Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

IPs of SETD1A COMPASS-HUMAN LC-MSMS

ABSTRACT: Mapping physical interactions of SETD1A COMPOASS in HEK293T cells using endogenous immunoprecipitation followed by label-free quantitative proteomics. We found a novel protein interacts with SETD1A, which is RAD18 (DNA damage repair protein).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Manal Alsulami

LAB HEAD: Gerard Cagney

PROVIDER: PXD012549 | Pride | 2019-06-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	170313kw_Nyla_HEK_ASH2_1.raw	Raw
	170313kw_Nyla_HEK_ASH2_2.raw	Raw
	170313kw_Nyla_HEK_ASH2_3.raw	Raw
	170313kw_Nyla_HEK_IgG_CONTROL_1.raw	Raw
	170313kw_Nyla_HEK_IgG_CONTROL_2.raw	Raw

Items per page:

1 - 5 of 41

Publications

SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18.

Alsulami Manal M Munawar Nayla N Dillon Eugene E Oliviero Giorgio G Wynne Kieran K Alsolami Mona M Moss Catherine C Ó Gaora Peadar P O'Meara Fergal F Cotter David D Cagney Gerard G

Molecular & cellular proteomics : MCP 20190510 7

SETD1A is a SET domain-containing methyltransferase involved in epigenetic regulation of transcription. It is the main catalytic component of a multiprotein complex that methylates lysine 4 of histone H3, a histone mark associated with gene activation. In humans, six related protein complexes with partly nonredundant cellular functions share several protein subunits but are distinguished by unique catalytic SET-domain proteins. We surveyed physical interactions of the SETD1A-complex using endoge ...[more]

PMID: 31076518

Similar Datasets

Physical and functional screening of Polycomb Repressor Complex 2 highlights novel regulators of histone H3 lysine 27 methylation status

Project description:Polycomb Repressor Complex 2 (PRC2) is a multi-protein epigenetic regulator complex that plays critical roles in early development and tissue differentiation. The complex catalyzes the methylation of histone H3 lysine 27 (H3K27). The tri-methyl state (H3K27me3) is well studied as an agent of gene repression, but more recently distinct roles for the mono- and di-methyl states have been discovered. In order to more fully understand how PRC2-associated factors might influence H3K27 status, we screened for physical associations of PRC2 subunits. Knockdown of these factors was used to produce functional interaction maps focused on H3K27 methylation, including proteins that have positive and negative effects on the levels each histone mark.

2018-04-05 | PXD005381 | Pride

Comparisons between fully and partially reprogrammed iPS cells induced by pMX-Klf4, pMX-Oct4 and pMX-Sox2 retroviruses

Project description:Induced pluripotent stem (iPS) cell reprogramming is a gradual epigenetic process that reactivates the pluripotent transcriptional network by erasing and establishing heterochromatin marks. Here, we characterize the physical structure of heterochromatin domains in full and partial mouse iPS cells by correlative Electron Spectroscopic Imaging (ESI). In somatic and partial iPS cells, constitutive heterochromatin marked by H3K9me3 is highly compartmentalized into chromocenter structures of densely packed 10 nm chromatin fibers. In contrast, chromocenter boundaries are poorly defined in pluripotent ES and full iPS cells, and are characterized by unusually dispersed 10 nm heterochromatin fibers in high Nanog-expressing cells, including pluripotent cells of the mouse blastocyst prior to differentiation. This heterochromatin reorganization accompanies retroviral silencing during conversion of partial iPS cells by Mek/Gsk3 2i inhibitor treatment. Thus, constitutive heterochromatin reorganization serves as a novel biomarker with retroviral silencing for identifying iPS cells in the very late stages of reprogramming. We compared the expression profiles of partially and fully reprogrammed iPS cell lines derived from CD1 mouse embryonic fibroblasts (MEFSs) by retroviral reprogramming (pMX-Oct4, pMX-Klf4 and pMX-Sox2). to the differentiated MEFS and the J1 embryonic stem cell line. We also studied the effect of a 2i cocktail treatment in partially reprogrammed iPS cells.

2011-09-21 | E-GEOD-21595 | biostudies-arrayexpress

Comprehensive proteomics analysis of polyhydroxyalkanoate (PHA) biology in Pseudomonas putida KT2440: the outer membrane lipoprotein OprL is a newly identified phasin Dataset 3

Project description:Pseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins are incompletely understood but genetic disruption of their function causes PHA-related phenotypes. To improve our understanding of these proteins, we investigated the PHA pathways of P.putida KT2440 using three types of experiment. First, we profiled cells grown in nitrogen-limited and nitrogen-excess media using global expression proteomics, identifying sets of proteins found to co-ordinately increase or decrease within clustered pathway. Next, we analysed the protein composition of isolated carbonosomes, identifying two new putative components. We carried out physical interaction screens focused on PHA-related proteins, generating a protein-protein network comprising 434 connected proteins. Finally, we confirmed that the outer membrane protein OprL (the Pal component of the Pal-Tol system) localizes to the carbonosome and shows a PHA-related phenotype, and therefore is a novel phasin. The combined datasets represent a valuable overview of the protein components of the PHA system in P.putida highlighting the complex nature of regulatory interactions responsive to nutrient stress.

