Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

KIN interactome - Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin

ABSTRACT: BioID experiment of KIN protein to determine its interactors

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Christian Poitras

LAB HEAD: Benoit Coulombe

PROVIDER: PXD010487 | Pride | 2019-10-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin.

Cloutier Philippe P Lavallée-Adam Mathieu M Faubert Denis D Blanchette Mathieu M Coulombe Benoit B

Journal of proteomics 20131016

Kin17 is a protein that was discovered through its immunoreactivity towards an antibody directed against prokaryotic RecA. Further study of Kin17 revealed a function in DNA replication and repair, as well as in pre-mRNA processing. Recently, it was found that Kin17 is methylated on lysine 135 by the newly discovered methyltransferase METTL22. To better understand the function of Kin17 and its regulation by methylation, we used multiple cell compartment protein affinity purification coupled with ...[more]

PMID: 24140279

Similar Datasets

PCNA interactome - SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair

Project description:We examined the complexity of replication fork composition upon DNA damage by employing a PCNA-based proteomic screen to uncover known and new players involved in replication and replication stress response. We used camptothecin or ultraviolet radiation, that lead to fork-blocking lesions, to establish a comprehensive proteomics map of the replisome under such replication stress conditions. We identified and examined two potential candidate proteins WIZ and SALL1 for their roles in DNA replication and replication stress response.

2018-12-14 | PXD011727 | Pride

TaqMan Peripheral blood mononuclear cell miRNA profiles of HIV-1 infected elite controllers, viremic patients, treated patients and uninfected control donors

Project description:Background: The emerging relationship between microRNAs (miRNA) and viral-control is a topic of interest in the field of HIV. Host-genome might play an important role in the control of viremia. The aim of this study was to assess the specific miRNA profile that could contribute to the control of HIV replication in Elite Controllers. Results: After adequate normalization, expression profile of 286 human miRNAs (hsa-miR) was evaluated in 29 individuals classified in 4 groups: 8 elite controllers (EC; viral load <50 cp/ml without treatment), 8 viremic progressors (VP; VL>5000 cp/ml without treatment), 8 patients under antiretroviral treatment (ART; VL<200cp/ml) and 5 uninfected individuals (HIV-) through TaqMan® Array Human microRNA Cards v3.0. A differential expression pattern consisting of 23 miRNAs overcame significantly different when comparing EC and VP. Profiling analysis segregated the population in two different blocks: while EC and HIV- clustered together in the same block (EC/HIV-_block 1), VP and ART individuals clustered together in a second block (VP/ART_block 2). Two inversely expressed miRNA patterns were determined within those two blocks: a set of 4 miRNAs (hsa-miR-221, -27a, -27b and -29b) was up-expressed in EC/HIV-_block and down-expressed in VP/ART_block while 19 miRNAs were down-expressed in block 1 and up-expressed in block 2. Differential miRNAs were successfully validated through individual RT-qPCR assays. Conclusions: Profile in EC resembled HIV- and differentially clusters with VP and ART. Therefore, differential clustering does not rely on undetectable viremia. Peripheral blood mononuclear cell samples were from five uninfected controls, eight viremic HIV-1-infected patients, eight HIV-1 elite controllers with undetectable viral load and eight HIV-1antiretroviral treated individuals with undetectable viral load.

2014-05-06 | E-GEOD-57323 | biostudies-arrayexpress

Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function

Project description:Eph receptor tyrosine kinases participate in a variety of normal and pathogenic processes during development and throughout adulthood. This versatility is likely facilitated by the ability of Eph receptors to signal through diverse cellular signalling pathways: primarily by controlling cytoskeletal dynamics, but also by regulating cellular growth, proliferation, and survival. Despite many proteins linked to these signalling pathways interacting with Eph receptors, the specific mechanisms behind such links and their coordination remain to be elucidated. In a proteomics screen for novel EPHB2 multi-effector proteins, we identified human MYC binding protein 2 (MYCBP2 or PAM or Phr1). MYCBP2 is a large signalling hub involved in diverse processes such as neuronal connectivity, synaptic growth, cell division, neuronal survival, and protein ubiquitination. Our biochemical experiments demonstrate that the formation of a complex containing EPHB2 and MYCBP2 is facilitated by FBXO45, a protein known to select substrates for MYCBP2 ubiquitin ligase activity. Formation of the MYCBP2-EPHB2 complex does not require EPHB2 tyrosine kinase activity and is destabilised by binding of ephrin-B ligands, suggesting that the MYCBP2-EPHB2 association is a prelude to EPHB2 signalling. Paradoxically, the loss of MYCBP2 results in increased ubiquitination of EPHB2 and a decrease of its protein levels suggesting that MYCBP2 stabilises EPHB2. Commensurate with this effect, our cellular experiments reveal that MYCBP2 is essential for efficient EPHB2 signalling responses in cell lines and primary neurons. Finally, our genetic studies in C. elegans provide in vivo evidence that the ephrin receptor VAB-1 displays genetic interactions with known MYCBP2 binding proteins. Together, our results align with the similarity of neurodevelopmental phenotypes caused by MYCBP2 and EPHB2 loss of function, and couple EPHB2 to a signalling effector that controls diverse cellular functions.

2024-01-29 | PXD041786 | Pride

Identification of gamma-carboxyglutamic acid residues in mouse ERGP by LC-MS/MS.

Project description:Vitamin K (VK) is a micronutrient required for the gamma-carboxylation of secreted proteins. Clinical studies have recently implicated VK in the pathophysiology of diabetes. Our data indicate that rodent beta-cells lacking gamma-carboxylation fail to adapt their insulin secretion in response to glucose in the context of age-related insulin resistance or diet-induced beta-cell stress. In contrast, VK supplementation protects beta-cells from endoplasmic reticulum stress-induced apoptosis. Using anti-Gla immunoprecipitation, we identified ERGP as a putative gamma-carboxylated protein present in pancreatic beta-cells. We used LC-MS/MS to confirm the presence of gamma-carboxyglutamic residues in ERGP.

