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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 
TranscriptomicsTissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.
Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method t...
ORGANISM(S): Caenorhabditis elegans 
2011-12-05 | E-GEOD-31602 | biostudies-arrayexpress
TranscriptomicsCATCH-IT method for measuring nucleosome turnover
Direct measurement of nucleosome turnover dynamics by using co-translational incorporation of the methionine (Met) surrogate azidohomoalaine (Aha) into proteins and subsequent ligation of biotin to Aha-containing proteins through the [3+2] cycloaddition reaction between the azide group of Aha and an...
ORGANISM(S): Drosophila melanogaster 
2010-05-27 | E-GEOD-19788 | biostudies-arrayexpress
ProteomicsComprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding
Nuclear proteins bind chromatin to execute and regulate genome-templated processes. While structural and biochemical studies of individual nucleosome interactions have suggested that an acidic patch on the nucleosome disk surface may be a common site for recruitment to chromatin, the pervasiveness o...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2020-06-24 | PXD018690 | Pride
Anaphase-promoting complex/cyclosome Nucleosome Proteomics Elys Arginine anchor Nuclear pore Y-complex Chromatin Acidic patch 
GenomicsCo-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
In mammalian cells transcription factors (TFs) preferentially bind sites contained in regions of high nucleosomal occupancy, as determined by nucleotide-dependent computational analysis. This observation suggests that nucleosomes may act as gatekeepers of TF binding sites. We hypothesized that in ma...
ORGANISM(S): Mus musculus 
2014-05-08 | E-GEOD-50762 | biostudies-arrayexpress
TranscriptomicsNucleosome loss leads to global transcriptional upregulation and genomic instability during yeast replicative aging
All eukaryotic cells divide a finite number of times, termed replicative aging, but the reason for this is not clear. Consistent with the decreased total histone protein levels in aged Saccharomyces cerevisiae, which is a cause of aging (1), we find that nucleosome occupancy decreases 50% across the...
ORGANISM(S): Saccharomyces cerevisiae 
2014-02-26 | E-GEOD-47023 | biostudies-arrayexpress
TranscriptomicsCoupling p53 binding and nucleosome occupancy measurements at p53 binding sites
We were interested to explain why p53 binds some high affinity sites in contrast to other high affinity sites that are not bound by p53. p53 binding was measured using p53 ChIP-CHIP and in parallel nucleosome occupancy was measured on these same sites Comparison between p53 binding and nucleosome oc...
ORGANISM(S): Homo sapiens 
2010-08-09 | E-GEOD-22783 | biostudies-arrayexpress
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 
ProteomicsStructural basis of paralog-specific KDM2A/B nucleosome recognition
The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. In order to define the molecular basis of acidic patch recognition proteome-wide, we performed an amino acid resolution acidic patch interacto...
ORGANISM(S): Homo sapiens (Human) 
2023-02-14 | PXD032791 | Pride
Nucleosome Demethylase Kdm2b Jmjc Chromatin Acidic patch Kdm2a 
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 
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