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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 
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 
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 
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 
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 
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 
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 
ProteomicsA H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium
BackgroundThe ability to deposit histone H3K27-trimethyl (me3) marks is essential for transcriptional repression by Polycomb Repressive Complex 2 (PRC2). This is largely attributed to Polycomb repressive complex 1 (PRC1), whose recruitment is H3K27me3-dependent. Yet it is unclear how H3K27me3 contri...
ORGANISM(S): Paramecium tetraurelia 
2026-03-03 | PXD065449 | Pride
TranscriptomicsGenome-wide profiling of salt fractions maps physical properties of chromatin
We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-...
ORGANISM(S): Drosophila melanogaster 
2008-12-11 | E-GEOD-13217 | biostudies-arrayexpress
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