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-Maria Geissen

PROVIDER: BIOMD0000001078 | BioModels | 2024-09-02

REPOSITORIES: BioModels

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	BIOMD0000001078?filename=Hammaren-Geissen2022_PPToP_Model12_withParameterSets-biopax2.owl	Owl
	BIOMD0000001078?filename=Hammaren-Geissen2022_PPToP_Model12_withParameterSets-biopax3.owl	Owl
	BIOMD0000001078?filename=Hammaren-Geissen2022_PPToP_Model12_withParameterSets-matlab.m	Other
	BIOMD0000001078?filename=Hammaren-Geissen2022_PPToP_Model12_withParameterSets-octave.m	Other
	BIOMD0000001078?filename=Hammaren-Geissen2022_PPToP_Model12_withParameterSets.cps	Other

Items per page:

1 - 5 of 19

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

Redefining the role of eIF4E dose in development, cancer, and protein synthesis

Project description:eIF4E, the major cap-binding protein, has long been considered limiting for translating the mammalian genome. However, the requirement for eIF4E dose at an organismal level remains unexplored. By generating an Eif4e haploinsufficient mouse, we surprisingly found that 50% reduction in eIF4E, while compatible with normal development and global protein synthesis, significantly impeded cellular transformation and tumorigenesis. Genome-wide translational profiling uncovered a translational program induced by oncogenic transformation and revealed a critical role for eIF4E dose specifically in translating a network of mRNAs enriched for a unique 5’UTR signature. In particular, we demonstrate that eIF4E dose is essential for translating mRNAs regulating reactive oxygen species (ROS) that fuel transformation and cancer cell survival in vivo. Therefore, mammalian cells have evolved surplus eIF4E levels that cancer cells hijack to drive a translational program supporting tumorigenesis Total cellular RNA and high MW polysome associated RNA were isolated from matched untransformed and transformed WT and Eif4e+/- MEFs for analysis on Affymetrix Mouse Gene 1.0 ST arrays. The difference in log2 RMA intensity between matched polysomal RNA and total RNA was taken to quantify translational efficiency (TE).

2015-07-01 | E-GEOD-68238 | biostudies-arrayexpress

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

Project description:We have developed Halo-seq, an RNA proximity labeling method that allows the quantification of subcellular transcriptomes. We have demonstrated the efficacy of Halo-seq here by using it to quantify chromatin-proximal, nucleolar, and cytoplasmic transcriptomes. In Halo-seq, RNA molecules in close proximity to a spatially restricted protein are specifically marked and biotinylated, facilitating their separation from bulk cellular RNA and their quantification.

2021-04-19 | GSE172281 | GEO

In vivo and transcriptome-wide identification of RNA-binding protein target sites [RNA-Seq]

Project description:Animal mRNAs are regulated by hundreds of RNA binding proteins (RBPs). The identification of RBP targets is crucial for understanding their function. A recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to target RNAs in cells prior to immunoprecipitation. Here, we establish iPAR-CLIP (in vivo PAR-CLIP) to determine, at nucleotide resolution, transcriptome-wide target sites of GLD-1, a conserved, germline-specific translational repressor in C. elegans. We identified 439 reproducible targets and demonstrate an excellent dynamic range of target detection by iPAR-CLIP. Upon GLD-1 knock-down, protein but not mRNA expression of the 439 targets was specifically and highly significantly upregulated, demonstrating functionality. Finally, we discovered strongly conserved GLD-1 binding sites nearby the start codon of target genes. We propose that GLD-1 interacts with the translation machinery nearby the start codon, a so far unknown mode of gene regulation in eukaryotes. PolyA mRNA was extracted from young adult wildtype (N2) worms and young adult germline less worms (glp-4(bn2) TS) to identify and quantify genes expressed in the young adult germline by sequencing. 2x100 paired end sequencing was performed according to the protocol on the Illumina HiSeq 2000.

2011-12-09 | E-GEOD-33573 | biostudies-arrayexpress

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

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