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Nucleosome Distribution Data for Methylphenidate Treatment

ABSTRACT: Jurkat T-leukemic cells at 0, 15, 45, and 240 minutes post MPH treatment. Chromatin structure depends highly on the position and density of nucleosomes in the genome. The distribution of these nucleosomes likely plays a critical role in all processes for which DNA is the template, including: gene expression, DNA replication, recombination and repair. It has been proposed for more than half a century that although all the cells in a human body contain, essentially, the same genetic material, nucleosomes give access to different areas of the genome effectively giving access to cell-type specific areas of the genome. We hypothesized that alterations in nucleosome distribution might play a role in the MPH stimulated immune response. We measured chromatin structural changes in a human T-cell line (Jurkat T-leukemic) at high temporal resolution after MPH treatment. We mapped the nucleosome distribution at 4 different time points (0, 15, 45, 240 minutes). Nucleosomal DNA sequences were harvested via chromatin cross-linkage, MNase digestion and DNA extraction. Results were gathered by measuring differences in nucleosome distribution between the basal and the treated states at the different time points. We identified changes in nucleosome distribution. Interestingly, these changes in nucleosome distribution were transient, returning to their basal positions. Finally, these changes in nucleosome distribution exhibited different kinetics at different genes. We propose that the changes in nucleosomal distribution help potentiate differences in gene activity. The results allow us to understand the direct affects of MPH on chromatin structure and help reveal certain mechanistic processes by which it performs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE70292 | GEO | 2015/06/26

SECONDARY ACCESSION(S): PRJNA288176

REPOSITORIES: GEO

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Nucleosome Distribution Data for Methylphenidate Treatment

Project description:Jurkat T-leukemic cells at 0, 15, 45, and 240 minutes post MPH treatment. Chromatin structure depends highly on the position and density of nucleosomes in the genome. The distribution of these nucleosomes likely plays a critical role in all processes for which DNA is the template, including: gene expression, DNA replication, recombination and repair. It has been proposed for more than half a century that although all the cells in a human body contain, essentially, the same genetic material, nucleosomes give access to different areas of the genome effectively giving access to cell-type specific areas of the genome. We hypothesized that alterations in nucleosome distribution might play a role in the MPH stimulated immune response. We measured chromatin structural changes in a human T-cell line (Jurkat T-leukemic) at high temporal resolution after MPH treatment. We mapped the nucleosome distribution at 4 different time points (0, 15, 45, 240 minutes). Nucleosomal DNA sequences were harvested via chromatin cross-linkage, MNase digestion and DNA extraction. Results were gathered by measuring differences in nucleosome distribution between the basal and the treated states at the different time points. We identified changes in nucleosome distribution. Interestingly, these changes in nucleosome distribution were transient, returning to their basal positions. Finally, these changes in nucleosome distribution exhibited different kinetics at different genes. We propose that the changes in nucleosomal distribution help potentiate differences in gene activity. The results allow us to understand the direct affects of MPH on chromatin structure and help reveal certain mechanistic processes by which it performs. Jurkat T-leukemic cells at 0, 15, 45, and 240 minutes post MPH treatment.

2015-06-26 | E-GEOD-70292 | biostudies-arrayexpress

MARCS: Modification Atlas for Regulation by Chromatin States

Project description:Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by various combinatorial chromatin modifications found in different chromatin states such as promoters, enhancers and heterochromatin. To achieve this, recombinant modified nucleosomes representing different chromatin states were assembled from canonical histones, H2A.Z and modified ligated H3/H4 histone proteins and biotinylated nucleosomal DNAs. Assembled nucleosomes were immobilized on streptavidin-coated beads via biotinylated di-nucleosomal 601 DNA and used for nucleosome affinity purifications to identify proteins regulated by chromatin modifications 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. Initial trial experiments with biotinylated mono-, di- and tetra- 601 nucleosomes are also deposited along with the data for the di-nucleosome experiments. See also: Bartke et al., 2010. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143, 470–484; doi:10.1016/j.cell.2010.10.012. The H4K20me2 samples from this experiment were previously deposited with identifier PXD009281. These were published in: Nakamura et al., 2019. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature Cell Biology 21, 311–318; doi: 10.1038/s41556-019-0282-9.

