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ProteomicsUSP7, a protein involved in Hao-Fountain syndrome, controls neuronal differentiation via BCOR-ncPRC1.1
Pathogenic variants in the ubiquitin-specific protease 7 (USP7) gene cause a neurodevelopmental disorder called Hao-Fountain syndrome. However, which of its pleiotropic substrates are relevant for neurodevelopment is undetermined. Here, we present a combination of quantitative proteomics, transcript...
ORGANISM(S): Homo sapiens (Human) 
2025-09-08 | PXD051616 | Pride
Usp7 Prm Dia-ms Label free quantitative proteomics Neuronal differentiation Bcor Hao-fountain syndrome 
ProteomicsIn vivo Analysis Reveals that ATP-hydrolysis Couples Remodeling to SWI/SNF Release from Chromatin.
ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers, and the role of ATP hydrolysis in this process remain unclear. We used live-cell imaging of Drosophila polytene nuclei to monitor...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2022-01-20 | PXD025474 | Pride
Brahma Live-cell imaging Ecdysone receptor Swi/snf Atp-dependent chromatin remodeling Polytene chromosomes 
ProteomicsDDA1, a novel factor in transcription-coupled repair, modulates CRL4CSA dynamics at DNA damage-stalled RNA polymerase II
Transcription–blocking lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the physical stalling o...
ORGANISM(S): Homo sapiens (Human) 
2024-05-31 | PXD045415 | Pride
Dna damage-stalled rna polymerase ii Transcription-coupled repair Crl4csa dynamics Dda1 
ProteomicsProteome-wide ubiquitinome profiling reveals substrate-specific dynamics within the USP7 network
USP7 is a deubiquitylating enzyme, a hub of a multi-nodal network, that is involved in tumor suppression, neuro)development, chromatin regulation and the DNA damage response. How USP7 regulates these diverse pathways is still unclear. Here, we used data-independent acquisition and label free quantit...
ORGANISM(S): Homo sapiens (Human) 
2026-09-07 | PXD071773 | Pride
Neurodevelopment Hao-fountain syndrome Ubiquitin Polycomb Usp7 
ProteomicsUbiquitinome UPS - Quantitative proteomics reveals extensive changes in the ubiquitinome after perturbation of the proteasome by targeted dsRNA mediated subunit knockdown in Drosophila
In eukaryotic cells, short-lived, regulatory and misfolded or denatured proteins are degraded by the ubiquitin–proteasome system (UPS), a highly regulated mechanism including the active marking of proteins for proteasomal degradation by ubiquitin. The UPS is critical in regulating proteostasis and d...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2017-07-03 | PXD002552 | Pride
Ubiquitinome Digly Silac Proteasome Lc-ms/ms 
ProteomicsFrom incision to excision: active DNA damage eviction by HLTF stimulates repair
Nucleotide excision repair (NER) counteracts the onset of cancer and aging by removing helix-distorting DNA lesions via a ‘cut-and-patch’-type reaction. The regulatory mechanisms that drive NER through its successive damage recognition, verification, incision and gap restoration reaction steps remai...
ORGANISM(S): Mus musculus (Mouse) 
2023-05-10 | PXD031243 | Pride
Uv damage response Hltf Repair synthesis Damage eviction Dna damage Tfiih Genome stability Post-replication repair Nucleotide excision repair 
ProteomicsMulti-omics characterization of the USP7 regulatory circuitry reveals control of H2AK119ub1 dosage uncoupled from H3K27me3 .
Ubiquitin-specific protease 7 (USP7) has been implicated in multiple cellular and developmental pathways. However, its molecular network remains poorly defined. We combined quantitative proteomics, transcriptomics and epigenomics to define the core USP7 regulome. We found that USP7 forms a regulator...
ORGANISM(S): Homo sapiens (Human) 
2023-03-11 | PXD030707 | Pride
Ap-ms Histone h2a ubiquitylation Prc1 Prc2 Prm Ubiquitin Interactome Usp7 Polycomb 
ProteomicsTranscription-coupled DNA-Protein Crosslink repair by CSB and CRL4(CSA)-mediated degradation
DNA-protein crosslinks (DPCs), arise from enzymatic intermediates, endogenous metabolism or exogenous chemicals like chemotherapeutics. DPCs are highly cytotoxic as they will impede DNA transacting processes such as replication, which is counteracted by proteolysis-mediated DPC removal by the protea...
ORGANISM(S): Homo sapiens (Human) Caenorhabditis elegans 
2024-02-09 | PXD041679 | Pride
Tc-ner Silac Csb Csa 
ProteomicsDiscovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53
Ubiquitin-specific proteases (USPs) are the largest class of human deubiquitinases (DUBs) and comprise its phylogenetically most distant members USP53 and USP54, which are annotated as catalytically inactive pseudo-enzymes. Conspicuously, mutations in the USP domain of USP53 cause progressive famili...
ORGANISM(S): Homo sapiens (Human) 
2024-11-11 | PXD054748 | Pride
Ubiquitin chain length Dubs Ubiquitin signaling K63 linkage X-ray crystallography Cholestasis Deubiquitinating enzymes Protease mechanism Ubiquitin probes Ubiquitin Polyubiquitin specificity Usp54 Usp53 
ProteomicsDistinct functions of dimeric and monomeric Alix in regulating F-actin assembly and loading of exosomal cargo
Alix is a ubiquitously expressed scaffold protein that participates in numerous cellular processes, relating to the remodeling/repair of membranes and the actin cytoskeleton. Alix exists in monomeric and dimeric/multimeric configurations, but how dimer formation occurs and what role the dimer has ...
ORGANISM(S): Mus musculus (Mouse) 
2022-10-14 | PXD031450 | Pride
Exosome Cytoskeleton Disulfide Syntenin Alix Dimerization Actin Homeostasis 
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