Browse
Submit Data
Databases
API
Help

Dataset Information

398 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of chromatin-associated non-histone proteins using SILAC proteomic analysis

ABSTRACT: Not available

INSTRUMENT(S): instrument model

ORGANISM(S): Schizosaccharomyces Pombe

SUBMITTER: Attila Csordas

LAB HEAD: Attila Csordas

PROVIDER: PRD000509 | Pride | 2012-07-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_18235.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_18235.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_18235.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_18236.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_18236.pride.mztab.gz	Mztab

Items per page:

1 - 5 of 33

Similar Datasets

Quantitative proteomic analysis of chromatin-associated factors

Project description:Not available

2012-07-26 | PRD000481 | Pride

Xenopus chromatin proteome survey

Project description:Not available

2007-10-16 | PRD000033 | Pride

Non-ionic Detergent Phase Extraction for the Quantitative Proteomic Analysis of Heart Membranes Proteins using Label-Free LC-MS

Project description:Not available

2008-08-21 | PRD000043 | Pride

Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis.

Project description:The large number of chemical modifications that are found on the histone proteins of eukaryotic cells form multiple complex combinations, which can act as recognition signals for reader proteins. We have used peptide capture in conjunction with super-SILAC quantification to carry out an unbiased high-throughput analysis of the composition of protein complexes that bind to histone H3K9/S10 and H3K27/S28 methyl-phospho modifications. The accurate quantification allowed us to perform Weighted correlation network analysis (WGCNA) to obtain a systems-level view of the histone H3 histone tail interactome. The analysis reveals the underlying modularity of the histone reader network with members of nuclear complexes exhibiting very similar binding signatures, which suggests that many proteins bind to histones as part of pre-organized complexes. Our results identify a novel complex that binds to the double H3K9me3/S10ph modification, which includes Atrx, Daxx and members of the FACT complex. The super-SILAC approach allows comparison of binding to multiple peptides with different combinations of modifications and the resolution of the WGCNA analysis is enhanced by maximizing the number of combinations that are compared. This makes it a useful approach for assessing the effects of changes in histone modification combinations on the composition and function of bound complexes.

| S-EPMC4330348 | biostudies-literature

Predicting chromatin organization using histone marks.

Project description:Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interactions, we have developed a computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries. Our model accurately and robustly predicts these features across datasets and cell types. Cell-type specific histone mark information is required for prediction of chromatin interaction hubs but not for TAD boundaries. Our predictions provide a useful guide for the exploration of chromatin organization.

| S-EPMC4549084 | biostudies-literature

Effects of polyamines on prostatic chromatin- and non-histone-protein-associated protein kinase reactions.

Project description:Studies are presented on the influence of polyamines on prostatic chromatin- and non-histone-protein-associated protein kinase reactions involving both exogenous and endogenous substrates. The activities toward the model acidic protein substrate, dephosphophosvitin, were maximal at 160--200mM-NaCl (or -KCl or -NH4Cl). Under these conditions, spermidine and spermine added in concentrations up to 2mM were essentially without effect. However, without addition of NaCl to the medium, marked stimulation of these reactions was elicited by these polyamines at 1--2mM concentrations. The stimulatory effects were not due to non-specific changes in the ionic strength or to substitution of spermine for Mg2+, as maximal stimulation by 1 mM-spermine was observed only at optimal (2--4mM) Mg2+ concentrations. Qualitatively similar effects of polyamines were observed with enzyme preparations from the prostates of castrated rats, and with chromatin and non-histone-protein preparations from other tissues besides ventral prostate. When phosphorylation of endogenous non-histone proteins of the chromatin was measured, spermine stimulated both the initial rates and the final extent of transphosphorylation, even in the presence of optimal concentration of NaCl. By contrast, spermine or spermidine had no effect on the chromatin- and non-histone-protein-associated protein kinase reactions determined with lysine-rich histones as substrates. Chemically NN-dimethylated dephosphophosvitin was a less active substrate for the chromatin-associated protein kinase, but its phosphorylation was more markedly stimulated by spermine in comparison with unmodified dephosphophosvitin. These observations hint that the polyamine stimulations of the various protein kinase reactions may be due to effects on the conformations of the non-histone protein substrates rather than on the kinases themselves.

| S-EPMC1186296 | biostudies-other

Identification of deubiquitinase targets of isothiocyanates using SILAC-assisted quantitative mass spectrometry.

Project description:Cruciferous vegetables such as broccoli and kale have well documented chemopreventative and anticancer effects that are attributed to the presence of isothiocyanates (ITCs). ITCs modulate the levels of many oncogenic proteins, but the molecular mechanisms of ITC action are not understood. We previously reported that phenethyl isothiocyanate (PEITC) inhibits two deubiquitinases (DUBs), USP9x and UCH37. DUBs regulate many cellular processes and DUB dysregulation is linked to the pathogenesis of human diseases including cancer, neurodegeneration, and inflammation. Using SILAC assisted quantitative mass spectrometry, here we identify 9 new PEITC-DUB targets: USP1, USP3, USP10, USP11, USP16, USP22, USP40, USP48 and VCPIP1. Seven of these PEITC-sensitive DUBs have well-recognized roles in DNA repair or chromatin remodeling. PEITC both inhibits USP1 and increases its ubiquitination and degradation, thus decreasing USP1 activity by two mechanisms. The loss of USP1 activity increases the level of mono-ubiquitinated DNA clamp PCNA, impairing DNA repair. Both the inhibition/degradation of USP1 and the increase in mono-ubiquitinated PCNA are new activities for PEITC that can explain the previously recognized ability of ITCs to enhance cancer cell sensitivity to cisplatin treatment. Our work also demonstrates that PEITC reduces the mono-ubiquityl histones H2A and H2B. Understanding the mechanism of action of ITCs should facilitate their use as therapeutic agents.

| S-EPMC5584250 | biostudies-literature

Quantitative proteome analysis of human blister fluids using 18O labeling

Project description:Not available

2008-05-14 | PRD000059 | Pride

Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase

Project description:Not available

2008-03-05 | PRD000046 | Pride

Proteomic changes associated with inactivation of the Candida glabrata ACE2 virulence-moderating gene

Project description:Not available

2007-05-04 | PRD000763 | Pride