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Nuclesome Distribution data for KSHV reactivation

ABSTRACT: 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 Kaposi’s 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 “spring” 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE52453 | GEO | 2013/11/19

SECONDARY ACCESSION(S): PRJNA228974

REPOSITORIES: GEO

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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

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

Nucleosome Distribution Data for Methylphenidate Treatment

2015-06-26 | GSE70292 | GEO

Homo sapiens

Project description:Nuclesome Distribution data for KSHV reactivation

| PRJNA228974 | ENA

Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner

Project description:We assessed the interplay between DNA sequences and ATP-dependent chromatin remodelers in defining the nucleosomal organization of the eukaryotic genome. We compared the genome-wide distribution and impact on chromatin of NURD, (P)BAP, INO80 and ISWI representing four major families of Drosophila remodelers. Each remodeler has a unique set of genomic targets, and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two ways: NURD, (P)BAP and INO80 increase histone density at their target sequences, which disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Thus, both selective targeting and distinct mechanisms of remodeling underlie the functional differentiation of remodelers. We conclude that chromatin organization involves a class-specific antagonism between remodeler activity and DNA sequence-driven nucleosome placement. The supplementary bed files (P)BAP_sites.bed, NURD_sites.bed, INO80_sites.bed, ISWI_sites.bed contain high quality binding sites for each remodeler obtained by intersecting the sets of significant ChIP-chip peaks for each antibody.

2011-12-12 | GSE32404 | GEO

Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome

Project description:In the yeast genome, a large proportion of nucleosomes occupy well-defined positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genomic context remains controversial. Through genome-wide, quantitative analysis of nucleosome positioning and high-resolution mutagenenesis of mononucleosomal DNA, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes. This effect is equally detected in transcribed and non-transcribed regions, suggesting the existence of sequence elements contributing to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open up the possibility of designing coding and non-coding DNA molecules capable of directing their own nucleosomal organization.

2016-09-20 | GSE84910 | GEO

Global host gene expression changes in KSHV+ PEL cells upon KSHV reactivation

Project description:Kaposi's sarcoma-associated herpesvirus (KSHV) is a human oncogenic virus, which maintains the persistent infection of the host by intermittently reactivating from latently infected cells to produce viral progenies. Here, we performed a comprehensive time course transcriptome analysis during KSHV reactivation in KSHV+ primary effusion B-cell lymphoma cells (PEL). For this we used a recombinant PEL cell line called TRExBCBL1-3xFLAG-RTA. The expression of the N-terminally 3xFLAG-tagged RTA was induced by adding 1 μg/ml doxycycline (Dox) to the medium. Total gene expression changes were identified in TRExBCBL1-3xFLAG-RTA cells at 0, 6, 12, and 24 hours post-induction (hpi).

2019-01-09 | GSE123898 | GEO

Next Generation Sequencing analysis of KSHV lytic replication in TREx-BCBL1-RTA cells

Project description:Purpose: miR-Seq was utilised to identify miRNAs which are altered during the course of KSHV lytic replication at 0, 16 and 24 hours post reactivation in TREx-BCBL1-RTA cells. Methods: Virus lytic replication was induced via addition of 2 µg/mL doxycycline hyclate (Sigma-Aldrich). Total RNA was extracted from TREx-BCBL-1s at 0, 16 and 24 hours post lytic induction. Small RNA libraries were prepared using the TruSeq Small RNA Library Prep Kit (Illumina). Quality filtered (Q < 20), and adapter trimmed reads (Trimmomatic v0.39) [59] were aligned to the GRCh38/hg38 assembly of the human genome using Bowtie2 (V 2.4.2).

2022-02-09 | GSE186652 | GEO

Kaposi’s Sarcoma-associated Herpesvirus Reactivation by Bacteria Promotes the Hypoxia Response and Epigenetic Regulation

Project description:Herpesviruses are frequently co-present with bacterial infection at multiple sites within the body, including the mouth, gut, and genitourinary tract. The detection of replicating virus in these compartments prompted investigation into the relationship between bacterial infection and Kaposi’s Sarcoma-associated Herpesvirus (KSHV) reactivation. Using a cell line latently infected with KSHV, we examined the ability of crude spent media containing metabolic products from periodontal and gut pathogens to reactivate KSHV. Upon incubation with crude spent media, KSHV was reactivated and we detected the up-regulation of viral early and late genes, linear viral genomes, and virions. Furthermore, KSHV reactivation was associated with global increases in histone H3 and histone H4 acetylation, consistent with viral expression. To explore the transcriptional consequences of spent media, we compared the gene expression changes following reactivation by P. gingivalis spent medium to those of two well-established pharmacological activators of KSHV reactivation, tetradecanolyl phorbol acetate and sodium butyrate. Microarray analyses revealed a unique gene expression signature with P. gingivalis-associated reactivation. Concurrent with KSHV reactivation, P. gingivalis spent medium increased the hypoxia response. Hypoxia was associated with effects on epigenetic regulators, including down-regulation of UHRF1, a modulator of DNA methylation. Our findings demonstrate that products secreted by oral bacteria not only stimulate a hypoxia response, but also result in global changes in epigenetic modifications and modifiers. These findings suggest that epigenetic changes induced by P. gingivalis underlie the KSHV reactivation pathway.

2018-03-20 | GSE67532 | GEO

Genome-wide mapping of RTA binding sites in KSHV+ PEL cells during KSHV reactivation.

Project description:Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) analysis was performed during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation in KSHV+ recombinant primary effusion B-cell lymphoma cells (PEL). RTA binding sites were identified genome-wide in a recombinant PEL cell line called TRExBCBL1-3xFLAG-RTA cells at 12 hours post-induction (hpi) of RTA expression.

2019-01-09 | GSE123897 | GEO

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