Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Yeast Histone ChIP-chips_Evidence for nucleosome depletion at active regulatory regions genome-wide (Lee et al. 2004)

ABSTRACT: The identification of nuclease-hypersensitive sites in an active globin gene and in the 5' regions of fruit fly heat shock genes first suggested that chromatin changes accompany gene regulation in vivo. Here we present evidence that the basic repeating units of eukaryotic chromatin, nucleosomes, are depleted from active regulatory elements throughout the Saccharomyces cerevisiae genome in vivo. We found that during rapid mitotic growth, the level of nucleosome occupancy is inversely proportional to the transcriptional initiation rate at the promoter. We also observed a partial loss of histone H3 and H4 tetramers from the coding regions of the most heavily transcribed genes. Alterations in the global transcriptional program caused by heat shock or a change in carbon source resulted in an increased nucleosome occupancy at repressed promoters, and a decreased nucleosome occupancy at promoters that became active. Nuclease-hypersensitive sites occur in species from yeast to humans and result from chromatin perturbation. Given the conservation of sequence and function among components of both chromatin and the transcriptional machinery, nucleosome depletion at promoters may be a fundamental feature of eukaryotic transcriptional regulation. Keywords: ChIP-chip

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE4727 | GEO | 2006/04/28

SECONDARY ACCESSION(S): PRJNA95587

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effects of MBD3 depletion on nucleosome occupancy in MCF-7 cells

Project description:We and others have identified that MBD3/NuRD localizes at active promoters and enhancers, suggesting an active role of NuRD at open chromatin region. Because NuRD includes nucleosome remodelers, CHD3 and CHD4, we hypothesized that NuRD regulates nucleosome organization at open chromatin region. To test this idea, we performed micrococcal nuclease digestion followed by massively parallel sequencing (MNase-seq) in MBD3 knockdowned MCF-7 cells. We observed the decrease of nucleosome occupancy at promoters and enhancers in MBD3 knockdowned cells. Our results suggest a regulatory role of MBD3/NuRD at open chromatin region. Mapped nucleosome positioning in control (shLuc) and MBD3 knockdowned MCF-7 cells, in duplicate.

2013-10-31 | E-GEOD-51097 | biostudies-arrayexpress

Effects of MBD3 depletion on nucleosome occupancy in MCF-7 cells

2013-10-31 | GSE51097 | GEO

Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers [MNase-Seq]

Project description:In higher eukaryotes, enhancers and promoters share many properties, including binding of transcription factors, existing in open chromatin, and bidirectional transcription. Yet the structural features that distinguish enhancers and promoters are unclear. Genome-wide micrococcal nuclease (MNase) studies previously interpreted MNase hypersensitivity to indicate that active enhancers and promoters are nucleosome-free, yet other studies found histone variants and post-translational modifications at active enhancers. We find that prior MNase genomic studies have an overdigestion bias and that low-level MNase digestion, coupled with mapping core histones, reveals two classes of MNase-hypersensitive sites: at active promoters, which are nucleosome depleted, and at tissue-specific enhancers, which retain core histones and co-bound transcription factors substantially more than promoters. Hypersensitivity of active enhancer nucleosomes may reflect their preferential exposure in chromatin and can be maintained by pioneer transcription factors such as FoxA. These findings unveil fundamental differences in the chromatin structure of active enhancers and promoters.

2016-04-08 | GSE57558 | GEO

Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers [ChIP-Seq]

2016-04-08 | GSE57557 | GEO

Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers [ChIP-exo]

2016-04-08 | GSE57556 | GEO

MNase-chip of maize B73 immature ears and seedlings

Project description:The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. Using micrococcal nuclease (MNase) to map nucleosome positions, we show that in the maize genome, nucleosome occupancy signals are remarkably uniform between different tissues, whereas particular genomic regions are highly susceptible to variation. We demonstrate that much of this variation is associated with the degree to which chromatin is digested with MNase. Using high-density DNA microarrays, we exploited this digestion-linked variation to identify protein footprints in the maize genome that are hypersensitive to MNase digestion, a method we term Differential Nuclease-Sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5’ and 3’ ends of genes, associated with gene-expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the homeobox transcription-factor Knotted1, suggesting a functional role in genome regulation. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints in gene promoters. These results demonstrate the value of DNS-chip for revealing biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on how chromatin organization might influence protein-DNA interactions and genome regulation.

