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TIAR represses c-Myc biosynthesis following ultraviolet light irradiation

ABSTRACT: RNA was isolated from material that had been subjected to immunoprecipitation (IP) from RKO cells that were either left untreated or irradiated with 20 J/m2 UVC and collected 1h later; IP assays were carried out using either an antibody recognizing RNA-binding protein TIAR, or using a control IgG1 antibody. RNA was reverse-transcribed in the presence of [alpha-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays. The experiment was repeated using three independent sample sets. The samples were numbered Tc-1, Tc-2, Tc-3, Tuv-1, Tuv-2, Tuv-3, IgG1c-1, IgG1c-2, IgG1c-3, IgG1uv-1, IgG1uv-2, and IgG1uv-3. ‘Tc’ denotes RNA from IP reactions using untreated cells and anti-TIAR antibody, ‘Tuv’ denotes RNA from IP reactions using UVC-treated cells and anti-TIAR antibody, ‘IgG1c’ denotes RNA from IP reactions using untreated cells and anti-IgG1 antibody, and ‘IgG1uv’ denotes RNA from IP reactions using UVC-treated cells and anti-IgG1 antibody. The numbers 1, 2 and 3 correspond to the three independent experimental datasets. Keywords = post-transcriptional / translation / nascent protein synthesis / stress response / ribonomics Keywords: ordered

ORGANISM(S): Homo sapiens

PROVIDER: GSE1433 | GEO | 2004/05/27

SECONDARY ACCESSION(S): PRJNA89969

REPOSITORIES: GEO

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TIAR represses c-Myc biosynthesis following ultraviolet light irradiation

Project description:RNA was isolated from material that had been subjected to immunoprecipitation (IP) from RKO cells that were either left untreated or irradiated with 20 J/m2 UVC and collected 1h later; IP assays were carried out using either an antibody recognizing RNA-binding protein TIAR, or using a control IgG1 antibody. RNA was reverse-transcribed in the presence of [alpha-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays. The experiment was repeated using three independent sample sets. The samples were numbered Tc-1, Tc-2, Tc-3, Tuv-1, Tuv-2, Tuv-3, IgG1c-1, IgG1c-2, IgG1c-3, IgG1uv-1, IgG1uv-2, and IgG1uv-3. âTcâ denotes RNA from IP reactions using untreated cells and anti-TIAR antibody, âTuvâ denotes RNA from IP reactions using UVC-treated cells and anti-TIAR antibody, âIgG1câ denotes RNA from IP reactions using untreated cells and anti-IgG1 antibody, and âIgG1uvâ denotes RNA from IP reactions using UVC-treated cells and anti-IgG1 antibody. The numbers 1, 2 and 3 correspond to the three independent experimental datasets. Keywords = post-transcriptional / translation / nascent protein synthesis / stress response / ribonomics Keywords: ordered

2010-06-09 | E-GEOD-1433 | biostudies-arrayexpress

Concurrent Versus Individual Binding of HuR and AUF1 to Common Labile Target mRNAs

Project description:RNA was isolated from material that had been immunoprecipitated (IP) from Hela cells using antibodies recognizing RNA-binding proteins HuR or AUF1, as well as using a control IgG1 antibody. RNA was reverse-transcribed in the presence of [alpha-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays. The experiment was repeated using three independent sample sets. The samples were numbered HuR-1, HuR-2, HuR-3, AUF1-1, AUF1-2, AUF1-3, IgG1-1, IgG1-2, IgG1-3. HuR represents RNA from IP reactions using an anti-HuR antibody, AUF1 represents RNA from IP reactions using an anti-AUF1 antibody and, IgG1 represents RNA from IP reactions using an anti-IgG1 antibody. The numbers 1, 2 and 3 correspond to the three independent experimental datasets. Keywords = RNa-binding protein Keywords = mRNA stability Keywords = exosome Keywords = polysome Keywords = RNA motif Keywords: ordered

2004-05-04 | GSE1361 | GEO

Concurrent Versus Individual Binding of HuR and AUF1 to Common Labile Target mRNAs

2010-06-09 | E-GEOD-1361 | biostudies-arrayexpress

Genome-wide analysis of TIAR RNA ligands in mouse macrophages before and after LPS stimulation

2016-02-05 | GSE77577 | GEO

Genome-wide analysis of TIAR RNA ligands in mouse macrophages before and after LPS stimulation

Project description:TIA-1 related protein (TIAR) is a RNA-binding protein involved in several steps of gene expression such RNA splicing and translation. TIAR contains three RNA recognition motifs (RRMs) allowing its interaction with specific sequences localized in the untranslated regions (UTRs) of several mRNAs. In myeloid cells, TIAR has been shown to bind and regulate the translation and stability of various mRNAs encoding proteins important for the inflammatory response, such as TNFÎ±, Cox-2 or IL-8 . Here, we generated two macrophage-like RAW 264.7 cell lines expressing either a tagged full-length TIAR protein or a RRM2-truncated mutant unable to bind RNA with high affinity . By a combination of RNA-IP and microarray analysis (RIP-chip), we identified mRNAs specifically bound by the full-length protein both in basal conditions and in response to LPS. Microarray hybridization was performed on TIAR-FLAG-associated mRNAs or TIARÎRRM2-FLAG-associated mRNAs in unstimulated and LPS-stimulated RAW264.7 cells. Enrichment of TIAR-FLAG-associated mRNAs and TIARÎRRM2-FLAG-associated mRNAS were normalized to total transcriptome of TIAR-FLAG and TIARÎRRM2-FLAG expressing-RAW264.7 cells respectively. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.

