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Identification of biotinylated papaverine interactors from HEK293 total cell extract by LC-MS/MS

ABSTRACT: Aim of the project was to identify interactors of the phytochemical papaverine, modified with a biotin moiety, from HEK293 total cell extract by LC-MS/MS.

INSTRUMENT(S): Orbitrap Fusion Lumos, nanoACQUITY UPLC

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Fabian Fischer

LAB HEAD: Michael Ristow

PROVIDER: PXD021808 | Pride | 2021-11-02

REPOSITORIES: Pride

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			Action	DRS
	20190627_12_P2Vexp_biotin_3.raw	Raw
	20190627_13_P2Vexp_P2V_2.raw	Raw
	20190627_14_P2Vexp_P2V_1.raw	Raw
	20190627_16_P2Vexp_biotin1.raw	Raw
	20190627_17_P2Vexp_P2V_3.raw	Raw

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1 - 5 of 9

Publications

Grainyhead 1 acts as a drug-inducible conserved transcriptional regulator linked to insulin signaling and lifespan.

Grigolon Giovanna G Araldi Elisa E Erni Reto R Wu Jia Yee JY Thomas Carolin C La Fortezza Marco M Laube Beate B Pöhlmann Doris D Stoffel Markus M Zarse Kim K Carreira Erick M EM Ristow Michael M Fischer Fabian F

Nature communications 20220110 1

Aging is impacted by interventions across species, often converging on metabolic pathways. Transcription factors regulate longevity yet approaches for their pharmacological modulation to exert geroprotection remain sparse. We show that increased expression of the transcription factor Grainyhead 1 (GRH-1) promotes lifespan and pathogen resistance in Caenorhabditis elegans. A compound screen identifies FDA-approved drugs able to activate human GRHL1 and promote nematodal GRH-1-dependent longevity. ...[more]

PMID: 35013237

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Identification of human GRHL1 interactors and post-translational modifications by LC-MS/MS

Project description:Aim of the project was to identify interactors and post-translational modifications of recombinant 3xFLAG-6xHis-tagged human GRHL1, tandem-affinity purified from isolated HEK293 nuclei treated with DMSO as control or with the phytochemical papaverine.

2021-11-02 | PXD021768 | Pride

Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin

Project description:This SuperSeries is composed of the following subset Series: GSE32694: Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin [gene expression profile] GSE32695: Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin [microRNA expression profile] Refer to individual Series

2011-12-31 | E-GEOD-32696 | biostudies-arrayexpress

Four Hi-C datasets from mESCs and 2C-like cells generated by knocking down the histone chaperone CAF-1 in mESCs

Project description:In this experiment, we've examined chromatin conformation of mESCs and 2C-like cells generated from a CAF-1 knockdown. The method to generate the knockdown was described in (). We performed a modified in situ Hi-C protocol from (Rao et al., 2014) and that can be found in detail at (Díaz et al., 2017, under revision). Samples were digested with MboI restriction enzyme having as starting material 100k cells with two biological replicates per sampling point. The aim of the experiment was to analyze the potential chromatin conformational changes that accompany the mESC to 2C-like transition.

2023-11-16 | E-MTAB-6330 | biostudies-arrayexpress

Chromatin contact maps of 24 and 48 hours post-fertilisation zebrafish (Danio rerio) embryos and 48 hours post-fertilisation fibroblasts

Project description:In this experiment, we've examined chromatin conformation of zebrafish embryos at 24 and 48 hours post-fertilization (hpf), as well as 48 hpf fibroblasts. The aim of this study was to characterise the 3D chromatin structure of zebrafish and perform an evolutionary comparison with mammalian genomes (Homo sapiens and Mus musculus) focusing on syntenic regions and zebrafish ohnologs (duplicated genes that were kept in the genome after the third round of whole-genome duplication).

2023-11-17 | E-MTAB-6313 | biostudies-arrayexpress

Six in situ Hi-C libraries of control and mESC auxin-inducible degrons for Scc1 and Ring1b.