2023-12-12 | PXD018966 | Pride

Stable nucleosome positions in HOX clusters; human K562 and HeLa cells

Project description:The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes where nucleosome positions have not been examined beyond isolated loci and promoter regions. Towards this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of inter-nucleosome distances, specific loci contain regular nucleosomal arrays with 195bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3’ ends of genes. Through comparison of different cell lines, we find that increased gene expression correlates with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes. Keywords: human chromatin nucleosome positions, nucleosomes, ChIP-chip

2008-02-20 | GSE10042 | GEO

H4K20me2 SILAC Nucleosome Affinity Purification

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

Nuclesome Distribution data for KSHV reactivation

Project description:iSLK.219 cells at 0, 6, 12, 24, and 48 hours post KSHV reactivation. Nucleosome occupancy plays a key role in regulating access to the eukaryotic genomes. Although various chromatin regulatory complexes are known to regulate nucleosome occupancy, the role of DNA sequence in this regulation remains unclear, particularly in mammals. To address this problem, we measured nucleosome distribution at high temporal resolution in human cells at hundreds of genes during the reactivation of KaposiM-bM-^@M-^Ys sarcoma-associated herpesvirus (KSHV). We show that nucleosome redistribution peaks at 24 hours post KSHV reactivation and that the nucleosomal redistributions are widespread and transient. To clarify the role of DNA sequence in these nucleosomal redistributions, we compared the genes with altered nucleosome distribution to a sequence-based computer model and in vitro assembled nucleosomes. We demonstrate that both the predicted model and the assembled nucleosome distributions are concordant with the majority of nucleosome redistributions at 24 hours post KSHV reactivation. We suggest a model in which loci are held in unfavorable chromatin architecture and M-bM-^@M-^\springM-bM-^@M-^] to a transient intermediate state directed by DNA sequence information. We propose that DNA sequence plays a more considerable role in the regulation of nucleosome positions than was previously appreciated. The surprising findings that nucleosome redistributions are widespread, transient, and DNA-directed shift the current perspective regarding regulation of nucleosome distribution in humans. iSLK.219 cells at 0, 6, 12, 24, and 48 hours post KSHV reactivation.

2013-11-19 | E-GEOD-52453 | biostudies-arrayexpress

Histone octamer structure is altered early in ISW2 ATP-dependent remodeling of nucleosomes

Project description:Histone octamers are thought to be a rigid part of nucleosomes that shape chromatin and block cellular machinery from accessing DNA. ATP-dependent chromatin remodelers like ISW2 mobilize nucleosomes to provide DNA access. We find evidence for histone octamer distortion preceding DNA being moved into nucleosomes and processive movement of the ATPase motor of ISW2 on nucleosomal DNA. DNA entering nucleosome is uncoupled from the ATPase activity of ISW2 and alterations of the histone octamer structure mediated by ISW2 by deletion of the SANT domain from the C-terminus of the Isw2 catalytic subunit. We also find that restricting histone movement by chemical crosslinking traps remodeling intermediates resembling those seen by loss of the SANT domain, further supporting the importance of changes in histone octamer structure early in ISW2 remodeling. Transient octamer distortions are stabilized by H3-H4 tetramer disulfide crosslinking, thereby linking intrinsic histone octamer flexibility to chromatin remodeling.

