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Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins

ABSTRACT: The aim of the MS analysis is to identify fatty acids modifying Cys3 of GNAI3 in cells exposed to high C16:0 or C18:0 concentrations. Detailed description in the manuscript Nuskova et al. submitted to NatComms.

INSTRUMENT(S): ultraflex

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Hana Nuskova

LAB HEAD: Aurelio Teleman

PROVIDER: PXD027064 | Pride | 2021-08-26

REPOSITORIES: Pride

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Nuclear condensates of p300 formed though the structured catalytic core can act as a storage pool of p300 with reduced HAT activity.

Zhang Yi Y Brown Kyle K Yu Yucong Y Ibrahim Ziad Z Zandian Mohamad M Xuan Hongwen H Ingersoll Steven S Lee Thomas T Ebmeier Christopher C CC Liu Jiuyang J Panne Daniel D Shi Xiaobing X Ren Xiaojun X Kutateladze Tatiana G TG

Nature communications 20210729 1

The transcriptional co-activator and acetyltransferase p300 is required for fundamental cellular processes, including differentiation and growth. Here, we report that p300 forms phase separated condensates in the cell nucleus. The phase separation ability of p300 is regulated by autoacetylation and relies on its catalytic core components, including the histone acetyltransferase (HAT) domain, the autoinhibition loop, and bromodomain. p300 condensates sequester chromatin components, such as histon ...[more]

PMID: 34326347

Similar Datasets

Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins

Project description:The aim of the MS analysis is to identify fatty acids modifying Cys3 of GNAI3. Detailed description in the manuscript Nuskova et al. submitted to NatComms.

2021-07-22 | PXD021517 | Pride

mRNA binding - Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

Project description:RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV crosslinking of RBPs to RNA, we describe a systematic, unbiased, and comprehensive approach, termed "interactome capture," to define the mRNA interactome of proliferating human HeLa cells. We identify 860 proteins that qualify as RBPs by biochemical and statistical criteria, adding more than 300 RBPs to those previously known and shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism, RNA-binding kinases, and RNA-binding architectures. Unexpectedly, we find that many proteins of the HeLa mRNA interactome are highly intrinsically disordered and enriched in short repetitive amino acid motifs. Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings.

2015-09-11 | PXD002880 | Pride

CTCF loss has limited effects on genome architecture in Drosophila despite critical regulatory functions.

Project description:Proteins co-purifying with recombinantly purified and N-terminally GFP-3C-tagged CTCF N-terminus (amino acids 1-293) produced in bacteria were identified by incubating the tagged bait with soluble nuclear protein extracts from 0-12h hour-old wildtype (OregonR strain) Drosophila melanogaster embryos.

2021-01-18 | PXD019487 | Pride

Illumina Microarray of MRC5 cell with or without KDM7A-DT overexpression

Project description:KDM7A Divergent Transcript (KDM7A-DT) is a stress-induced lncRNAs. In our previous studies, KDM7A-DT showed the most robust cellular phenotype alteration and a significant TP53-dependency upon oxidative and oncogenic stress induction. To investigate the functional roles of KDM7A-DT, we first performed overexpression experiments using fibroblasts. We found that MRC5 cells overexpressing KDM7A-DT escaped cell cycle proliferation and long-term survival ability and were associated with a distinct stress-related morphology (enlarged and flattened cells) compared to cells expressing just the vehicle control. To examine the effects of KDM7A-DT overexpression on the transcriptome, we performed a differential expression gene (DEG) analysis comparing a group of four independent biological replicates of MRC5 overexpressing KDM7A-DT to a group of samples from control cells.

2023-05-01 | E-MTAB-11819 | biostudies-arrayexpress

Illumina Microarray of T47D cell with or without KDM7A-DT silencing under normal and oxidative stress conditions

Project description:KDM7A Divergent Transcript (KDM7A-DT) is a stress-induced lncRNAs. In our previous studies, KDM7A-DT showed the most robust cellular phenotype alteration and a significant TP53-dependency upon oxidative and oncogenic stress induction. Since about 50% of human breast cancers have mutant p53 and associated genetic alterations, it is essential to determine what effect a mutant p53 would have on acquired pro-oncogenic functions of KDM7A-DT. In these experiments, we used four antisense LNA Gapmer sequences designed by Exiqon (Vedbaek, Denmark). One of these was a negative control, while the other 3 were designed to target the end of the transcript representing the full-length lncRNA KDM7A-DT (lncRNA; GRCh38/hg38, chr7: 140,178,951-140,179,640). To test the effect of KDM7-DT in the context of mutant p53, we selected the p53-negative luminal BC cells T47D. For each of the LNA gapmers, we utilized 3 technical replicates across two main experimental conditions (normal vs. oxidative stress induced via 30 mins of 0.2 mM H2O2 treatment). Overall, we measured the signals for 47,323 Illumina array probes across 24 individual experiments (4 LNA gapmers * 3 technical replicates * 2 main experimental conditions).

2023-05-01 | E-MTAB-11818 | biostudies-arrayexpress

ChIP-seq analysis of the Cib1 transcription factor with and without clp1 overexpression.