2024-06-16 | PXD045993 | Pride

Dynamic protein interactions of the Polycomb Repressive Complex 2

Project description:Polycomb proteins assemble to form complexes with important roles in epigenetic regulation. The Polycomb Repressive Complex 2 (PRC2) modulates the di- and tri-methylation of lysine 27 on histone H3, each of which are associated with gene repression. Although three subunits, EZH1/2, SUZ12 and EED, form the catalytic core of PRC2, a wider group of proteins associate with low stoichiometry. This raises the question of whether dynamic variation of the PRC2 interactome results in alternative forms of the complex during differentiation. Here we compared the physical interactions of PRC2 in undifferentiated and differentiated states of NTERA2 pluripotent embryonic carcinoma cells. Label-free quantitative proteomics was used to assess endogenous immunoprecipitation of the EZH2 and SUZ12 subunits of PRC2. A high stringency dataset reflecting the endogenous state of PRC2 was produced that included all previously reported ‘core’ and ‘associated’ PRC2 components, and several novel interacting proteins. Comparison of the interactomes obtained in undifferentiated and differentiated cells revealed candidate proteins that favoured either one or other state. For example, SALL4 and ZNF281 associate with PRC2 in pluripotent cells, while PCL1 and SMAD3 more associate with PRC2 in differentiating cells. Analysis of the mRNA and protein levels of these factors found that their association with PRC2 correlated with their cell state-specific expression. Taken together, we propose that dynamic changes to the PRC2 interactome during differentiation may contribute to directing its activity during cell fate transitions.

2016-09-27 | PXD004462 | Pride

The role of PCNA ubiquitylation during unperturbed genome replication in S.pombe

Project description:To establish if PCNA ubiquitylation affects the DNA replication kinetics of specific loci, we compared rates of DNA replication across the genome between rad18+ and rad18-delta cells using the BrdU-IP sequencing method.

2017-05-12 | GSE70033 | GEO

Quantitative Proteomics Illuminates A Functional Interaction Between Mouse Homolog Of Diaphanous 2 (mDia2) And The Proteasome

Project description:Formin mDia2 is a cytoskeleton-regulatory protein that switches reversibly between a closed, auto-inhibited and an open, active conformation. Although the open conformation of mDia2 induces actin assembly thereby controlling many cellular processes, mDia2 possesses also actin-independent and conformation-insensitive scaffolding roles related to microtubules and p53, respectively. Thus, we hypothesise that mDia2 may have other unappreciated functions and regulatory modes. Here we identify and validate proteasome and Ubiquitin as genuine mDia2-interacting partners using quantitative proteomics and a multi-disciplinary approach, respectively.

2016-12-14 | PXD002066 | Pride

The length of a ubiquitin chain is a general determinant for selective recognition by ubiquitin-binding proteins.

Project description:The attachment of differently linked ubiquitin (Ub) chains of varying length to proteins is a prevalent posttranslational modification in eukaryotic cells. The fate of a modified protein is determined by Ub-binding proteins (UBPs) that interact with Ub chains in a linkage-selective manner. Therefore, proteome-wide interaction studies using differently linked Ub chains have become a focus of research activities. However, the impact and functional consequences of chain length on the binding selectivity of UBPs remain mostly elusive, due to a lack of available tools and sufficient amounts of pure, length-defined Ub chains. Here we generated linkage- and length-defined Ub chains using click-chemistry and gel-free fractionation and employed such defined polymers in affinity-based enrichment assays to identify length- and linkage-selective interactors on a proteome-wide scale. For the first time, this revealed that the length of a Ub chain has generally a major impact on its ability to be selectively recognized by UBPs.

2020-04-20 | PXD015877 | Pride

Interactome of S65 phosphorylated NEDD8 and Ub

Project description:In this project we present for the first time a proteome-wide interaction study of S65 phosphorylated NEDD8 and ubiquitin (Ub). By using cell extracts and affinity enrichment coupled to mass spectrometry, we show that pNEDD8 and pUb have different interactomes that are also distinct from those of the non-modified forms. Among the preferential pNEDD8 interactors are HSP70 family members and, indeed, pNEDD8 stimulates HSP70 ATPase activity more pronouncedly than non-modified NEDD8. Our findings provide evidence that phosphorylation of Ub and NEDD8 at S65 is involved in stress response signaling and underscore the importance of studying non-covalent interactions of NEDD8 in particular and post-translational modifications of Ubls in general.

2021-11-03 | PXD021143 | Pride

HipSci project pilot submission for 18 IPS cell lines

Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Raw data files for this study can be accessed from the PRIDE database at EMBL-EBI under accession number PXD003903: http://www.ebi.ac.uk/pride/archive/projects/PXD003903.

2016-06-22 | E-PROT-5 | biostudies-arrayexpress

Exploring roles of the chitinase ChiC in modulating Pseudomonas aeruginosa virulence phenotypes

Project description:Proteins were precipitated using chloroform and methanol, by the protocol described by Wessel and Flügge (1984). Following precipitation, the proteins were reduced and alkylated before being digested, cleaned and desalted using STrap tips (Zougman A, Selby PJ, Banks RE. 2014). The peptide samples were analyzed by a nano UPLC (nanoElute, Bruker) coupled to a trapped ion mobility spectrometry and a quadrupole time of flight mass spectrometer (timsTOF Pro, Bruker).

2024-04-30 | PXD048597 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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