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GenomicsPromoters Active in Interphase are Bookmarked during Mitosis by Ubiquitination
We analyzed genome-wide modification of chromatin by ubiquitination in human cells and whether this mark changes through the cell cycle using modified ChIP-seq technique (ChAP-seq). Chromatin affinity purification was based on a standard ChIP method with modification of a two-step affinity purificat...
ORGANISM(S): Homo sapiens 
2013-04-04 | E-GEOD-45771 | biostudies-arrayexpress
GenomicsThe Mediator complex subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination
The Mediator complex orchestrates multiple transcription factors with the Pol II apparatus for precise transcriptional control. However, its interplay with the surrounding chromatin remains poorly understood. Here, we analyze differential histone modifications between WT and MED23-/- (KO) cells and ...
ORGANISM(S): Mus musculus 
2015-09-16 | E-GEOD-59518 | biostudies-arrayexpress
ProteomicsZnf598-mediated Rps10/eS10 Ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ubiquitination of the ribosomal proteins plays a pivotal role in translational control and ribosome-associated quality control (RQC). However, little is known about the d...
ORGANISM(S): Danio Rerio 
2023-10-11 | PXD039560 | JPOST Repository
ProteomicsCalcium-triggered (de)ubiquitination events in synapses
Neuronal communication relies on neurotransmitter release from synaptic vesicles (SVs), whose dynamics are controlled by Ca2+-dependent pathways, as many thoroughly studied phosphorylation cascades. However, little is known about other post-translational modifications, as ubiquitination. To address ...
ORGANISM(S): Homo Sapiens Rattus Norvegicus 
PXD053470 | panorama
ModelsNguyenLK2011 - Ubiquitination dynamics in Ring1B/Bmi1 system
NguyenLK2011 - Ubiquitination dynamics in Ring1B-Bmi1 system This theoretical model investigates the dynamics of Ring1B/Bmi1 ubiquitination to identify bistable switch-like and oscillatory behaviour in the system. Michaelis-Menten (MM) equations are used to formulate the model. However, the authors ...
2024-09-02 | BIOMD0000000622 | BioModels
ProteomicsProtein ubiquitination in Aspergillus nidulans
Protein ubiquitination, an evolutionarily conserved post-translational modification process in eukaryotes, and plays an important role in many biological processes. Aspergillus nidulans, a model filamentous fungus, contributes to our understanding of cellular physiology, metabolism and genetics, but...
ORGANISM(S): Aspergillus 
2015-09-10 | PXD002299 | Pride
Lc-msms Aspergillus nidulans Ubiquitination Mycelial dvelopment 
ProteomicsA COFRADIC protocol to study protein ubiquitination
We here apply the COmbined FRActional DIagonal Chromatography (COFRADIC) technology to enrich for ubiquitinated peptides and identify sites of ubiquitination by mass spectrometry. Our technology bypasses the need to ectopically overexpress tagged variants of ubiquitin and the use of sequence-biased ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080780 | MassIVE
ProteomicsActive protein ubiquitination regulates xylem vessel functionality
Xylem vessels function in the long-distance conduction of water in land plants. The NAC transcription factor VASCULAR-RELATED NAC-DOMAIN7 (VND7) is a master regulator of xylem vessel cell differentiation in Arabidopsis (Arabidopsis thaliana). We previously isolated seiv (suppressor of ectopic xylem ...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2024-10-17 | PXD048830 | Pride
Vnd7 Xylem vessel Ubiquitination 
ProteomicsThe identification of ubiquitination sites of IBTK by shotgun proteomics
Previous study reported that eIF4A1 protein stability is subject to control by the ubiquitin-proteasome pathway, and deubiquitinase USP9X elevated eIF4A1 protein level by promoting eIF4A1 deubiquitination. However, the E3 ubiquitin ligases responsible for eIF4A1 proteolysis is not determined. Our re...
ORGANISM(S): Homo sapiens (Human) 
2024-05-10 | PXD039031 | Pride
Ibtk Ubiquitination Shotgun 
ProteomicsIdentification of ubiquitination sites on protein CSDE1 in SHSY5Y cells.
This bottom-up proteomics dataset provides a global map of post-translational modifications (PTMs) on the RNA-binding protein CSDE1 in human neuroblastoma SHSY5Y cells. The data was acquired to survey the modification landscape of CSDE1, with a particular observation that lysine (K) residues display...
ORGANISM(S): Homo sapiens (Human) 
2026-03-02 | PXD073844 | Pride
Mkrn2 Csde1 Ubiquitination site 
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