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ProteomicsNitrogen signaling factor triggers a respiration-like gene expression program
Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, nitrogen signaling factor (NSF) is part of such communication system, ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-06-25 | PXD047795 | Pride
Nsf Cell communication Nitrogen metabolism Nitrogen signaling 
OtherConvergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells.
Data from ProteomeXchange, PXD ID: PXD000554. Experiment: SILAC_SC_Rap048_2ndrep_SCX, file: folder summary. Published as part of Mol Cell Proteomics. 2014 Aug;13(8):1979-92 . From the Abstract: {{i}} ... Here, we used a mass-spectrometry-based proteomics approach for the parallel quantification of ...
ORGANISM(S): Yeast 
GPM32320003896 | GPMDB
Resource Reanalysis 
ProteomicsThe HP1 protein interactome of mouse embryonic stem cells
The family of Heterochromatin Protein 1 (HP1) consists of highly conserved proteins, which have important functions in the nucleus of eukaryotic cells. In mammals there are three HP1 paralogs: HP1(alpha), Hp1(beta), and Hp1(gamma)They are encoded by the Cbx5, Cbx1, and Cbx3 genes, respectively. Hp1 ...
ORGANISM(S): Mus musculus (Mouse) 
2018-05-22 | PXD006226 | Pride
Lc-orbitrap fusion Mouse es-cells Tandem purification Chd4 Maxquant. Hp1 Cbx3 Adnp Cbx1 Hp1 Flag-avi-tag Cbx5 Hp1 
ProteomicsThe histone acetyltransferase Mst2 protects active chromatin from epigenetic silencing by acetylating the ubiquitin ligase Brl1
Faithful propagation of functionally distinct chromatin states is crucial for maintaining cellular identity, and its breakdown can lead to diseases such as cancer. Whereas mechanisms that sustain repressed states have been intensely studied, regulatory circuits that protect active chromatin from ina...
ORGANISM(S): Schizosaccharomyces pombe 
2017-06-28 | PXD005714 | Pride
Mst2 Acetylome Ms3 Acetylation Brl1 Heterochromatin 
ProteomicsSir4 H-BRCT domain interacts with multiple phospho-proteins to regulate heterochromatic repression
In Saccharomyces cerevisiae, the Silent Information Regulator (SIR) proteins Sir2/3/4 form a complex suppressing transcription of genes at subtelomeric regions and the homothallic mating type (HM) loci. Here we identify a non-canonical BRCA1 C-terminal domain (H-BRCT) in Sir4 which is responsible fo...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-09-13 | PXD014119 | Pride
Tom1 Sir complex Heterochromatin Brct Dbf4 
ProteomicsProtein Tyrosine Phosphatase SHP2 Controls Interleukin-8 Expression in Breast Cancer Cells
Our work highlights a new role of SHP2 in regulating breast cancer progression by enhancing the production and secretion of the pro-metastatic cytokine IL-8. We also provide mechanistic insights into the effects of SHP2 inhibition and its downstream repercussions. Overall, this work enforces the rat...
ORGANISM(S): Homo sapiens (Human) 
2022-06-23 | PXD017219 | Pride
Phosphatase Mapk Breast cancer Cytokines Il-8 Ets1 Shp2 
ProteomicsNovel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites
Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. He...
ORGANISM(S): Mus musculus (Mouse) 
2023-09-07 | PXD029392 | Pride
Ccdc174 Spliceosome Protein-rna interactions Splicing factors Rna-binding proteins Nrde2 
ProteomicsBANP is an essential transcription factor that opens chromatin and activates CpG island regulated genes
While the majority of RNA polymerase II initiation events in mammalian genomes take place within CpG island (CGI) promoters, our understanding of their regulation remains limited. Here we combine single-molecule footprinting with interaction proteomics to identify BANP as a critical CGI regulator an...
ORGANISM(S): Mus musculus (Mouse) 
2021-06-16 | PXD024794 | Pride
Cpg island Single-molecule footprinting Cgi promoters Banp Tf binding Paqman 
ProteomicsModeling of DNA methylation in cis reveals principles of chromatin folding in vivo in the absence of crosslinking and ligation
Mammalian chromosomes are folded into intricate hierarchies of interaction domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current understanding of chromosome folding largely relies on chromoso...
ORGANISM(S): Mus musculus (Mouse) 
2019-06-03 | PXD013507 | Pride
Proteomic ruler Tads Chromosomal interactions Mouse embryonic stem cells Ctcf-associated loops Topologically associating domains Chromosome folding 
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