Project description:In this experiment, we've examined chromatin conformation differences of E14 mESC against cohesin and Ring1b degrons. We performed a modified in situ Hi-C protocol from (Rao et al., 2014) that can be found in detail at (Díaz et al., 2018). Samples were digested with MboI restriction enzyme. The aim of the experiment was to characterize the role of cohesin and polycomb on the 3D structure of mouse chromatin.

2020-01-23 | E-MTAB-7816 | biostudies-arrayexpress

Biotinylated H3K9me2 and H3S10ph peptides pull down analysis

Project description:To further explore the interacting proteins associated with histone modifications, we synthesized biotin labelled peptides for pull down examination.

2023-03-11 | PXD039496 | Pride

iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

Project description:Analysis of UNR (CSDE1) binding to RNA targets by iCLIP transcriptome-wide mapping.

2016-11-07 | E-MTAB-3818 | biostudies-arrayexpress

Ancistrocladinium A induces cell death in drug-resistant myeloma cells via targeting transcription and RNA splicing machinery and ATF4-dependent apoptotic pathway: a promising candidate as a drug for multiple myeloma

Project description:N,C-coupled naphthylisoquinoline alkaloids like the natural product ancistrocladinium A, was known for its strong antiprotozoal activity, but had never explored for its antitumor activity. We found the alkaloid to be a very efficient anti-myeloma agent in various cell lines, including proteasome inhibitor-resistant cell lines and patient's primary CD138+ myeloma cells either alone or in combination approaches with the compounds carfilzomib or panobinostat. To gain further insight, we used an MS-based approach with the biotinylated derivative of Ancistrocladinium A, leading to an enrichment of RNA splicing associated proteins. We validated alternative pre-mRNA splicing by analyzing RNA gene expression and splicing using the human Clariom D gene array after treatment of INA-6 cells with the alkaloid. Important pathways with altered RNA expression levels included RNA processing, transcription and splicing, and the ribonucleoprotein complex. Pathways with altered RNA splicing included PSMB5 target genes and, therefore, a driver of unfolded protein response (UPR) along with transcription-associated and cell cycle-associated genes. Furthermore, we confirmed the splicing-induced protein expression of activating tran-scription factor 4 (ATF4), a key regulator of UPR. Finally, histone 2A (H2A) phosphorylation and PARP-1 cleavage as an indicator of apoptosis indicator was also detected. Taken together, an-cistrocladinium A can be considered as a potent agent against PI-resistance in MM either alone or in combination with clinically approved drugs.

2023-10-24 | PXD043261 | Pride

Low input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells

Project description:In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with MboI restriction enzyme having as starting material 1 million (M), 100 thousand (k), 50k, 25k, 10k or 1k cells. As well as, to 2 samples digested with HindIII restriction enzyme that had as starting material 5M or 100k cells. Traditional in situ Hi-C protocols recommend 5-10 million starting cells. The aim of the experiment was to assess the impact of decreasing the cell number on reproducibility, library complexity, chromatin structure visualization in order to adapt the method to the study of rare cell populations. Furthermore, we have characterised the 3D structure of peripheral blood mononuclear cells (PBMCs) obtained from a blood extraction from a healthy donor and from a lymph node biopsy from a DLBCL patient as a proof of concept for the suitability of Low-C for rare cell population analysis.

2018-11-30 | E-MTAB-5875 | biostudies-arrayexpress

Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

Project description:We evolved Escherichia coli cells over 500 generations under five environments that include four abiotic stressors: osmotic, acidic, oxidative, n-butanol, and control The goal of the experiment: Bacterial populations have a remarkable capacity to cope with extreme environmental fluctuations in their natural environments. In certain cases, adaptation to one stressful environment provides a fitness advantage when cells are exposed to a second stressor, a phenomenon that has been coined as cross-stress protection. A tantalizing question in bacterial physiology is how the cross-stress behavior emerges during adaptation and what the genetic basis of acquired stress resistance is. RNA profiles were obtained for six E. coli strains evolved for 500 generations under abiotic stressors; two technical replicates for each strain where sequenced by Illumina GAII analyzer

2013-02-28 | E-GEOD-39926 | biostudies-arrayexpress

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