2020-05-27 | PXD013967 | Pride

Drosophila melanogaster S2 cells nucleosome occupancy data after simulation by heat killed Staphylococcus aureus

Project description:The innate immune response is among the strongest genomic responses and is conserved across all metazoa. Although transcription during the innate immune response has been well studied, the associated chromatin reorganizations are largely uncharacterized. Here we show that Drosophila S2 cells stimulated with Staphylococcus aureus display a dynamic change in genome-wide nucleosome occupancy and sensitivity. We found a widespread and transient nucleosomal loss peaking at 30 minutes post stimulation, and we demonstrated that the regulatory potentials of nucleosomes differ following stimulation. In addition, we identified differentially sensitive nucleosomes with response-specific potentials. Our results provide high-resolution nucleosome-distribution maps of the fly genome, revealing chromatin's role in: the innate immune response to Gram-positive bacteria, response-specific regulatory-factor binding, and nucleosome sensitivity. We identify functional chromatin regulatory features associated with immune response, and lay a foundation for a framework linking general and locus-specific roles for nucleosomes in immune regulation. Drsophila S2 cells at 0hr, 30minutes, 1hr and 4hr post heat-killed Staphylococcus aureus stimulation

2015-02-28 | E-GEOD-66367 | biostudies-arrayexpress

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

Nucleosome recognition and DNA distortion by the Chd1 remodeler revealed at 2.6 Å resolution

Project description:Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. The Chd1 remodeler specializes in shifting nucleosomes into evenly spaced arrays, a defining characteristic of chromatin in gene bodies that blocks spurious transcription initiation. Linked to some forms of autism and commonly mutated in prostate cancer, Chd1 is essential for maintaining pluripotency in stem cells. Here we report a complex of yeast Chd1 bound to a nucleosome in a nucleotide-free state, determined by cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. The structure shows a bulge of the DNA tracking strand where the ATPase motor engages the nucleosome, consistent with an initial stage in DNA translocation. Unlike other remodeler-nucleosome complexes, nucleosomal DNA compensates for the remodeler-induced bulge with a bulge of the complementary DNA strand one helical turn downstream from the ATPase motor. Unexpectedly, the structure also reveals an N-terminal binding motif, called ChEx, which binds on the exit-side acidic patch of the nucleosome. The ChEx motif can displace a LANA-based peptide from the acidic patch, which suggests a means by which Chd1 remodelers may block competing chromatin remodelers from acting on the opposite side of the nucleosome.

2022-02-23 | PXD025287 | Pride

Chemical map of S. pombe reveals species-specific features in nucleosome positioning

Project description:Knowing the exact positions of nucleosomes not only advances our understanding of their role in gene regulation, but also the mechanisms that underlie between-species variation in chromatin structure. We have generated a chemical map of nucleosomes in vivo in Schizosaccharomyces pombe at base pair resolution. This new map reveals that S.pombe genome shares a similar periodic linker length distribution with Saccharomyces cerevisiae, but with major distinctions in nucleosomal/linker DNA sequence features. In S.pombe, A/T rich sequences are enriched in the nucleosome core region, particularly +/-20 bp of dyad, while they are disfavored in S.cerevisiae nucleosomes. The poly (dA-dT) tracts only slightly affect the nucleosome occupancy in S.pombe; and they possess preferential rotational positions within the nucleosome core with significant enrichment in the 10-30 bp region from the dyad for longer tracts. S.pombe does not have well-defined nucleosome free region immediately upstream of most transcription start sites (TSS), instead the -1 nucleosome is positioned with regular distance to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. The nucleosomes around TSS show more pronounced bidirectional phasing when the intergenic distance is relatively short, and the downstream nucleosome positioning is strongly correlated with DNA sequence features. We discovered that heterochromatin regions tend to have sparse nucleosome positioning, mixed with both well-positioned and fuzzy nucleosomes. The S.pombe map suggests that some of nucleosome positioning codes, formerly thought to be intrinsic, may largely depend on species-specific extrinsic factors including linker histone, chromatin remodelers and other DNA-binding proteins. 2 samples were analyzed with high throughput paired-end parallel sequencing. Both samples were created using the same chemical mapping protocol

2013-11-12 | E-GEOD-46975 | biostudies-arrayexpress

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