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ProteomicsDNA damage-induced chromatome analysis in yeast reveals recruitment of Ubiquitin ligases for efficient DNA repairtest1
Eukaryotic cells package their genomes around histone octamers. In response to DNA damage checkpoint kinase-induced core histone degradation leads to a 20-40% reduction in nucleosome density in yeast. To gain insights into this process we report the first comprehensive proteomic analysis of yeast ch...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-02-02 | PXD022369 | Pride
Hmgb1/nhp6 Dna dynamics S. cerevisiae Teschromatome Chromatin proteomics Ino80 Ubiquitin ligases Proteasome Zeocin Homologous recombination Dna damage response Histone degradation 
ProteomicsCross-linking MS of S. cerevisiae ORC bound to DNA and Cdc6
During DNA replication initiation, the Origin Recognition Complex (ORC) and Cdc6 co-associate on DNA to load replicative helicases onto origins of replication. We apply DSSO crosslinking mass spectrometry of reconstituted ORC-DNA-Cdc6 to identify interactions between different subunits and domains i...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-02-28 | PXD031033 | Pride
Cleavable Cid Xlms Xlinkx Crosslinking ms Dsso Phosphorylation Ms2_ms3 Orc 
ProteomicsDeep quantification of substrate turnover definesprotease subsite cooperativity. Working title: Massively parallel mapping of dipeptidyl peptidase cleavage sites reveals substrate motifs
Proteases play a crucial role in processing or breaking down proteins. They exhibit varying levels of substrate specificity that determine their physiological or pharmacological functions. However, this specificity is not well-understood. To address this, we have developed hiMAPS (high-throughput ma...
ORGANISM(S): Homo sapiens (Human) 
2024-11-01 | PXD042089 | Pride
Dpp4 Tmt Dipeptidyl peptidase Hela digest Multiplexing Proteome discoverer Sequence motif Himaps Einprot Dpf-3 
ProteomicsRegulatory phosphosite on Mec1 and control of RNAP11 and PIII during replication stress
Yeast sensor checkpoint kinase Mec1 is phosphorylated at Ser1991 upon HU replication stress. The phospho-accepter mutant (mec1-S1991A) confers HU sensitivity and synthetic sickness with the mutants that aggravate replication and transcription collision. To understand how the entire chromatin proteom...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-09-28 | PXD027337 | Pride
Lc-msms Mec1 Yeast Chromatome Phosphoproteomics Replication stress 
ProteomicsNucleosomes gate cofactor access to the transcription factor p53 P53-pos8-NCP
In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.
ORGANISM(S): Homo sapiens (Human) 
2025-07-31 | PXD054140 | Pride
Proteome discoverer Transcription factor Xlinkx Dsso Nucleosomes Ubiquitin proteasome system Xl-ms Cofactors Crosslinking 
ProteomicsNucleosomes gate cofactor access to the transcription factor p53 P53_USP7TRAF_FL_NCP
In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.
ORGANISM(S): Homo sapiens (Human) 
2025-07-31 | PXD054141 | Pride
Proteome discoverer Transcription factor Xlinkx Dsso Nucleosomes Ubiquitin proteasome system Xl-ms Cofactors Crosslinking 
ProteomicsLarge-scale interactome screen for predicted transcription factors in fission yeast using IP-MS.
Large-scale interactome screen for 89 transcription factors (TFs) in fission yeast. TFs are tagged at the endogenous locus with a 3xFLAG affinity epitope. Cells cultured under optimal conditions (30°C, rich medium) were subjected to IP-MS at 150 mM an 500 mM NaCl.
ORGANISM(S): Schizosaccharomyces pombe 927 
2024-08-30 | PXD054070 | Pride
Pulldown Fission yeast Protein interactions Lc-ms Schizosaccharomyces pombe Ip-ms Maxquant Orbitrap fusion lumos Einprot Transcription factors 
ProteomicsInteractions between basic helix-loop-helix transcription factors and nucleosomes
In solution crosslinking mass spectrometry of transcription factors in complex with nucleosomes
ORGANISM(S): Homo sapiens (Human) 
2023-05-23 | PXD033181 | Pride
Dsso crosslinking xlinkx pd transcription factor nucleosome human 
ProteomicsChromatin-dependent motif syntax defines differentiation trajectories 
Proteome quantification using TMT reagents and off-line basic peptide fractionation was done as described previously in Grand, 2021, with the exception that the isolated nuclei were used as a starting material rather than whole cells to enable detection of transcription factors which are generally l...
ORGANISM(S): Mus musculus (Mouse) 
2025-08-21 | PXD054143 | Pride
Myod1 Proteome discoverer Mutliplexing Tmt Myogenesis Ngn2 Nucleoplasm proteome Neurogenesis 
UnknownHow the Brain Understands Spoken and Sung Sentences.
Not available
S-EPMC7017195 | biostudies-literature
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