2016-02-05 | E-GEOD-77577 | biostudies-arrayexpress

Single Cell RNA-seq on Human PBMC

Project description:To assess the impact of IgG1 and IgG4 variants of a TIGIT-Fc-LIGHT fusion protein on human PBMC expression, each fusion protein or an untreated control were incubated with human PBMC for 2 days in AIMV lymphoproliferative media. Both IgG1 and IgG4 variants of TIGIT-Fc-LIGHT induced broad immune cell activation on T, NK, and myeloid cells.

2022-05-27 | GSE201999 | GEO

Expression data at 24 hours after the blocking of Shh signaling in tooth germs at embryonic day 14

Project description:The genetic mechanism governing the spatial patterning of teeth still remains to be elucidated. Sonic hedgehog (Shh) is one of key signaling molecules involved in the spatial patterning of teeth. By utilizing maternal transfer of 5E1 (an IgG1 monoclonal antibody against Shh protein) through the placenta to block Shh signaling, we investigated the changes in tooth patterning and in gene expression. We used microarrays to detect specific genes related with Shh signaling in tooth germs and identified some specific genes up- or down-regulated after blocking of Shh signaling activity. Gene-chip expression analysis was performed with RNA from mandibular tooth germs from embryos of pregnant mice at one day after injection of 5E1 (an IgG1 monoclonal antibody against Shh protein; number of replicates =2), 40-1a (an IgG1 monoclonal antibody against β-galactosidase; number of replicates=2), cyclopamine (a specific Smo antagonist; number of replicates=2) or PBS (Phosphate buffered saline; number of replicates=2), using a Affymetrix mouse gene microarray.

2011-02-22 | E-GEOD-27429 | biostudies-arrayexpress

SHR-1210 in Combination With BP102 and XELOX in Patient With Metastatic Colorectal Cancer

Project description:This is an open label, single-arm, multi-center, phase II study of SHR-1210 in metastatic colorectal cancer patients with the recurrent lesion(s) post-surgery or the untreated mCRC. SHR-1210 is a humanized monoclonal antibody against Programmed death 1(PD-1).BP102 is a humanized recombinant monoclonal IgG1 antibody. The primary objective of this study is to investigate the safety and efficacy of the subjects who given the combination therapy.

| 2282196 | ecrin-mdr-crc

Changes in histone modifications H3K4me2, H3k27me3 and H3K36me3 due to phenobarbital in mice

Project description:29-32 days old male mice where either treated with Phenobarbital or untreated Replicated control/treated study with IP and Input per group and antibody

2012-11-10 | E-GEOD-41399 | biostudies-arrayexpress

ECT2 and AURKB Modulate Formation of Stress Granules Containing Transcripts from Diverse Cellular Pathways in Astrocytoma Cells

Project description:Stress granules are small RNA-protein granules that modify the translational landscape during cellular stress to promote survival. The RhoGTPase RhoA is implicated in the formation of RNA stress granules. Our data demonstrate that the cytokinetic proteins ECT2 and AurkB are localized to stress granules in human astrocytoma cells. AurkB and its downstream target histone-3 are phosphorylated during arsenite-induced stress. Chemical (AZD1152-HQPA) and siRNA inhibition of AurkB results in fewer and smaller stress granules when analyzed utilizing high throughput fluorescent based cellomics assays. RNA immunoprecipitation with the known stress granule aggregates TIAR and G3BP1 was performed on astrocytoma cells and subsequent analysis revealed that astrocytoma stress granules harbour unique mRNAs for various cellular pathways including cellular migration, metabolism, translation and transcriptional regulation. Human astrocytoma cell stress granules contain mRNA that are known to be involved in glioma signaling and the mTOR pathway. These data provide evidence that RNA stress granules are a novel form of epigenetic regulation in astrocytoma cells, which may be targetable by chemical inhibitors and enhance astrocytoma susceptiblity to conventional therapy such as radiation and chemotherapy. Astrocytoma cells were either untreated or treated with arsenite to induce stress granule formation and RNA immunoprecipitates were analyzed by exon array analysis. RNA species that were enriched in TIAR RIPs and G3BP1 RIPS, respectively were compared to compared to TIAR and G3BP1 RIPs from untreated cells and input controls. Ingenuity pathway analysis was performed on the stress granule enriched mRNAs from the TIAR and G3BP1 RIPs to identify significant functional biology networks.

2016-02-29 | E-GEOD-76814 | biostudies-arrayexpress

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