Project description:For ChIPseq analyses JB1 and UVO151 (JB1 Pcrg:clp1) were transformed with a Cib1-3xHA fusion construct was expressed under control of the endogenous promoter. The fusion construct was integrated at the endogenous locus replacing the native Cib1 gene.

2019-04-04 | E-MTAB-7460 | biostudies-arrayexpress

Genome-wide sequences bound by the transcription factors BLUEJAY and JACKDAW in Arabidopsis thaliana roots

Project description:We report the genomic sequences bound by the C2H2 transcription factors BLUEJAY and JACKDAW as profiled by chromating immunoprecipitation experiments followed by Illumina high sequencing. Plants were carrying constructs of proteins (translational) fusions of these transcription factors to the yellow fluorescent protein. Gene fusions were expressed under all their genomic regulatory regions using recombineering. The recombineering technique was used to recombine the fluorecent protein at the 3' end of their genomic regions in a JATY clone carrying these genes. Subsequently the JATY clones carrying these translational fusions were introgressed into plants. We performed ChIP on roots grown under standard conditions and fixed with formaldehyde in PBS-EDTA. Sequences bound by BLUEJAY and JACKDAW were immunoprecipitated with a-GFP AbCam290 at 4 Â°C overnight. Biological replicate samples were make into libraries of ~100 bp insert size and 50 bp of single ends sequenced through Illumina High Sequencing. Two biological replicates of samples of plants expressing the C2H2 transcription factors fused to the yellow fluorescent protein; and of control wild type plants processed through the same protocol.

2015-11-02 | E-GEOD-60011 | biostudies-arrayexpress

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 disease specific mechanisms and vulnerabilities.

Project description:Coronaviruses constitute a constant threat as documented by the recent emergence of SARS-CoV-2 that has caused more than 2,5 million deaths worldwide. Despite this our understanding of coronaviruses and how they interact with their host is very limited. Here we describe a novel phage display library for the discovery of viral short linear interaction motifs (SLiMs) from RNA viruses that mediate binding to human host factors. We utilize this library to uncover the unique patterns of viral SLiMs mediating SARS-CoV-2 - host factor interactions. This established a specific interaction between the human G3BP1/2 proteins and an xFG peptide motif in the viral nucleocapside (N) protein that when disrupted reduce viral replication and infection. We show that the N protein through this xFG motif modulates the G3BP1/2 host interactome by competing with numerous cellular xFG containing proteins and inhibits G3BP1/2 mediated stress granule formation. Collectively our work outlines a strategy for system-wide understanding of viral-host factor interactions that provides both mechanistic insight and pinpoints therapeutically relevant interactions for development of novel antiviral strategies.

2021-10-29 | PXD025410 | Pride

Chaperonin CCT Checkpoint Function in Basal Transcription Factor TFIID Assembly

Project description:TFIID is a cornerstone of eukaryotic gene regulation. Distinct TFIID complexes with unique subunit composition exist and several TFIID subunits are shared with other complexes, conveying intricate cellular decision making to control subunit allocation and functional assembly of this essential transcription factor. However, the underlying molecular mechanisms remain poorly understood. Here, we used quantitative proteomics to examine TFIID submodules and assembly mechanisms in human cells. Structural and mutational analysis of the cytoplasmic TAF5/TAF6/TAF9 submodule identified novel interactions crucial for TFIID integrity, and for allocating TAF9 to TFIID or the SAGA co-activator complex. We discover a key checkpoint function for the chaperonin CCT, which specifically associates with nascent TAF5 for subsequent handover to TAF6/TAF9 and ultimate holo-TFIID formation. Our findings illustrate at the molecular level how multisubunit complexes are crafted in the cell, involving checkpoint decisions facilitated by a chaperone machine.

2022-03-02 | PXD011211 | Pride

Translatome and transcriptome profiling of FK866 response in Jurkat cells

Project description:We treated Jurkat cells for 48 hr with a sublethal dose of FK866 (5 nM) and DMSO (Mock, control treatment). RNA samples for microarrays derived from fractionated samples by sucrose gradient (sub-polysomes, polysomes), giving us the chance to perform an analysis among polysomal/subpolysomal distribution in treated or untreated cells and the possibility to identify the multi-level gene expression regulation effects of FK866. We are interested to find differentially expressed genes, in the early phase of cell response to FK866, and genes that account for a specific post-transcriptional regulation exerted by the cell in response to the drug. Keywords: polysomal profiling, translatome profiling, polysomal RNA, subpolysomal RNA, translational profiling, polysome profiling, post-transcriptional regulation, FK866, translational efficiency. Gene expression signals derived from the polysomal and subpolysomal RNA populations were compared by microarrays analysis to those obtained from total RNAs (derived from the sum of all the fractions in the polysomal gradient). Polysomal RNA, subpolysomal RNA and total RNA were isolated from Jurkat cells treated with FK866 5 nM or DMSO (mock, control treatment) for 48 hr. Cells lysates were collected from control cells (mock) and from treated cells (FK866). All experiments were run in biological quadruplicates.

2015-04-01 | E-GEOD-53772 | biostudies-arrayexpress

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