BRCA2-N-terminus interacting proteins in HEK293T cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap XL
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Embryonic Cell, Kidney
SUBMITTER: 
Valentin SABATET
LAB HEAD: Damarys Loew
PROVIDER: PXD018979 | Pride | 2021-01-27
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| BRCA2-NT.dat | Other | |||
| Design.xls | Xls | |||
| F6152BL.RAW | Raw | |||
| F6152BL.dat | Other | |||
| F6153BL.RAW | Raw |
Items per page: 5 1 - 5 of 97 |
Similar Datasets
Project description:Mlh3 internally tagged with Flag was pulled down from synchronous meiotic cells at t = 4 h in meiosis, in order to identify its interacting partners involved in meiotic crossover formation
2020-11-06 | PXD014180 | Pride
Project description:The small heat shock protein Hsp27 has been long demonstrated as a major driver of Castration Resistant Prostate Cancer (CRPC) progression via an androgen receptor-independent pathway. In the light of identification of its molecular mechanisms, we found that the RNA helicase protein DDX5 was an interactor of Hsp27 and DDX5 expression was regulated by Hsp27 through its cytoprotective function. We showed that DDX5 was overexpressed in a large collection of human samples in aggressive PCs, especially CRPC. Here, we described the protein-protein interaction network of DDX5 which were identified in four human prostate cell lines (PNT1A, LNCaP, DU-145 and PC-3) representing different disease stages using immunoaffinity purification and quantitative mass spectrometry. The DDX5 interactome in CRPC cells was enriched in several functions (DNA damage response, translation, transcription, RNA stability, and DNA conformation changes) involved in disease progression. Furthermore, we found a new critical function of DDX5 in DNA damage repair in CRPC and validated the interaction of DDX5 with the DNA repair complex Ku70/Ku86 which plays a pivotal role in the NHEJ process. We also showed that DDX5 overexpression conferred resistance to DNA damage poisoners (such as irradiation and cisplatin) in CRPC, a feature that could lead to genome maintenance, tumor progression and treatment resistance.
2022-08-21 | PXD023252 | Pride
Project description:Extracellular vesicles (EVs) are present in all body fluids. Shed by cells, their molecular make-up reflects that of their cell of origin and/or tissue pathological situation. Our working hypothesis was that analyzing the protein composition, protein abundance, and functional clustering of EVs released by peritoneal exudate cells (PECs) in the pristane experimental lupus model would allow us to identify predictive or diagnostic biomarkers that might discriminate the autoimmunity process in lupus from inflammatory reactions and/or normal physiological processes. Three pools of PE-EVs were isolated from pristane-treated mice (WT versus Cd38-/- mice) by qEV size exclusion column methodology (F5-12, F5-10 and F11-12). Protein extracts were analyzed by LC-MS/MS. Protein identification was performed with ProteinScape, and MASCOT data searching using Swiss-Prot database. For relative quantification the emPAI-based method was used. The functional enrichment analysis was based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO + CluePedia apps within Cytoscape environment. STRING app and EnrichR tools were also used. Gene Ontology (GO) and signaling pathways enrichment analyses of F5-10 and F11-12 PE-EVs via ClueGO analyses showed that the proteins clustered in functionally distinct GO terms and signaling pathways. Moreover, the predominance of given GO terms in PE-EVs seemed to vary with the extent of the inflammatory/autoimmune reaction to pristane. Compared with the protein content and protein abundance in PECs (mainly Ly6Chi inflammatory monocytes and neutrophils), PE-EVs showed an enrichment in neutrophil-associated functions, in particular in PE-EVs from Cd38-/- mice.
2022-10-20 | PXD035257 | Pride
Project description:In this study, we have carried out a broad census of histone PTMs in Ectocarpus chromatin and have developed a method to evaluate the genome-wide distribution of specific marks. We show that modulation of the expression of sporophyte-biased genes during the life cycle is correlated with marked changes in the pattern of three histone PTMs. In contrast, the expression patterns of gametophyte-biased genes were not correlated with modifications to the histone PTMs assayed, suggesting that gametophyte-biased and sporophyte-biased gene expression are mediated by different epigenetic processes.
