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TranscriptomicsA Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT
Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A-H2B deposition during transcript...
ORGANISM(S): Saccharomyces cerevisiae 
2016-08-10 | E-GEOD-80831 | 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
TranscriptomicsNucleosome Mapping in S. pombe Centromeres
A key element for defining the centromere identity is the incorporation of a specific histone H3, CENP-A, known as Cnp1p in S. pombe. Previous studies have suggested that functional S. pombe centromeres lack nucleosome arrays and may involve chromatin remodeling as a key step of kinetochore assembl...
ORGANISM(S): Schizosaccharomyces pombe 
2008-05-30 | E-GEOD-10742 | 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
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
TranscriptomicsThe Nucleosome Landscape of P. falciparum Reveals Chromatin Architecture and Dynamics of Regulatory Sequences
In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-related processes. For P. falciparum, the causative agent of human malaria, the nucleosome landscape of the extremely AT-rich intergenic regulatory regions is largely unexplored. With the aid of a highly controlled MN...
ORGANISM(S): Plasmodium falciparum 
2015-11-25 | E-GEOD-66185 | biostudies-arrayexpress
GenomicsGenome-wide nucleosome position data for 3 yeast species
Genome-wide nucleosome position data for wildtype and mutant strains in S. cerevisiae, C. albicans, and S. pombe Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe). S. pombe samples were grown in YES medium at permissive t...
ORGANISM(S): Candida albicans 
2011-08-01 | E-GEOD-28839 | biostudies-arrayexpress
GenomicsGenome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq]
We determined genome-wide nucleosome occupancy in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell type and protein specific binding preferences of transcription fact...
ORGANISM(S): Mus musculus 
2012-10-21 | E-GEOD-40910 | 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
TranscriptomicsMechanisms that specify promoter nucleosome location and identity
The chromatin architecture of eukaryotic gene promoters is generally characterized by a nucleosome-free region (NFR) flanked by at least one H2A.Z variant nucleosome. Computational predictions of nucleosome positions based on thermodynamic properties of DNA-histone interactions have met with limite...
ORGANISM(S): Saccharomyces cerevisiae 
2009-04-30 | E-GEOD-13446 | biostudies-arrayexpress
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