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H3K27ac, H3K4me and H3K4me3 binding examined by ChIP-seq in the CHP-134 neuroblastoma cell line

ABSTRACT: Super-enhancers are defined by peaks in H3K27 acetylation and H3K4 mono-methylation, and the lack of H3K4 tri-methylation. They have been found to play a role in oncogene transcription and tumour maintenance. Using ChIP-Seq, we profiled H3K27ac, H3K4me and H3K4me3 binding in CHP-134 neuroblastoma cells. We identified H3K27ac, H3K4me and H3K4me3 binding sites in the CHP-134 neuroblastoma cell line.

ORGANISM(S): Homo sapiens

PROVIDER: GSE113139 | GEO | 2019/06/23

REPOSITORIES: GEO

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H3K27ac, H3K4me and H3K4me3 binding examined by ChIP-seq in the CHP-134 neuroblastoma cell line

Project description:H3K27ac, H3K4me and H3K4me3 binding examined by ChIP-seq in the CHP-134 neuroblastoma cell line

| PRJNA450134 | ENA

Pol2 binding examined by ChIP-seq in inducible JMJD6 knockdown neuroblastoma cells

Project description:JMJD6 is an important oncogene that is upregulated in 17q21-ter gained neuroblastoma.It plays a role in E2F and N-Myc-regulated gene pathways and neuroblastoma tumorigenesis Using ChIP-Seq, We profiled RNA polymerase 2 binding in doxycycline inducible JMJD6 shRNA CHP-134 neuroblastoma cells, treated with either doxycycline or vehicle control. We identified a list of genes with reduced RNA Pol II binding peaks at their gene promoters as a result of the JMJD6 knockdown. GSEA analysis showed that the top four gene sets, with most considerable reduction in RNA Pol II binding peaks at gene promoters, were E2F target genes, G2M checkpoint genes, mitotic spindle genes, and Myc target genes.

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ChIP-seq of neuroblastoma IMR-32, CLB-GA, NGP, IMR-5/75, GI-M-EN, CHP-212, and IMR-5 cell lines to identify TBX2, MYCN, H3K27ac, H3K4me1 and H3K4me3 binding sites

Project description:ChIP-seq to define bindings sites for TBX2, MYCN, H3K27ac, H3K4me1, H3K4me3 and Input in the cell lines IMR-32, CLB-GA, NGP, IMR-5/75, GI-M-EN, CHP-212, and IMR-5.

2018-10-16 | E-MTAB-6570 | biostudies-arrayexpress

Direct Targeting of MYCN Gene Amplification by CRISPR/Cas9 in Neuroblastoma Cells (CHP-134)

Project description:