Browse
Submit Data
Databases
API
Help

Dataset Information

185 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

R2TP_TAP-MS - R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein

ABSTRACT: The R2TP/Prefoldin-like (R2TP/PFDL) complex is a cochaperone complex involved in the assembly of a number of critical protein complexes. Here we use multiple target tandem affinity purification (TAP) coupled to mass spectrometry to map out the interaction network around R2TP/PFDL.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Christian Poitras

LAB HEAD: Benoit Coulombe

PROVIDER: PXD006198 | Pride | 2018-10-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein.

Cloutier Philippe P Poitras Christian C Durand Mathieu M Hekmat Omid O Fiola-Masson Émilie É Bouchard Annie A Faubert Denis D Chabot Benoit B Coulombe Benoit B

Nature communications 20170531

The R2TP/Prefoldin-like (R2TP/PFDL) complex has emerged as a cochaperone complex involved in the assembly of a number of critical protein complexes including snoRNPs, nuclear RNA polymerases and PIKK-containing complexes. Here we report on the use of multiple target affinity purification coupled to mass spectrometry to identify two additional complexes that interact with R2TP/PFDL: the TSC1-TSC2 complex and the U5 small nuclear ribonucleoprotein (snRNP). The interaction between R2TP/PFDL and the ...[more]

PMID: 28561026

Similar Datasets

R2TP_SILAC_FLAG-MS - R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein

Project description:The R2TP/Prefoldin-like (R2TP/PFDL) complex is a cochaperone complex involved in the assembly of a number of critical protein complexes. Here we use stable isotope labeling with amino acids in cell culture (SILAC) and FLAG tag affinity purification coupled to mass spectrometry to assess whether siRNA-driven knockdown of cofactors or subunits of R2TP/PFDN affects composition of U5 snRNP and TSC complex.

2017-11-02 | PXD006199 | Pride

Paf1C plays novel subunit-specific roles in alternative cleavage and polyadenylation

Project description:The PAF complex (Paf1C) has been shown to regulate chromatin modifications, gene transcription, and PolII elongation. Here, we provide the first genome-wide analysis of chromatin occupancy by the entire PAF complex in mammalian cells. We show that Paf1C is recruited not only to promoters and gene bodies, but also to regions downstream of cleavage/polyadenylation (pA) sites at 3â ends, a profile that sharply contrasted with the yeast complex. Remarkably, our studies identified novel, subunit-specific links between Paf1C and regulation of alternative cleavage and polyadenylation (APA) and upstream antisense transcription. Moreover, we found that depletion of Paf1C subunits also resulted in the accumulation of RNA polymerase II (PolII) over gene bodies, which coincided with APA. Depletion of specific Paf1C subunits leads to global loss of histone H2B ubiquitylation, but surprisingly, there is little impact of Paf1C depletion on other histone modifications, including the tri-methylation of histone H3 on lysines 4 and 36 (H3K4me3 and H3K36me3), previously associated with this complex. Our results provide surprising differences with yeast, while unifying observations that link Paf1C with PolII elongation and RNA processing, and suggest that Paf1C could play a role in protecting transcripts from premature cleavage by preventing PolII accumulation at TSS-proximal pA sites. ChIP-seq, RNA-seq and 3'READS of Paf1C factors in mouse C2C12 myoblast cells

2016-01-15 | E-GEOD-72574 | biostudies-arrayexpress

ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

Project description:ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

2010-06-25 | E-MTAB-214 | biostudies-arrayexpress

The E2F4/p130 repressor complex cooperates with oncogenic Np73 to promote cell survival

Project description:Tumor suppressor p53 and its related proteins, p63 and p73, can be synthesized as multiple isoforms lacking part of the N- or C-terminal regions. Specifically, high expression of the Np73 isoform is notoriously associated with poor prognosis in cancer. Here, we have performed proteomics analysis of Np73 using as a cellular model human papillomavirus type 38-transformed keratinocytes (38HK) that express high levels of this isoform. We find that Np73 associates with the E2F4/p130 repressor complex through a direct interaction with E2F4. Remarkably, this interaction is favored by the N-terminal truncation of p73 characteristic of Np73 isoforms and is independent of the C-terminal splicing status. We show that the Np73-E2F4/p130 complex is recruited to the promoters of specific genes, thereby enforcing inhibition of their expression both in 38HK and in cancer-derived cell lines. Consistently, silencing of E2F4 in 38HK and in cancer cells resulted in induction of senescence. In conclusion, we have identified and characterized a novel transcriptional regulatory complex that exerts pro-proliferative functions in transformed cells

