Nucleosome profiles in strains with different numbers of nucleosomes at HML and HMR
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA564006 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report nucleosome positions by using native Mnase-seq. The results strongly suggest that nucleosome positions don't change at the heterochromatic locus HMR upon removal of adjacent nucleosomes via deletion of nucleosomal DNA. Positions of nucleosomes at HML are also quantified.
2019-09-06 | GSE136897 | GEO
Project description:Heterochromatin is a complex structure comprised of nucleosome arrays that are bound by silencing factors. This composition suggests that certain configurations of nucleosome arrays are permissible for heterochromatic silencing. We tested this idea in S. cerevisiae by systematically altering the distance between heterochromatic Nucleosome Depleted Regions (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can be packed between NDRs. Consistent with this prediction, some inter-NDR distances led to poorly positioned nucleosome arrays within heterochromatin. Furthermore, these conditions that caused poor nucleosome positioning also led to defects in both heterochromatin stability and the ability of cells to generate and inherit a silenced transcriptional state. These findings strongly suggest that nucleosome positioning contributes to formation and maintenance of functional heterochromatin.
2020-02-06 | GSE144808 | GEO
Project description:Nucleosome profiles in strains with different inter-NDR distances at HML
| PRJNA604986 | ENA
Project description:Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are well- and consistently positioned, some nucleosomes and nucleosome-like structures are more sensitive to nuclease digestion or transitory in nature. To better understand the role of nucleosome remodeling factors in generating and clearing these alternative nucleosome structures, we depleted murine embryonic stem cells of the remodeler ATPases BRG1 and SNF2H then performed MNase-seq in murine embryonic stem cells. We performed MNase-seq under high- and low-MNase conditions to assess the effects of nucleosome remodeling factors on nuclease-sensitive or “fragile” nucleosome occupancy. In parallel, we gel-extracted MNase-digested fragments to enrich for another alternative nucleosome structure, the overlapping dinucleosome. Overlapping dinucleosomes are composed of two canonical nucleosomes, asymmetrically lacking one H2A:H2B dimer and wrapped by ~250 bp of DNA. In vitro studies of nucleosome remodeling have suggested that the collision of adjacent nucleosomes by nucleosome sliding can stimulate formation of overlapping dinucleosomes. Using these methods, we were able to identify fragile nucleosomes and overlapping dinucleosomes near transcription start sites and gene-distal DNaseI hypersensitive sites in mouse embryonic stem cells, among other loci. We find that BRG1 consistently stimulates occupancy of fragile nucleosomes but represses occupancy of overlapping dinucleosomes through its nucleosome remodeling function, while SNF2H expression slightly increases fragile nucleosome occupancy.
2023-03-14 | GSE216057 | GEO
Project description:Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by di-methylation of lysine 20 on histone H4 (H4K20me2). To achieve this unodified and H4K20me2-modified histone H4 were generated by native chemical ligation and assembled into recombinant di-nucleosomes. The di-nucleosomes were immobilized on streptavidin-coated beads via the biotinylated di-nucleosomal DNA and used for nucleosome affinity purifications to identify proteins regulated by H4K20me2 from SILAC-labelled HeLaS3 nuclear extracts (Arg10 and Lys8). SILAC affinity purifications were carried out in "forward" (heavy extract on modified nucleosome and light extract on unmodified nucleosome) and "reverse" (light extract on modified nucleosome and heavy extract on unmodified nucleosome) label-swap experiments and protein abundances were quantified by MaxQuant.
2019-02-27 | PXD009281 | Pride
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization. Comparing nucleosome occupancy under different MNase digestion levels and growth conditions.
2011-01-24 | E-GEOD-26412 | biostudies-arrayexpress
Project description:Nuc-MS characterizes histone modifications and variants directly from intact
endogenous mono-nucleosomes. Preserving whole nucleosome particles enables
precise interrogation of their protein content, as for H3.3-containing nucleosomes which
had 6-fold co-enrichment of variant H2A.Z over bulk chromatin. Moreover, Nuc-MS
showed co-occurrence of oncogenic H3.3K27M with euchromatic marks (e.g., H4K16ac
and >40-fold enrichment of H3K79me2). By capturing the entire epigenetic landscape,
Nuc-MS provides a new, quantitative readout of nucleosome-level biology.
2020-04-06 | MSV000085238 | MassIVE
Project description: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 harbouring the natural epigenetic signature, suitable for biochemical manipulation. Combined with deep sequencing, this library was used to investigate the stability of individual nucleosomes, and – as proof of principle - the nucleosome preference of the chromatin remodeling complex, RSC. In order to generate a library of native yeast nucleosomes, we developed a three-step purification protocol: first, purified yeast nuclei were incubated with micrococcal nuclease (MNase), which preferentially digests naked DNA to generate short chromatin fragments. The resulting fragments were extracted from the nuclei, then bound to and eluted from DEAE sepharose. This was followed by ultracentrifugation through a sucrose gradient to separate the fragments by length to further remove contaminating proteins and free DNA. We chose a simple disassembly assay, which involves incubating the nucleosome library with ATP and the histone chaperone Nap1, with or without RSC. In this assay, RSC binds to nucleosomes and transfers the histones to Nap1, thereby releasing ‘naked’ DNA. Under certain conditions, reaction intermediates can be observed (tetramers or hexasomes), but for simplicity we chose to compare the input nucleosomes with the final naked DNA product. To separate the RSC-dependent released DNA from the non-remodeled nucleosomes, the reactions were subjected to native agarose gel electrophoresis, and DNA of the four bands isolated by gel-extraction. The upper bands, harboring nucleosomes, were named NUC (no RSC) and NUCR (with RSC), whereas the lower, ‘naked’ DNA bands were named DNA (no RSC) and DNAR (with RSC).
2019-05-08 | E-MTAB-7926 | biostudies-arrayexpress
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.
2011-01-24 | GSE26412 | GEO
Project description:HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes). During acute infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the acute infection, but that they are not evenly positioned like cell DNA, with a 200bp repeat pattern. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is strong (6hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152kb). Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (NFR or NDR), or occupied at a low frequency in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during acute infection. On average, DNA encoding Immediate Early, Early and Late genes appear to have a similar density of nucleosomes. This distribution of nucleosomes is discussed in relation to genome DNA sequence and gene expression.
2015-06-01 | GSE59108 | GEO