2020-11-06 | PXD013535 | Pride
Project description:Comparitive proteomics on Clematis terniflora leaves with VIGS-CtPPO and VIGS-vector
2018-12-21 | PXD011439 | Pride
Project description:Identifying the proteins associated with the polyribosomes in astrocytes from the mouse brain to unveil translation regulation mechanisms in these cells.
2023-07-20 | PXD033121 | Pride
Project description:Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the understanding of fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing from several major and deep-branching eukaryotic groups, such as the marine model diatom Phaeodactylum tricornutum. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans. Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on P. tricornutum histones, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining active or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes. This study is the first genome-wide characterization of the histone code from a Stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.
2015-05-08 | PXD002148 | Pride
Project description:CCCTC-binding factor (CTCF) is a DNA-binding protein that plays important roles in chromatin organization, though the mechanism by which CTCF carries out these functions is not fully understood. Recent studies show that CTCF recruits the cohesin complex to insulator sites and that cohesin is required for insulator activity. Here we have shown that the DEAD box RNA helicase p68 (DDX5) and its associated noncoding RNA, steroid receptor RNA activator (SRA), form a complex with CTCF that is essential for insulator function. p68 was detected at CTCF sites in the IGF2/H19 imprinted control region (ICR) as well as other genomic CTCF sites. In vivo depletion of SRA or p68 reduced CTCF-mediated insulator activity at the IGF2/H19 ICR, increased levels of IGF2 expression, and increased interactions between the endodermal enhancer and IGF2 promoter. p68/SRA also interacts with members of the cohesin complex. Depletion of either p68 or SRA does not affect CTCF binding to its genomic sites, but it does reduce cohesin binding. The results suggest that p68/SRA stabilizes the interaction of cohesin with CTCF, by binding to both, and is required for proper insulator function. Identification of p68-binding sites in Hela cells using ChIP-Seq.
2010-11-16 | E-GEOD-24126 | biostudies-arrayexpress
Project description:DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we found that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also found that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.
2020-08-14 | PXD020608 | Pride
Project description:Ddx5 inhibition in RN2 cells slows cell proliferation and induces apoptosis within 48-72hrs. The aim of this analysis was to gain insight into how Ddx5 inhibition causes this outcome by analyzing gene expression changes in RN2 cells that occur at early timepoints after Ddx5 inhibition that precedes the timepoint when RN2 proliferation/cell death becomes evident in tissue culture (72hrs after inhibition). Derivatives of RN2 AML cells were prepared that encode doxycycline-inducible expression of either of two different shRNAs targeting Ddx5 (shDdx5.1322 and shDdx5.2086) or a negative control shRNA that targets Renilla Luciferase (shRen.713). Six independent cultures of each derivative RN2 cell line (shDdx5.1322, shDdx5.2086, or shRen.713) were treated with doxycycline at timepoint 0 days to induce expression of the indicated shRNA in the RN2 cells. Each shRNA is co-expressed with dsRed in a doxycycline-induced manner and flow cytometry analysis indicated that doxycycline induced expression of dsRed and the shRNA in 70-to-80% of the cells in each culture. RNA was isolated from three independent cultures of each derivative RN2 cell line at either 24hrs and 48hrs after dpxycycline treatment. Therefore this study consists of 18 samples, sequencing results from biological triplicate samples of RN2-shDdx5.1322, RN2-shDdx5.2086, and RN2-shRen.713 at 24hrs post-doxycycline and sequencing results from biological triplicate samples of RN2-shDdx5.1322, RN2-shDdx5.2086, and shRen.713 at 48hrs post-doxycycline.
2013-12-26 | E-GEOD-53599 | biostudies-arrayexpress