2023-05-10 | PXD032955 | Pride

Identification of vitamin K-dependent proteins in mouse liver by LC-MS/MS

Project description:Vitamin K (VK), a fat-soluble vitamin, functions as a co-factor during the gamma-carboxylation reaction that converts glutamic acid residues to gamma-carboxyglutamic acid residues in proteins transiting through the endoplasmic reticulum. Two enzymes are involved which together form the VK cycle: gamma-glutamyl carboxylase (GGCX), and vitamin K oxidoreductase (VKORC1). GGCX requires reduced VK (VKH2) as an essential cofactor, which upon carboxylation, is oxidized to VK epoxide and then reconverted to VKH2 by VKORC1. Physiologically, gamma-carboxylation is essential in the liver for the activity of several coagulation factors (e.g., prothrombin, factor IX, etc.), and in arteries and cartilage to modulate the activity of Matrix Gla Protein (MGP) which prevents extra-osseous tissue mineralization. Gamma-carboxylation also negatively regulates the function of osteocalcin, a bone-derived hormone that promotes glucose homeostasis. Our objective is to identify unrecognized gamma-carboxylated proteins.

2023-05-10 | PXD032920 | Pride

BirA*-RAB18 proximity biotinylation in HeLa cells

Project description:Proximity labelling using transient expression of the same exogenous BirA*-RAB18 construct in wild-type HeLa cells and in otherwise isogenic RAB3GAP1-, RAB3GAP2- and TRAPPC9-null HeLa cell lines.

2024-01-26 | PXD016336 | Pride

Transmembrane nuclease NUMEN/ENDOD1 regulates DNA repair pathway choice at the nuclear periphery

Project description:Proper repair of DNA damage lesions is essential to maintaining genome integrity and preventing the development of human diseases including cancer. Increasing evidence suggests the importance of the nuclear envelope in the spatial regulation of DNA repair, although the mechanisms of such regulatory processes remain poorly defined. Through a genome-wide synthetic viability screen for PARP inhibitor (PARPi) resistance using an inducible CRISPR/Cas9 platform and BRCA1-deficient breast cancer cells, we identified a transmembrane nuclease (renamed NUMEN) that could facilitate compartmentalized and NHEJ-dependent repair of DNA double-strand breaks at the nuclear periphery. Collectively, our data demonstrate that NUMEN generates short 5’ overhangs through its endonuclease and 3’-5’ exonuclease activities, promotes the repair of DNA lesions including heterochromatic LAD breaks as well as deprotected telomeres, and functions as a downstream effector of DNA-PKcs. These findings underline NUMEN’s role as a key player in DNA repair pathway choice and genome stability maintenance and have implications for ongoing research into the development and treatment of genome instability disorders.

2023-04-19 | PXD041562 | Pride

AIN-2::GFP IP of mRNAs associated with miRISC in stage sychronized C. elegans populations

Project description:AIN-2::GFP IP were used to purify miRISC from stage sychronized C.elegans populations (Egg, L1, L2, L3 and L4 stages). The mRNA composition of the IP results and the corresponding total RNA samples were analyzed by WUSTL Caenorhabditis elegans Whole Genome 23k Oligo Array. The miRISC associated mRNAs (miRNA targets) in each stage were identified by measuring the relative enrichment of each mRNA in the IP sample versus the corresponding total RNA sample The mRNAs in AIN-2::GFP IP results (IP) and the corresponding input total lysate (tot) were analyzed for each stage (Egg, L1, L2, L3, and L4 stages). At least three independent biological replicates were analyzed for each stage.

2009-05-21 | E-GEOD-16208 | biostudies-arrayexpress

The MYO6 interactome using BioID

Project description:The intracellular function of myosin motors requires a number of adaptor molecules, which control cargo attachment, but also fine-tune motor activity in time and space. These motor-adaptor-cargo interactions are often weak, transient or highly regulated. To overcome these problems we use a proximity labelling-based proteomics strategy (BioID) to map the interactome of the unique minus end-directed actin motor MYO6. Our analysis identified several distinct MYO6-adaptor modules including two complexes containing RHO GEFs which we screened using further BioID baits (LRCH3, DOCK7, GIPC1 and ARHGEF12). These complexes emphasise the multifunctionality of MYO6 provides the first in vivo interactome of a myosin motor protein, highlighting the power of this approach in uncovering dynamic and functionally diverse myosin motor complexes.

2018-02-27 | PXD008686 | Pride

Genome wide analysis of gene expression of rat ES cells, rat embryonic fibroblast cells and mouse ES cells

Project description:Rat ES cells were derived using 3I medium from E4.5 blastocysts. Rat embryonic fibroblast cells were derived form E14.5 embryos. To analyze the mechanism under the selfrenewal of rat ES cells, microarrays were used for the genome wide analysis of gene expressoin profiles in rat ES cells. Rat embryonic fibroblast cells and mouse ES cells were tested at same time as control. Our results from clustering analysis demonstrated that the gene expression profile of rat ES cells resembles mouse ES cells, but not REFs. Keyword: 3I medium; rat embryonic stem cells; mouse ES cells; rat embryonic fibroblast cells Rat ES cells were cultured in 3I medium; rat embryonic fibroblast cells were derived and cultured GMEM/10% FBS; mouse ES cells (C57/BL6)were cultured in GMEM/10% FBS added LIF and feeder cells were removed before RNA extraction. Three replicates each.

2010-05-15 | E-GEOD-13681 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data