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ProteomicsIdentifying Specific Protein Interactors of Nucleosomes Carrying Methylated Histones using Quantitative Mass Spectrometry
Chemical modification of histone proteins by methylation plays a central role in chromatin regulation by recruiting epigenetic ‘readers’ via specialized binding domains. Depending on the degree of methylation, the exact modified amino acid, and the associated reader proteins histone methylations are...
ORGANISM(S): Homo sapiens (Human) 
2022-08-11 | PXD027238 | Pride
H3k4me3 Nucleosome pull-down affinity purification H3k9me3 Histone ptms 
ProteomicsProteomics analysis of ligated and recombinant human histones H3 and H4
A library of unmodified and differentially modified human histones H3 and H4 was prepared using native chemical ligation as described previously (Bartke et al., 2010; Nakamura et al., 2019). The modification status of histone H3 and H4 products was confirmed by LC-MS/MS.
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD020773 | Pride
Recombinant histones Ligated histones 
ProteomicsH4K20me2 SILAC Nucleosome Affinity Purification
Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by di-methylation of lysine 20 on histone H4 (H4K20me2). To achieve this unodified and H4K20me2-modified histone H4 were generated by native chemical ligation and assembled into re...
ORGANISM(S): Homo sapiens (Human) 
2019-02-27 | PXD009281 | Pride
H4k20me2 H4k20me0 Snap Silac Nucleosome affinity purification 
ProteomicsExamining the stability of nucleosomal modifications during pull-down affinity purification
Here we investigated the stability of nucleosomal modifications during pull-down affinity purification with HeLa nuclear extracts. Unmodified di-nucleosomes and di-nucleosomes decorated with H3K4me3K9acK14acK18acK23acK27ac, H4K5acK8acK12acK16acK20me2 and incorporating histone variant H2A.Z were incu...
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD042823 | Pride
Nucleosome pull-down 
ProteomicsTesting the effect of histone native chemical ligation on protein binding to di-nucleosomes
Here we examined whether histones H3 and H4 produced using native chemical ligation reaction affect protein binding to di-nucleosomes. To test this we performed a set of affinity purification pull-downs using di-nucleosomes containing the following histones H3 and H4: 1. unmodified ligated histone ...
ORGANISM(S): Homo sapiens (Human) 
2023-12-12 | PXD042390 | Pride
Nucleosome pull-down Native chemical ligation 
ProteomicsExamining the effect of the linker DNA length on protein binding to di-nucleosomes decorated with H3K9me3 and H3K27me3
Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from between 35-55 bp (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 bp in nucleosome-depleted regions (NDRs...
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD042368 | Pride
Nucleosome pull-down Linker dna H3k27me3 H3k9me3 
ProteomicsMARCS: Modification Atlas for Regulation by Chromatin States
Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by various combinatorial chromatin modifications found in different chromatin states such as promoters, enhancers and heterochromatin. To achieve this, recombinant modified nucleos...
ORGANISM(S): Homo sapiens (Human) 
2023-12-12 | PXD018966 | Pride
H3k14ac H3k27me3 H3k27me2 Snap H4k20me3 H4k20me2 H3k9me2 H2a.z H3k9me3 Chromatin Nucleosome affinity purification H3k18ac H4k12ac H4k5ac H4k16ac H4k8ac H3k4me3 H3k4me1 H3k27ac H3k23ac Mecpg H3k9ac Dna methylation Silac Epigenetics 
ProteomicsIP-MS analysis of the human INO80 complex composition and interactome
The project aimed to investigate the composition/interactome of the human INO80 complex. To this end, INO80B - a core INO80 complex subunit - was endogenously tagged with V5 epitope tag at its C terminus in MCF-7 cells, and co-immunoprecipitation followed by LC-MS/MS analysis was performed using ant...
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD020712 | Pride
Ip-ms Ino80 
ProteomicsPull-down affinity purifications using di-nucleosomes decorated with enhancer-associated modifications and incorporating 200bp linker DNA
Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from around 35-55 bp in most eu- and heterochromatin domains (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 ...
ORGANISM(S): Homo sapiens (Human) 
2023-12-12 | PXD041443 | Pride
Ndrs H3k4me1 H3k27ac Pull-down 
ProteomicsDissecting the effect of a long linker DNA on protein binding to di-nucleosomes decorated with promoter-associated PTMs
Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from around 35-55 bp in most eu- and heterochromatin domains (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 ...
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD041835 | Pride
Ndrs Sv40 promoter H3k4me3 Pull-down H4ac H3ac 
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