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ProteomicsExonuclease-1 interactome and phosphorylation sites
To help shedding light on regulatory aspects of DNA repair and remodeling pathways in which EXO1 participates and to help revealing novel cellular processes in which EXO1 is involved, we set out to identify proteins interacting with EXO1. Both a small-scale approach and a comprehensive analysis of t...
ORGANISM(S): Homo sapiens (Human) 
2019-01-31 | PXD002780 | Pride
Human Exo1 Phosphorylation Affinity tag purification 
TranscriptomicsMemory CD8+ T cells require stress-levels of acetate for optimal function
How systemic metabolic alterations during acute infections impact immune-cell function remains poorly understood. Hess and colleagues demonstrate that acetate rapidly increases during infections, which drives acetylation of GAPDH in memory CD8+ T cells and thereby catalyzes the rapid recall response...
ORGANISM(S): Mus musculus 
2016-05-18 | E-GEOD-79600 | biostudies-arrayexpress
ProteomicsZc3h13/Flacc is required for adenosine methylation by bridging the mRNA binding factor Rbm15/Spenito to other components of the m6A machinery
N6-methyladenosine (m6A) is an abundant RNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of Mettl3, which depends on additional proteins whose precise functions remain poorly understood. Here we identified Flacc/Zc3h13 as a nove...
ORGANISM(S): Mus musculus (Mouse) Drosophila melanogaster (Fruit fly) 
2018-12-20 | PXD008111 | Pride
Rna modifications Flacc Methyltransferase complex M6a Sex determination Zc3h13 
ProteomicsRif1 S-acylation mediates DNA double-strand break repair at the inner nuclear membrane
Rif1 is involved in telomere homeostasis, DNA replication timing, and DNA double-strand break (DSB) repair pathway choice from yeast to human. The molecular mechanisms that enable Rif1 to fulfill its diverse roles remain to be determined. Here, we demonstrate that Rif1 is S-acylated within its conse...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-04-15 | PXD012137 | Pride
Non-homologous end-joining Dna double-strand break repair Palmitoylation Yeast Rif1 s-acylation 
ProteomicsThe interactomes of Ubn1 and Ubn2 in mouse embryonic stem cells
Ubn1 and Ubn2 are essential subunits of the Histone Regulator A (HiRA) complex, the H3.3 histone variant chaperone for euchromatin. We pulled-down Ubn1 and Ubn2 with a C-terminal AVI-tag in mouse embryonic stem cells and identified, besides all known components of the complex, transcription factors ...
ORGANISM(S): Mus musculus (Mouse) 
2021-07-14 | PXD025466 | Pride
Mus musculus Stem cel Cell culture l 
ProteomicsThe interactome of Zbtb2 in mouse embryonic stem cells
Zbtb2 is a transcription factor that plays a role in mouse embryonic stem cell (mESC) differentiation. We pulled-down endogenously tagged Zbtb2-FLAG in mESCs and found a complex interactome. We characterized the Zbtb2 complex further by co-pull-downs of overexpressed Zbtb2-AVI, after mutation of ind...
ORGANISM(S): Mus musculus (Mouse) 
2021-07-14 | PXD025520 | Pride
Zbtb2 interactome Development Mouse embryonic stem cells 
ProteomicsSystematic assessment of ISWI subunits reveals that NURF creates local accessibility for proper CTCF function
Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediates these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of...
ORGANISM(S): Mus musculus (Mouse) 
2024-03-13 | PXD042945 | Pride
Snf2h Chromatin remodelers Ip-ms Iswi Mesc 
TranscriptomicsRNA-seq comparing WT to HDAC3 knock-out clones in naïve mESCs, as well as SL and EpiLC differentiation conditions at two distinct time points (1 and 2 days)
Determine the transcriptomic effects that are associated with the distinct differentiation phenotypes of HDAC3 knock-out vs wildtype mESCs.
This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.
ORGANISM(S): Mus musculus 
2021-03-14 | E-MTAB-9446 | biostudies-arrayexpress
ProteomicsReadout of histone methylation by Trim24 locally restricts chromatin opening by p53
The genomic binding sites of the transcription factor (TF) and tumour suppressor p53 are unusually diverse in regards to their chromatin features, including histone modifications, opening the possibility that chromatin provides context-dependence for p53 regulation. Here, we show that the ability of...
ORGANISM(S): Mus musculus (Mouse) 
2023-05-05 | PXD039553 | Pride
Trim24 p53 mouse 
ProteomicsInvestigation upon the state of p53 as well as interaction partners, in so much as can be learned from using the multi-component v5-dTag system.
Chromatin modifications provide additional context-dependence for DNA sequence-based gene regulation. Binding sites of the transcription factor (TF) and important tumour suppressor p53 are unusually diverse with regards to their chromatin accessibility and histone modifications, suggesting different...
ORGANISM(S): Mus musculus (Mouse) 
2023-05-05 | PXD033674 | Pride
Trim24 Gene regulation Chromatin P53 
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