeneChip. After-ripened seeds were generated by storing dormant seeds at room temperature for 10 months.

2013-12-15 | E-GEOD-41949 | biostudies-arrayexpress

mRNA oxidation data from dry dormant and after-ripened wheat seeds

2013-12-15 | GSE41949 | GEO

Identification of the binding DNA of ONECUT2 by ChIP in Neuro-2a cells

Project description:These ChIP-seq analyses identified binding DNAs of ONEUCT2 in Neuro-2a (mouse neuroblastoma)cells. We overexpressed OC2ΔHOX (a gain-of-function mutant) in Neuro-2a cells, and infected the cells with HSV-1 at 40 hours post transfection. Samples infected for 5 hours were sequenced by ChIP for binding DNAs of the OC2 mutant in Neuro-2a cells.

2023-09-18 | GSE241863 | GEO

NAT8L mRNA oxidation is linked to neurodegeneration in multiple sclerosis

Project description:RNA oxidation has been implicated in neurodegeneration, but the underlying mechanism for such effects is unclear. Recently, we demonstrated extensive RNA oxidation within the neurons in multiple sclerosis (MS) brain. In this report we identified selectively oxidized mRNAs in neuronal cells that pertained to neuropathological pathways. N-acetyl aspartate transferase 8 like (NAT8L) mRNA is one such transcript, whose translated product enzymatically synthesizes N-acetyl aspartic acid (NAA), a neuronal metabolite essential for myelin synthesis. We reasoned that impediment of translation of an oxidized NAT8L mRNA will result in reduction in its cognate protein, thus lowering NAA level. This assertion is directly supported by our studies on a model cellular system, an MS animal model and postmortem human MS brain. Reduced NAA level in the brain could hamper myelin synthesis causing neuronal damage, which results in MS neurodegeneration. Overall, this work provides a framework for mechanistic understanding of the link between RNA oxidation and neurodegenerative diseases.

2020-01-28 | GSE144294 | GEO

RNA-seq identification of herpes simplex virus type 1 transcription in Neuro-2a cells overexpressing ONECUT2

Project description:This is a part of the study that shows that a host gene,ONECUT2 (OC2), promote herpes simplex virus 1 (HSV-1) transcription. These RNA-seq analyses viral genes transcription in Neuro-2a cells. Neuro-2a cells were transfected with pOC2△HOX2 and pcDNA plasmids for 42 hours then infected with herpes simple virus1 for 5 hours.

2023-09-18 | GSE241029 | GEO

Pax3 plays a role in Neuro-2a cells proliferation and neurite outgrowth

Project description:Our fingdings suggested that Pax3 not only inhibited the cell viability and proliferation, but also affected the cell cycle and the neurite outgrowth of Neuro-2a cells.RNA sequencing analysis showed upregulated genes in Pax3 overexpressed group were involved in cell cycle machinery, which may reveal the potential mechanism of proliferation.

2021-01-26 | GSE146058 | GEO

Hydrogen peroxide positively regulates brassinosteroid signaling through oxidation of the BRASSINAZOLE-RESISTANT1 transcription factor

Project description:Hydrogen peroxide (H2O2) is an important signaling molecule in plant developmental processes and stress responses. However, whether H2O2-mediated signaling can crosstalk with plant hormone signaling is largely unclear. Here, we show that H2O2 induces oxidation of the BRASSINAZOLE-RESISTANT1 (BZR1) transcription factor, which functions as a master regulator of Brassinosteroid (BR) signaling. Oxidative modification enhances BZR1 transcriptional activity by promoting its interaction with regulators of auxin- and light-signaling, including AUXIN RESPONSE FACTOR6 (ARF6) and PHYTOCHROME INTERACTING FACTOR4 (PIF4). Genome-wide analysis shows that H2O2-dependent regulation of BZR1 activity plays a major role in modifying gene expression related to several BR-mediated biological processes. Furthermore, we show that the thioredoxin TRXh5 can interact with, and catalyze reduction of, BZR1. We conclude that reversible oxidation of BZR1 connects H2O2- and thioredoxin-mediated redox signaling to BR signaling to regulate plant development

2018-03-21 | GSE110488 | GEO

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