Ubiquitin chain types

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Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
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PC 16:0/16:0 (1)

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1 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry,Germany. 2 NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (1)
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New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China. (1)
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R602, Institute of Biological Chemistry, Academia Sinica (1)
Research Director, Professor Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen (1)
The Francis Crick Institute 1 Midland Road London, NW1 1AT United Kingdom (1)

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Proteomic Analysis of Ubiquitin Chain Types in Murine Cells and Tissues

Mass spectrometry-based proteomics has become an integral approach for characterising ubiquitin chain-linkage compositions and architectures. In this study, we optimised sample preparation and chromatographic separation of Ubiquitin peptides for Absolute Quantification by Parallel Reaction Monitorin...

ORGANISM(S): Mus musculus (Mouse)

2020-09-28 | PXD017754 | Pride

Ubiquitin chain types on ubiquitinated VPS34 in the presence or absence of UBE3C in vitro LC-MSMS

We identified VPS34 as the direct substrate of UBE3C E3 ligase in vivo and in vitro. Next, to analyze the ubiquitin chain on VPS34 that was assembled by UBE3C in vitro.

ORGANISM(S): Homo sapiens (Human)

2021-02-17 | PXD023986 | Pride

Ubiquitin chain types Vps34 Ube3c

Ubiquitin chain editing promotes p97/VCP dependent removal of RPA from DNA

PRJNA1223807 | ENA

Ubiquitin diGly site ampping on ZNFX1 autoubiquitination reactions

This experiment aimed to characterise ubiquitin chain linkage preferences generated and autoubiquitination sistes during ZNFX1 E3 reactions using diGly remnant mass spectrometry. GlyGly-modified lysine residues were identified as a qualitative proxy for ubiquitin linkage types. Spectral counts of ra...

ORGANISM(S): Homo sapiens (Human)

2026-05-22 | PXD073484 | Pride

Znfx1 ubiquitin chains

Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome maintenance

Linkage-specific ubiquitin (Ub) chains dictate the functional outcome of many critical Ub-dependent signaling processes. However, the functions and targets of several poly-Ub topologies remain poorly understood due to a lack of tools for their specific detection and manipulation. To remedy this know...

ORGANISM(S): Homo sapiens (Human)

2025-09-18 | PXD056493 | Pride

Ubiquitin ubiquitin-proteasome system k29-linked ubiquitylation chromatin epigenome

Ubiquitin chain editing promotes p97/VCP dependent removal of RPA from DNA

How eukaryotic cells choose which DNA repair pathways to use is incompletely understood, yet these decisions are critical to maintain genome stability. Here, we show how error-free DNA repair is controlled by a ubiquitin-dependent mechanism. Central to this is a multi-component ubiquitin chain editi...

ORGANISM(S): Homo sapiens

2026-09-16 | GSE289609 | GEO

Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome integrity

PRJNA1171407 | ENA

Light-Activatable Ubiquitin for Studying Linkage-Specific Ubiquitin Chain Formation Kinetics.

Not available

S-EPMC11809417 | biostudies-literature

Branched-K29/K48 and K48/K29 polyUb_LC-MSMS

The E3 ubiquitin ligase Ufd4/TRIP12 and the E4 enzyme Ufd2 are capable of catalyzing branched ubiquitination. Here, we employ LC-MS/MS to characterize the specific ubiquitin linkage types involved in these branched ubiquitin chains.

ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast)

2025-04-10 | PXD062799 | Pride

Branched ubiquitin chain lc-msms

Central catalytic domain of BRAP (RNF52) recognizes the types of ubiquitin chains and utilizes oligo-ubiquitin for ubiquitylation.

Not available

S-EPMC5628404 | biostudies-literature

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