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GenomicsDistribution of macroH2A1 nucleosomes in mouse liver chromatin
We produced a genome-wide map of the distribution of macroH2A1 histone variants in mouse liver chromatin using high-throughput sequencing of DNA from macroH2A1 nucleosomes. Although macroH2A1 nucleosomes are widely distributed across the genome, their local concentration varies over a range of 100-f...
ORGANISM(S): Mus musculus 
2010-11-10 | E-GEOD-18963 | biostudies-arrayexpress
GenomicsNucleosomes are context-specific, H2A.Z modulated barriers to RNA polymerase
Nucleosomes are barriers to transcription in vitro, however, their effects on RNA polymerase in vivo are unknown. Here we describe a simple and general strategy to comprehensively map the positions of elongating and arrested RNA Polymerase II (RNAPII) at nucleotide resolution. Our results suggest th...
ORGANISM(S): Drosophila melanogaster 
2014-03-06 | E-GEOD-49106 | 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 
ProteomicsThe structure and composition of native human nucleosomes
In this study, we analysed the composition of histone modifications on native nucleosomes purified from HEK293 cells.
ORGANISM(S): Homo sapiens (Human) 
2026-01-12 | PXD064241 | Pride
Ptms Cryoem Nucleosomes Histones 
ProteomicsThe interaction between DNMT3A with H3Kc36me2 modified nucleosomes
DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns, essential for the dynamic organization of vertebrate genomes. However, the mechanisms underlying DNMT3A1's recruitment and function within different chromatin environments remain unclear...
ORGANISM(S): Homo sapiens (Human) 
2024-12-07 | PXD046529 | Pride
Dnmt3a Crosslink Nucleosomes 
TranscriptomicsMNase-Seq of isolated mono-nucleosomes from strains W303 (wild-type) and htz1∆.
Chromatin transactions are typically studied in vivo, or in vitro using artificial chromatin lacking the epigenetic complexity of the natural material. Attempting to bridge the gap between these approaches, we established a system for isolating the yeast genome as a library of mono-nucleosomes harbo...
ORGANISM(S): Saccharomyces cerevisiae S288c 
2019-05-08 | E-MTAB-7926 | biostudies-arrayexpress
GenomicsThe CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres
Plant and animal centromeres comprise megabases of highly repeated satellite sequences, yet centromere function can be specified epigenetically on single-copy DNA by the presence of nucleosomes containing a centromere-specific variant of histone H3 (cenH3). We determined the positions of cenH3 nucle...
ORGANISM(S): Oryza sativa 
2013-11-06 | E-GEOD-50755 | biostudies-arrayexpress
TranscriptomicsStructural basis for retroviral integration into nucleosomes
Retroviral integration is catalyzed by a tetramer of integrase (IN) assembled on viral DNA ends in a stable complex, known as the intasome. How the intasome interfaces with chromosomal DNA, which exists in the form of nucleosomal arrays, is currently unknown. Here we show that the prototype foamy vi...
ORGANISM(S): Homo sapiens 
2015-06-10 | E-GEOD-67730 | biostudies-arrayexpress
GenomicsDual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in PlantsM-BM-
DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT...
ORGANISM(S): Arabidopsis thaliana 
2012-11-11 | E-GEOD-39097 | biostudies-arrayexpress
GenomicsTwo distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription
In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, b...
ORGANISM(S): Saccharomyces cerevisiae 
2014-10-01 | E-GEOD-61596 | biostudies-arrayexpress
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