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ProteomicsPARP1 proximity proteomics reveals interaction partners at stressed replication forks
PARP1 mediates poly-ADP-ribosylation of proteins on chromatin in response to different types of DNA lesions. PARP inhibitors are used for the treatment of BRCA1/2-deficient breast, ovarian, and prostate cancer. Loss of DNA replication fork protection is proposed as one mechanism that contributes to ...
ORGANISM(S): Homo sapiens (Human) 
2022-10-11 | PXD037154 | Pride
Parp1 Proximity proteomics Ipond Olaparib Adp-ribosylation Tpx2 Replication stress 
ProteomicsInduced degradation of Ufd1 reveals regulation of cohesin by the VCP/p97Ufd1-Npl4 complex
The AAA ATPase VCP/p97 has emerged as a critical regulator of ubiquitin and chromatin-associated processes but progress in understanding has been hampered by the complexity of p97 functions and the various p97 cofactors involved. Here, we combined ubiquitin profiling with acutely induced degradation...
ORGANISM(S): Homo sapiens (Human) 
2026-08-31 | PXD082712 | Pride
Dna damage Replication Ubiquitin Vcp Cohesin 
ProteomicsMitotic bookmarking redundancy by nuclear receptors mediates robust post-mitotic reactivation of the pluripotency network.
Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate post-mitotic gene reactivation. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the significance and import...
ORGANISM(S): Mus musculus (Mouse) 
2023-11-20 | PXD038950 | Pride
Nuclear receptors Pluripotency Esrrb Nr5a2 Es cells Mitotic bookmarking 
ProteomicsLinkage Reprogramming by Tailor-made E3s Reveals Polyubiquitin Chain Requirements in DNA Damage Bypass
A polyubiquitin chain can adopt a variety of shapes, depending on how the ubiquitin monomers are joined. However, the relevance of linkage for the signaling functions of polyubiquitin chains is often poorly understood because of our inability to control or manipulate this parameter in vivo. Here we ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-04-25 | PXD030735 | Pride
Ubiquitin E3 ligase Dna damage bypass Pcna 
ProteomicsAlterations in proteome and proteostasis networks during replicative senescence
The accumulation of senescent cells constitutes a pivotal hallmark of tissue ageing, contributing to disruption of tissue homeostasis and thus, to the development of several aging-related diseases. Despite this, our knowledge about the molecular, spatial and temporal changes that drive aging on a ce...
ORGANISM(S): Homo sapiens (Human) 
2026-07-16 | PXD069085 | Pride
Ubiquitin profilling Replicative senescence 
ProteomicsATR inhibition rewires cellular signaling networks in response to pathologic replication stress
DNA replication stress is the major cause of genomic instability in human cells. The ataxia telangiectasia and Rad3-related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy for the treatment of cancer. Howev...
ORGANISM(S): Homo sapiens (Human) 
2015-11-24 | PXD002135 | Pride
Atr Phosphoproteomics Phosphorytion 
ProteomicsHakai is required for stabilization of core components of the m6A mRNA methylation machinery
N6-methyladenosine (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mam...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2021-04-29 | PXD022294 | Pride
Rna modification M6a Sex determination Hakai 
ProteomicsProteomic analysis of tyrosine phosphorylation induced by oncogenic kinase fusions identified in lung adenocarcinoma
Kinase fusions are considered oncogenic drivers in numerous types of cancer. In lung adenocarcinoma 5-10% of patients harbor kinase fusions. The most frequently detected kinase fusion involves the Anaplastic Lymphoma Kinase (ALK) and Echinoderm Microtubule-associated protein-Like 4 (EML4). In additi...
ORGANISM(S): Homo sapiens (Human) 
2021-04-27 | PXD021904 | Pride
Kinase fusion Ros1 Lung cancer Phosphoproteomics Ret Alk 
ProteomicsLoss of the E3 ubiquitin ligases UBR-5 or HECD-1 restores Caenorhabditis elegans development in the absence of SWI/SNF function
SWItch/Sucrose Non-Fermenting (SWI/SNF) complexes are a family of chromatin remodellers that are conserved across eukaryotes. Mutations in subunits of SWI/SNF cause a multitude of different developmental disorders in humans, most of which have no current treatment options. Here we identify an alanin...
ORGANISM(S): Caenorhabditis elegans 
2023-01-24 | PXD037497 | Pride
Hecd-1 Ubr-5 Development Swi/snf Ubiquitination Ubr5 Hectd1 C. elegans 
ProteomicsThe MYCN oncoprotein is an RNA-binding protein that promotes nascent RNA turnover via the NEXT targeting complex of the nuclear exosome
The MYCN oncoprotein forms a DNA-binding heterodimer with its partner protein MAX. MYCN-driven tumor cells depend on the nuclear exosome, a 3`-5` RNA exonuclease complex, to progress through S phase. Here we show that MYCN forms stable high molecular weight complexes with the nuclear exosome and add...
ORGANISM(S): Homo sapiens (Human) 
2024-07-18 | PXD044446 | Pride
Neuroblastoma Exosome Mycn Next Mxd Zcchc8 Myc Intron Max Mnt Eclip 
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