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GenomicsEffects of DNA Methylation on Nucleosome Stability
Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted high-throughput nucleosome reconstitution experiments on 572 KB of human DNA and 668 KB of mouse DNA that wa...
ORGANISM(S): Mus musculus 
2013-01-28 | E-GEOD-37224 | biostudies-arrayexpress
GenomicsPartitioning the C. elegans genome by nucleosome modification, occupancy, and positioning
We have characterized two post-translational histone modifications in C. elegans on a genomic scale. Micrococcal nuclease digestion and immunoprecipitation were used to obtain distinct populations of single nucleosome cores, which were analyzed using massively parallel DNA sequencing to obtain pos...
ORGANISM(S): Caenorhabditis elegans 
2009-08-31 | E-GEOD-17284 | biostudies-arrayexpress
TranscriptomicsDeterminants of nucleosome positioning and their influence on plant gene expression
We report the global nuclesome posiitons to study the relationship between nucleosome occupancy and gene expression in response to Coronatine in Arabidopsis We examined nucleosome occupancy and mRNA abundance in response to Coronatine in Arabidopsis rosette leaves
ORGANISM(S): Arabidopsis thaliana 
2015-05-27 | E-GEOD-64397 | biostudies-arrayexpress
GenomicsEffects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [single-end MNase-seq]
Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted d...
ORGANISM(S): Saccharomyces cerevisiae 
2012-09-26 | E-GEOD-29291 | biostudies-arrayexpress
GenomicsNucleosome repositioning-coupled expression divergence between species
We describe the genome-wide nucleosome profiles for S. bayanus under standard conditions Nucleosomes from S. bayanus was isolated and sequenced using the Illumina GAII platform.
ORGANISM(S): Saccharomyces bayanus 
2011-11-10 | E-GEOD-24356 | biostudies-arrayexpress
GenomicsTOP1M-NM-1 functions on nucleosome density
DNA topoisomerases release supercoils in DNA introduced during replication or transcription. How DNA topoisomerases impact transcription in the context of eukaryotic chromatin is poorly understood. In this study, using a floral stem cell model in Arabidopsis, we uncovered a role of TOP1M-NM-1 in Pol...
ORGANISM(S): Arabidopsis thaliana 
2014-10-14 | E-GEOD-53950 | biostudies-arrayexpress
GenomicsA compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [Nuc-Seq]
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain...
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-22 | E-GEOD-44878 | biostudies-arrayexpress
GenomicsThe Nucleosome Map of the Mammalian Liver
We report the genome-wide map of nucleosome positions in the mouse liver, with emphasis on transcriptional start sites, CpG islands, Foxa2 binding sites, and their correlation with gene expression. Despite the heterogeneity of liver tissue, we could clearly discern the nucleosome pattern of the pred...
ORGANISM(S): Mus musculus 
2011-04-30 | E-GEOD-26729 | biostudies-arrayexpress
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
GenomicsNucleosome Positioning Dynamics Through the Yeast Metabolic Cycle
We present Micrococcal Nuclease digestion maps of S. cerevisiae through the progression of the Yeast Metabolic Cycle. We demonstrate that nucleosome positions at many promoters are dynamic, and remodeling events at promoters have significant consequences with respect to gene expression. Examination ...
ORGANISM(S): Saccharomyces cerevisiae 
2016-03-15 | E-GEOD-77631 | biostudies-arrayexpress
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