2014-08-06 | GSE60090 | GEO

MNase-chip of maize B73 immature ears, seedling shoots, and seedling roots

2014-08-06 | GSE60089 | GEO

Genome-wide reductions in active chromatin, paused RNA Polymerase II and nucleosome turnover during heat shock

Project description:Heat shock rapidly induces expression of a small set of genes while globally repressing transcription, making it an attractive system for studying alterations in the chromatin landscape that accompany changes in gene regulation. We have characterized these changes using low-salt extraction of intact micrococcal nuclease (MNase)-treated Drosophila S2 cell nuclei to determine the active nucleosomal and subnucleosomal chromatin landscapes. The low-salt-soluble fraction corresponds to classical "active" chromatin and includes distinct size fractions of MNase-protected particles that can be precisely mapped by paired-end sequencing. After heat shock, the distribution of low-salt-soluble nucleosomes showed an overall reduction over gene bodies, consistent with down-regulation of transcription. No global changes were detected in the subnucleosomal landscape upstream of transcriptional start sites, however, we observed a genome-wide reduction of paused RNA Polymerase II from the active chromatin fraction. Furthermore, nucleosome turnover decreased within gene bodies in a pattern similar to that observed when transcription elongation was artificially inhibited. These observations suggest that reduced Pol II affinity and processivity is the dominant nuclear mechanism for genome-wide repression during heat shock. Our ability to precisely map both nucleosomal and subnucleosomal particles directly from classical active chromatin extracts to assay changes in the chromatin landscape provides a simple general strategy for epigenome characterization. High-throughput sequencing (Illumina HiSeq 2000) We have characterized changes to the active nucleosomal and subnucleosomal landscape during the heat shock response in Drosophila cells by genome-wide profiling of low-salt extracted micrococcal nuclease-treated nuclei, paused RNA Polymerase II and CATCH-IT nucleosome turnover.

2011-11-15 | E-GEOD-30755 | biostudies-arrayexpress

Chromatin landscape of Leishmania major

Project description:We sought to identify nuclease-hypersensitive sites and to quantify nucleosome positions in an effort to identify cis-regulatory elements in the protozoan parasite Leishmania major. Using micrococcal nuclease digestion of chromatin (MNAse-seq), we report that few nuclease hypersensitive sites are present within the presumed regions of RNA polymerase II-mediated transcription initiation, and that similar numbers of nuclease hypersensitive sites were found in control datasets. However, utilizing an independent approach (FAIRE), we observe that a heterogeneous population of nuclease hypersensitive sites are present in and around these regions, and that nucleosomes within these regions are susceptible to MNAse overdigestion.

2020-03-31 | GSE60846 | GEO

Two Distinct Promoter Nucleosome Architectures at Protein-Coding Genes in Yeast

Project description:Previous studies indicate that eukaryotic promoters display a stereotypical chromatin landscape characterized by a well-positioned +1 nucleosome near the transcription start site and an upstream -1 nucleosome that together demarcate a nucleosome-free (or depleted) region. Here we present evidence that there are two distinct types of promoters distinguished by the resistance of the -1 nucleosome to micrococcal nuclease digestion. These different architectures are characterized by two sequence motifs that are broadly deployed at one set of promoters where a nuclease-sensitive ("fragile") nucleosome forms, but concentrated in a more narrow, nucleosome-free region at all other promoters. The RSC nucleosome remodeler acts through the motifs to establish stable +1 and -1 nucleosome positions, while binding of a small set of general regulatory (pioneer) factors at fragile nucleosome promoters plays a key role in their destabilization. We propose that the fragile nucleosome promoter architecture is adapted for regulation of highly expressed, growth-related genes. MNase-seq profiles obtained with various MNase concentrations from wild-type cells and cells depleted of different factors. ChIP-seq using anti-RNA polymerase II antibody, anti-histone H2A antibody, and anti-histone H3 antibody.

2015-11-05 | E-GEOD-73337 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data