Ontology highlight
ABSTRACT:
PROVIDER: PRJNA95673 | ENA |
REPOSITORIES: ENA
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Project description:The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Keywords: FAIRE
2006-08-11 | GSE4720 | GEO
Project description:The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Keywords: FAIRE
2006-08-11 | GSE4719 | GEO
Project description:The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Keywords: FAIRE
2006-08-11 | GSE4721 | GEO
Project description: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 of nucleosome positions and transcriptional output through metabolic oscillations in budding yeast.
2016-03-15 | E-GEOD-77631 | biostudies-arrayexpress
Project description:KaposiM-bM-^@M-^Ys sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus which establishes latent infection in endothelial and B cells, as well as in primary effusion lymphoma (PEL). During latency, the viral genome exists as a circular DNA minichromosome (episome) and is packaged into chromatin analogous to human chromosomes. Only a small subset of promoters, those which drive latent RNAs, are active in latent episomes. In general, nucleosome depletion (M-bM-^@M-^\open chromatinM-bM-^@M-^]) is a hallmark of eukaryotic regulatory elements such as promoters and transcriptional enhancers or insulators. We applied formaldehyde-assisted isolation of regulatory elements (FAIRE) followed by next-generation sequencing to identify regulatory elements in the KSHV genome and integrated these data with previously identified locations of histone modifications, RNA polymerase II occupancy, and CTCF binding sites. We found that (i) regions of open chromatin were not restricted to the transcriptionally defined latent loci; (ii) open chromatin was adjacent to regions harboring activating histone modifications, even at transcriptionally inactive loci; and (iii) CTCF binding sites fell within regions of open chromatin with few exceptions, including the constitutive LANA promoter and the vIL6 promoter. FAIRE-identified nucleosome depletion was similar among B and endothelial cell lineages, suggesting a common viral genome architecture in all forms of latency. Ten total samples analyzed by FAIRE-seq from latent KSHV-infected cell lines. Two replicates were performed for BC1, KSHV-BJAB, KSHV-HUVEC, and L1-TIVE cells using the Illumina HiSeq 2000 platform. For BCBL1 cells, 1 FAIRE-seq sample and 1 non-cross-linked control BCBL1 sample was analyzed using the Illumina GAIIx
2013-09-05 | E-GEOD-50581 | biostudies-arrayexpress
Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide to reveal new relationships between regulators of stress-dependent gene expression. Nucleosome occupancy was measured by MNase-Seq in response to .4mM H2O2 in the S288c yeast derivative BY4741. A single replicate was performed for the time-course experiment with time points at 0, 4, 12, 20, 40 and 60 minutes after treatment.
2012-06-18 | E-GEOD-30900 | biostudies-arrayexpress
Project description: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.
2016-03-15 | GSE77631 | GEO
Project description:The yeast Ssn6-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Ssn6-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of SSN6 or TUP1, and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of SSN6 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Ssn6 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of SSN6 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Ssn6-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation. nucleosomes were prepared from isogenic wild type (BY4742), ssn6 KO and tup1 KO cells after varying degrees of micrococcal nuclease (MNase) digestion, followed by isolation of mononucleosomal DNA and sequencing. Three replicates of each strain (9 samples) were subjected to Illumina sequencing.
2012-10-10 | E-GEOD-37465 | biostudies-arrayexpress
Project description:Nucleosome organization and dynamics play a central role in controlling the DNA accessibility to regulatory factors of many critical cellular functions, especially gene regulation. However, despite extensive studies, the main factors determining nucleosome positioning and its fluctuation during cell cycle still remain elusive. Here, we present a large-scale study of nucleosome plasticity throughout the cell cycle and its interplay with gene expression based on genome-wide nucleosome positioning and mRNA abundance. We have clusterized distinct nucleosome architectures around transcription start sites and replication origins and studied their dynamics during the cell cycle progression. The most significant cell cycle-dependent changes occur at G1-S and G2-M transitions due to a large changes in gene expression in cell cycle regulatory genes. Taken together, our accurate study provides a dynamic picture of chromatin organization along cell cycle and its interplay with gene expression.
2014-10-09 | E-MTAB-2839 | biostudies-arrayexpress
Project description:Cell cycle dependent nucleosome occupancy at cohesin binding sites in yeast chromosomes
| PRJNA101013 | ENA