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ProteomicsStreamlined identification of permissive non-canonical amino acid incorporation sites in mammalian cell lines with an expanded genetic code
The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2021-02-23 | PXD019815 | Pride
Genetic code expansion Unnatural amino acids Non-canonical amino acids Amber suppression 
ProteomicsChIP-MS of KAT7, H3K9me3 and H3K4me3 in naive, formative and primed mouse PSCs
The establishment of cellular identity is driven by transcriptional and epigenetic regulation exerted by the components of the chromatin proteome - the chromatome. However, chromatome composition and its dynamics in functional phases of pluripotency have not been comprehensively analyzed thus limiti...
ORGANISM(S): Mus musculus (Mouse) 
2023-02-27 | PXD039556 | Pride
Epigenetics Chip-ms Pluripotency Interactome 
ProteomicsComprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components
The establishment of cellular identity is driven by transcriptional and epigenetic regulators of the chromatin proteome - the chromatome. Comprehensive analyses of the chromatome composition and dynamics can therefore greatly improve our understanding of gene regulatory mechanisms. Here, we develope...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2023-02-27 | PXD034448 | Pride
Naive Dia Pluripotency Mass spectrometry Stem cells Formative Chromatin proteomics Primed 
ProteomicsDistinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency
Cytosine DNA bases can be methylated by DNA methyltransferases and subsequently oxidized by TET proteins. The resulting 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) are considered demethylation intermediates as well as stable epigenetic marks. To dissect the ...
ORGANISM(S): Mus musculus (Mouse) 
2020-07-24 | PXD019514 | Pride
Epigenetics Epiblast-like cells Mouse embryonic stem cells Dna methylation 
ProteomicsTET1 interactome in mESCs (via ChIP-MS)
Precise regulation of DNA methylation in mammals is critical for genome stability and epigenetic regulation. The discovery of the ten-eleven translocation (TET) proteins catalyzing the oxidation from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcyto...
ORGANISM(S): Mus musculus (Mouse) 
2022-08-31 | PXD028850 | Pride
Epigenetics Tet1 Mouse embryonic stem cells Dna methylation 
ProteomicsChIP-MS of HP1-beta (CBX1) and ubiquitylome of KAP1 (TRIM28) in mESCs
Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β-/- embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found th...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-24 | PXD025053 | Pride
Phase separation Pluripotency exit Chromocenter Heterochromatin Chromatin structure 
ProteomicsChIP-MS of DPPA3/STELLA in mouse embryonic stem cells
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. So far, it was unclear how mammals specifically achieve global DNA hypomethylation, given the high conservation of the DNA (de-)methylation machinery among vertebrates. We found that DNA deme...
ORGANISM(S): Mus musculus (Mouse) 
2020-10-12 | PXD019794 | Pride
Epigenetics Dna methylation Escs Chip-ms 
ProteomicsFull proteome analysis of WT and Ezh2-KO K562 cells
Chemotherapy resistance is the main impediment in the treatment of acute myeloid leukaemia (AML). Despite rapid advances, the various mechanisms that lead to resistance development remain to be defined in detail. Here we report that loss-of-function mutations (LOF) in the histone methyltransferase E...
ORGANISM(S): Homo sapiens (Human) 
2021-03-12 | PXD023139 | Pride
Aml K562 Human Cytarabine Ezh2 Epigenetics 
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