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ProteomicsElectrophile scanning by chemical prote-omics reveals a potent pan-active DUB probe for investigation of deubiquitinase activity in live cells
Deubiquitinases (DUBs) are proteases that hydrolyze isopeptide bonds linking ubiquitin to protein substrates, which can lead to reduced substrate degradation through the ubiquitin proteasome system. Deregulation of DUB activity has been im-plicated in many disease states, including cancer, neurodege...
ORGANISM(S): Homo sapiens (Human) 
2024-01-03 | PXD035417 | Pride
Ubiquitin-activity base probe Deubiquitinase Chemical probe Activity-based probe Electrophilic war-head Ubiquitin Dub Enzyme targeting Myc-deregulated cancer 
Proteomicsproteomics analysis of SDE2UBL base activity based probe immunoprecipitation
SDE2, a highly conserved and essential gene required for genome maintenance, coordinates essential processes ranging from pre-mRNA splicing and ribosome biogenesis to DNA repair and replication stress response. It is expressed as a full-length precursor (SDE2FL,) bearing an N-terminal ULD, which is ...
ORGANISM(S): Homo sapiens (Human) 
2026-06-24 | PXD064155 | Pride
Ubiquitin-like fusion proteins Sde2 Activity-based probe Proteolysis Immunoprecipitation 
GenomicsBase-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics
5-methylcytosine (5mC), the predominant epigenetic modification on DNA, plays critical roles in mammalian development and is dysregulated in various human pathologies. In mammals, the TET family of dioxygenases can oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5...
ORGANISM(S): Mus musculus 
2015-01-20 | E-GEOD-56429 | biostudies-arrayexpress
ProteomicsRegulation of the endosomal SNX27 retromer by OTULIN
OTULIN specifically hydrolyzes methionine1 (Met1)-linked ubiquitin chains conjugated by LUBAC (linear ubiquitin chain assembly complex). Using mass spectrometry, we discovered an interaction of OTULIN with SNX27 (sorting nexin 27), an adaptor of the endosomal retromer complex responsible for protein...
ORGANISM(S): Homo sapiens (Human) 
2019-09-25 | PXD012082 | Pride
Acitivity-based probe Otulin Interactome 
TranscriptomicsHeterologous microarrays for the study of drought stress in Musa
'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex, overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial...
ORGANISM(S): Musa sp. 
2009-07-04 | E-GEOD-16865 | biostudies-arrayexpress
ProteomicsUSP16 is an ISG15 cross-reactive deubiquitinase targeting a subset of metabolic pathway-related proteins
The ubiquitin-like modifier ISG15 can modulate host and viral proteins to restrict viral and microbial infections, and act as a cytokine. Its expression and conjugation are strongly up-regulated by type I interferons. Here we identify the deubiquitinating enzyme USP16 as an ISG15 cross-reactive prot...
ORGANISM(S): Homo sapiens (Human) 
2023-11-17 | PXD043553 | Pride
Usp16 Innate immunity Metabolic enzyme Isg15 
ProteomicsStructural Premise of Selective Deubiquitinase USP30 Inhibition by Small- Molecule Benzosulfonamides
Dampening functional levels of the mitochondrial deubiquitylating enzyme USP30 has been suggested as an effective therapeutic strategy against neurodegenerative disorders such as Parkinson’s Disease. USP30 inhibition may counteract the deleterious effects of impaired turnover of damaged mitochondria...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD036574 | Pride
Ubiquitin Usp30 Abpp Benzosulfonamides Hdx-ms 
TranscriptomicsRnf41 is associated with anxiety like behavior, major depression and beta carboline induced seizure
The molecular etiology of invididual differences in complex behavior traits and susceptibility to psychiatric illness remains incomplete. Using an unbiased genetic approach in a mouse model, Quantitative Trait Loci (QTL) influencing anxiety-like behaviors and beta-carboline-induced seizure vulnerabi...
ORGANISM(S): Mus musculus 
2010-05-25 | E-GEOD-8641 | biostudies-arrayexpress
ProteomicsIdentification of deubiquitinases controlled by extracellular matrix stiffness in cancer cells
The project was aimed at identifying deubiquitinases (DUBs) involved in cancer cell mechanosignaling. Lysates from cancer cells grown on collagen matrices with varying stiffnesses were incubated with an activity-based HA-tagged ubiquitin probe that covalently binds DUB active site. To identify DUBs ...
ORGANISM(S): Homo sapiens (Human) 
2025-08-22 | PXD054010 | Pride
Lc-ms/ms Immunopurification Dub abp Ecm stiffness 
GenomicsPost-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation (ChIP-seq)
SAGA is a highly conserved transcriptional co-activator complex involved in multiple steps of transcription with activities that function both pre and post initiation. Loss of individual subunits results in developmental defects, suggesting a role in development. To better understand the roles of SA...
ORGANISM(S): Drosophila melanogaster 
2011-08-22 | E-GEOD-29513 | biostudies-arrayexpress
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