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Epigenetic changes of Raji Epstein–Barr viral genome in reponse to byrostatin treatment

ABSTRACT: We report the application of cut&tag technology for high-throughput profiling of histone modifications Raji Epstein–Barr viral genome in reponse to bryostatin treatment. Dual- and tri-methylation of lysine 4 on histone H3 protein indicate genes that are actively expressed/regulated. Tri-methylation of lysine 27 on histone H3 protein marks genes that are negatively regulated or suppressed for expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE192837 | GEO | 2022/01/05

REPOSITORIES: GEO

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Genome-wide epigenetic changes of leukemia cell lines in reponse to byrostatin treatment

Project description:We report the application of cut&tag technology for high-throughput profiling of histone modifications in leuemia cells in reponse to bryostatin treatment. We generated genome-wide chromatin-state landscape of NALM6, REH and Raji cells. Dual- and tri-methylation of lysine 4 on histone H3 protein indicate genes that are actively expressed/regulated. Tri-methylation of lysine 27 on histone H3 protein marks genes that are negatively regulated or suppressed for expressiom. We compared differential peaks for cells treated with or without bryostatin to demonstrate genes responding to bryostatin treatment on epigenetic level.

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Effect of bryostatin-1 on gene expression profile of Raji cells

Project description:To investigate bryostain's effect on Raji , we performed a whole-transcriptome RNA sequencing experiment for Raji cells treated with Bryostatin and established differntial expression profile comparing to raji treated with DMSO.

2022-08-19 | GSE211351 | GEO

Epigenetic changes of Raji Epstein–Barr viral genome in reponse to byrostatin treatment

Project description:Epigenetic changes of Raji Epstein–Barr viral genome in reponse to byrostatin treatment

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Time makes histone H3 modifications drift

Project description:To disclose the epigenetic drift of time passing, we determined the genome-wide distributions of mono- and tri-methylated lysine 4 and acetylated and tri-methylated lysine 27 of histone H3 in the livers of healthy 3, 6 and 12 months old C57BL/6 mice. The comparison of different age profiles of histone H3 marks revealed global redistribution of histone H3 modifications with time, in particular in intergenic regions and near transcription start sites, as well as altered correlation between the profiles of different histone modifications. Moreover, feeding mice with caloric restriction diet, a treatment known to retard aging, preserved younger state of histone H3 in these genomic regions.

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Expression of the TM4SF member CD9 on the human Burkitts lymphoma cell line Raji

Project description:Expression of the TM4SF member CD9 on the human Burkitts lymphoma cell line Raji induced increased cell proliferation, motilty and adhesion to fibronectin. CD9 promoted increases in Raji cell proliferation was dependent upon histone deacetyalase (HDAC) activity as treatment with HDAC inhibitors trichostain A or cucurmin attenuated CD9 mediated increases in Raji cell proliferation. Gene expression of Raji cells stably expressing human CD9 via transfection with expression vector PRVCMVCD9 was compared with corresponding Mock transfected cell by microarray analysis using the Affymetrix U133 2.0 platform.

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ChIP-seq analysis of the Sordaria macrospora wild type and the developmental mutant delta-asf1 [ChIP-seq]

Project description:Genome-wide distribtuion of histone H3 and H3K27me3 (histone H3 tri-methylated at lysine 27) was analyzed in the wild type and the sterile mutant asf1. The asf1 gene encodes a conserved histone chaperone, and preliminary experimentes indicated changes in histone modifications in the mutant that were analyzed on a genome-wide basis in these experiments.

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Transcription profiling of human Burkitts lymphoma cells line Raji expressing the TM4SF member CD9

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Determine genes differentially expressed between Raji cells and a subline which is resistant to APTO-253 (Raji/253R)

Project description:To obtain further insight into the resistance mechanism, RNA-seq analysis was carried out on 3 independent samples of both the sensitive Raji and resistant Raji/253R cells. A gene-level differential expression analysis was performed by removing all genes with less than 50 reads across all 6 samples as genes with only low level expression can cause irregularities in differential expression analysis. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction. Among the 13,791 evaluable genes there were 1,012 that were significantly up-regulated in the Raji/253R cells and 704 genes that were significantly down regulated relative to the parental sensitive Raji cells. The ATP-binding cassette sub-family member ABCG2 was the most up-regulated gene with more than a thousand-fold increase in transcript level. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction.

2020-03-30 | GSE111928 | GEO

METTL14 Regulates Chromatin Bivalent Domains in Mouse Embryonic Stem Cells [ChIP-seq]

Project description:METTL14 (methyltransferase-like 14) is an RNA binding protein that partners with METTL3 to mediate N6-methyladenosine (m6A) methylation of mRNA. Recent studies identified a function for METTL3 in heterochromatin and transcription, but the role of METTL14 in these contexts remains unclear. Here we show that METTL14 binds and regulates mouse embryonic stem cell bivalent domains, which are marked with tri-methylation at lysine 27 of histone H3 (H3K27me3) and tri-methylation at lysine 4 of histone H3 (H3K4me3). Knockout of Mettl14 results in decreased H3K27me3 but increased H3K4me3 levels at bivalent regions, resulting in the resolution of the bivalency and in increased transcription. We demonstrate that bivalent domain regulation by METTL14 is independent of METTL3 or m6A modification. Instead, METTL14 enhances H3K27me3 and reduces H3K4me3 by interacting with and probably recruiting the histone 3 lysine 27 (H3K27) methyltransferase complex PRC2 and the histone 3 lysine 4 (H3K4) demethylases KDM5B to chromatin. Our findings identify a METTL3-independent function of METTL14, important for maintaining the bivalent domains in mESCs, thus revealing a new mechanism of bivalent domain regulation in mammals.

2023-06-19 | GSE206730 | GEO

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