2023-02-28 | PXD022947 | Pride

IGR_Itzykson_CMML

Project description:Genomic studies in chronic myeloid malignancies, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS) and MPN/MDS, have identified common mutations in genes encoding signaling, epigenetic, transcription and splicing factors. Analysis of 18 of these genes in a cohort of 224 chronic myelomonocytic leukemias (CMML), which is the most frequent MPN/MDS, identified at least one mutated gene in 95% of the patients, with some of the mutations affecting the disease phenotype. The number of mutated genes negatively affected progression-free and overall survival in multivariate analysis. Analysis of sorted progenitors indicated an early amplification of the CMML clone at the CD34+/CD38- stage of hematopoiesis, together with a premature granulomonocytic differentiation skewing. We interrogated the clone architecture by mutation-specific discrimination analysis of single-cell-derived colonies. The genetic classification of individual colonies allowed a designation of sub-clones and the assembly of putative evolutionary trees, indicating a linear acquisition of the studied mutations. Analysis of matched pre- and post-treatment samples demonstrated clonal persistence with limited and selective elimination of sub-clones. The disease was characterized by an amplification of multipotent and common myeloid progenitors in the CD34+ compartment, both fractions showing increased granulomonocytic differentiation at the expense of erythroid progenitors, contrasting with normal granulomonocytic progenitors. Altogether, early amplification of the leukemic clone and increased granulomonocytic differentiation of early progenitors may account for the specificity of CMML among myeloid neoplasms. This experiment correspond to the analysis of gene expression profiles in total CD34+ cells from the peripheral blood of 15 patients (Chronic Myelomonocytic Leukemia) and 4 healthy controls.

2013-01-17 | E-MTAB-1044 | biostudies-arrayexpress

TrxA-binding proteins of Salmonella

Project description:To identify binding partners of Salmonella’s thioredoxin protein encoded by the trxA gene, we performed tandem-affinity purification (TAP) using a C-terminal fusion of thioredoxin with calmodulin-binding peptide and Protein A. TrxA-binding molecules were identified by mass spectrometry (MS) analysis

2023-03-11 | PXD037199 | Pride

The Nuclear Exosome is Active and Important during Budding Yeast Meiosis

Project description:We have analysed the activity of the nuclear exosome during meiosis by deletion of TRF4, which encodes a key component of the exosome targeting complex TRAMP. We find that TRAMP mutants produce high levels of CUTs during meiosis that are undetectable in wild-type cells, showing that the nuclear exosome remains functional for CUT degradation. Lack of TRAMP activity stabilises ~1600 CUTs in meiotic cells, which occupy 40% of the binding capacity of the nuclear cap binding complex (CBC). One sample each of Cbc2-associated RNA from wild-type and trf4-deleted cells at 6 hours of meiosis

2014-08-09 | E-GEOD-60221 | biostudies-arrayexpress

Comparison of Mineralizing Synchronous UMR106-01 cells with UMR106-01 cells treated with Mineralization Inhibitor AEBSF

Project description:UMR106-01 osteoblastic cells are a model for studying bone mineralization. We have shown that mineralization is temporally synchronized within cultures grown under defined conditions . Cells are plated at time zero and differentiate into osteoblastic phenotype by 64 h later. If an exogenous phosphate source is added to the cultures, the cells form and deposit hydroxyapatite mineral within distinct extracellular supramolecular lipid protein complexes termed biomineralization foci (BMF) starting 12 h later. Mineralization is largely complete by 24 h later (88 h after plating). We have also shown that AEBSF, covalent serine protease inhibitor, blocks mineralization within BMF and inhibits the fragmentation of several proteins related to biomineralization. The present experiment was designed to test whether AEBSF treatment for 12 h has an effect on transcription by UMR106-01 osteoblastic cells. AEBSF is known to inactivate several serine proteases including SKI-1 (site 1, subtilisin kexin protease-1).SKI-1 functions intracellularly to activate transmembrane bound transcription factor precursors releasing the transcriptionally active N-terminal portions to imported into the nucleus. Thus, if AEBSF blocks transcription of mineralization related genes, it would support a role for SKI-1 in gene regulation in mineralizing UMR106-01 osteoblastic cells. Comparison of triplicate cultures treated with mineralizing conditions with triplicate cultures treated with AEBSF protease inhibitor for 12 h.

2010-11-13 | E-GEOD-21476 | biostudies-arrayexpress

Transcription profiling of human breast cancer samples

Project description:We measured baseline gene expression profiles for a set of breast tumors. Note: this experiment was modified in June 2008 when the CEL files associated with some hybridizations were changed.

2008-06-28 | E-TABM-158 | biostudies-arrayexpress

AopACT binding in adult gut and fat body upon its induction in Drosophila melanogaster

Project description:ChIP-chip on FLAG-tagged AopACT expressed in adult gut and fat body.

2014-08-18 | E-MTAB-1306 | biostudies-arrayexpress