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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 
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 
ProteomicsControl pull-downs testing 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. ligated unmodified histone H...
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD042630 | Pride
Nucleosome pull-down Native chemical ligation 
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 
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 
ProteomicsPhosphorylation of the FACT histone chaperone subunit SPT16 modulates Arabidopsis development and affects chromatin at RNA polymerase II transcriptional start sites
The heterodimeric histone chaperone FACT consisting of SSRP1 and SPT16 contributes to dynamic nucleosome rearrangements during various DNA-dependent processes including transcription. In search of post-translational modifications that may regulate the activity of FACT, SSRP1 and SPT16 were isolated ...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2022-06-09 | PXD028534 | Pride
Arabidopsis Fact complex Acetylation Phosphorylation 
ProteomicsMiddle-down MS analysis of intact and clipped histone H3 proteoforms
There is growing evidence that proteolytic cleavage of histone N-terminal tails, known as histone clipping, influences nucleosome dynamics and functional properties. Using middle-down MS analysis we characterized intact and proteolytically processed histone H3 proteoforms isolated from human hepatoc...
ORGANISM(S): Homo sapiens (Human) 
2022-03-14 | PXD002535 | Pride
Liver Hepg2/c3a Middle-down ms Histone post-translational modifications 
ProteomicsSingle-copy locus isolation identifies distinct proteomes of early- and late-firing DNA replication origin chromatin
The chromatin at origins of replication is the template for DNA replication initiation in eukaryotic genomes. However, whether the chromatin composition instructs individual origins to fire early-efficiently (EE) or late-inefficiently (LI) remains to be investigated. Here, we used site-specific reco...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-05-10 | PXD031984 | Pride
Replication timing Replication efficiency Affinity purification Locus-specific chromatin isolation Dna replication origin Histone ptms Site-specific recombination 
ProteomicsProteomic analysis of histone modifications present on nucleosomes bound by INO80 complex
The INO80 complex is a chromatin remodeler that regulates DNA replication, repair, and transcription. Although the INO80 complex plays a crucial role in various chromatin-associated processes, the mechanism of its recruitment to specific genomic loci is not well understood. Here we used a native ChI...
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD042210 | Pride
Native chip-ms Ino80 Histone ptms 
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