Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hammaren-Geissen2022_PPToP_Model12

ABSTRACT: The model encodes the general biological process of protein synthesis and post-translational modification (PTM, such as protein phosphorylation), viewed through the eyes of a specific, widely-used experimental method. Specifically, we model measurements of pulsed stable isotope labelling of amino acids in cell culture (pSILAC), which is a method often used to quantify protein turnover (i.e. the degradation of old and replacement with new) of proteins in a cell.

SUBMITTER: Eva Geissen

PROVIDER: BIOMD0000001078 | BioModels | 2024-01-29

REPOSITORIES: BioModels

ACCESS DATA

Json Xml

Publications

Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation.

Hammarén Henrik M HM Geissen Eva-Maria EM Potel Clement M CM Beck Martin M Savitski Mikhail M MM

Nature communications 20221202 1

Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods relying on pulsed metabolic labeling are popular to quantify turnover rates on a proteome-wide scale. Such data have traditionally been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture (pSILAC) for the study of protein phospho ...[more]

PMID: 36460637

Similar Datasets

Comparative analysis of four- and seven-day-old Arabidopsis thaliana plasmodesmata fractions using label free method

Project description:To compare four- and seven-day-old Arabidopsis thaliana plasmodesmata proteome, the identification and the relative amount of proteins in plasmodesmata, cell wall and total cell extracts were performed using fractions purified from four- and seven-day-old liquid culture cells of A. thaliana. The relative amount for each protein was determined with a label-free quantification method. Four biological replicates of each fraction were used for quantification.

2019-07-05 | PXD006806 | Pride

Testicular dysgenesis syndrome and long-lasting epigenetic silencing of mouse sperm genes involved in the reproductive system after prenatal exposure to DEHP

Project description:Prenatal exposure to 300 mg/kg/day of bis(2-ethylhexyl)phthalate (D300) was administered to pregnant mice during embryonic days 9th to 19th, inducing a Testicular Dysgenesis Syndrome (TDS), observed in 100 days old F1 derived C57BL/6J males. A transcriptomic analysis was performed from spermatozoa produced by D300 mice compared with CTL. We used an adapted RNAseq method able to quantify all RNAs molecules independently of the 5’ and 3’ modifications.

2017-01-09 | GSE86837 | GEO

Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast

Project description:Acetylation of histone H3 lysine 56 is a covalent modification best-known as a mark of newly-replicated chromatin, but has also been linked to replication-independent histone replacement. Here, we measured H3K56ac levels at single-nucleosome resolution in asynchronously growing yeast cultures, as well as in yeast proceeding synchronously through the cell cycle. We developed a quantitative model of H3K56ac kinetics, which shows that H3K56ac is largely explained by the genomic replication timing and the turnover rate of each nucleosome, suggesting that cell cycle profiles of H3K56ac should reveal most first-time nucleosome incorporation events. However, since the deacetylases Hst3/4 prevent use of H3K56ac as a marker for histone deposition during M phase, we also directly measured M phase histone replacement rates. We report a global decrease in turnover rates during M phase, and a further specific decrease in turnover among early origins of replication, which switch from rapidly-replaced in G1 phase to stable-bound during M phase. Finally, by measuring H3 replacement in yeast deleted for the H3K56 acetyltransferase Rtt109 and its two co-chaperones Asf1 and Vps75, we find evidence that Rtt109 and Asf1 preferentially enhance histone replacement at rapidly-replaced nucleosomes, whereas Vps75 appears to inhibit histone turnover at those loci. These results provide a broad perspective on histone replacement/incorporation throughout the cell cycle, and suggest that H3K56 acetylation provides a positive feedback loop by which replacement of a nucleosome enhances subsequent replacement at the same location.

2008-10-04 | GSE12822 | GEO

Transcriptome and proteome dynamics of cervical remodeling in the mouse during pregnancy

Project description:The transcriptomic patterns that drive cervical softening and ripening in early mid- and late pregnancy were identified in this study. Further we sought to evaluate protein turnover rates with a focus on ECM proteins. In early pregnancy there is a shift in immune cell and epithelial cell responses at the transcriptional level and an overall slowing down of protein turnover rates. By mid pregnancy transcriptomic patterns indicate there is an increase in extracellular matrix reorganization and by late pregnancy the transcriptional patterns of early and mid-pregnancy begin to reverse. Protein turnover rates for fibrillar collagen are high in the nonpregnant and pregnant cervix and thus allow for the rapid replacement of mature collagen with poorly crosslinked collagen through pregnancy.

2021-11-24 | GSE164059 | GEO

A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (H3K4me3 or H3K36me3 to input)

Project description:Chd proteins are ATP-dependent chromatin remodeling enzymes implicated in biological functions from transcriptional elongation to control of pluripotency. Here, we examine roles of Chd1 in replication- independent dynamics of histone H3 in yeast. Using genome-wide ChIP on chip analysis, we find that Chd1 influences histone turnover at the 5M-bM-^@M-^Y and 3M-bM-^@M-^Y ends of genes, accelerating H3 replacement at the 5M-bM-^@M-^Y ends of genes while protecting the 3M-bM-^@M-^Y ends of genes from excessive H3 turnover. Although consistent with a direct role for Chd1 in exchange, these results may indicate that Chd1 stabilizes nucleosomes perturbed by transcription. Curiously, we observe a strong effect of gene length on Chd1M-bM-^@M-^Ys effects on H3 turnover. Finally, we show that Chd1 also affects histone H3K4 and H3K36 methylation patterns over genes, likely as a consequence of its effects on histone replacement. In control experiments, we measure effects of deletion of CHD1 on RNA polymerase II distribution across the genome and on gene expression. We also examine the effect of deleting the TOP1 gene, alone and in combination with deletion of CHD1, on histone replacement. Taken together, our results emphasize a role for Chd1 in histone replacement in both budding yeast and Drosophila, and surprisingly show that the major effects of Chd1 on turnover occur at the 3M-bM-^@M-^Y ends of genes. ChIP on chip experiments, comparing IP to input.

2012-06-07 | E-GEOD-38492 | biostudies-arrayexpress

Drosophila melanogaster

Project description:CATCH-IT method for measuring nucleosome turnover

| PRJNA121809 | ENA

A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (Rpb3 to input)

2012-06-07 | E-GEOD-38493 | biostudies-arrayexpress

A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (gene expression)

2012-06-07 | E-GEOD-38496 | biostudies-arrayexpress

A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (Flag-tagged histone H3 to total histone H3)

2012-06-07 | E-GEOD-38491 | biostudies-arrayexpress

Nucleosome occupancy

Project description:Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states. Keywords: MNase, Nucleosomes Nucleosomal vs genomic DNA.

2007-05-16 | E-GEOD-6668 | 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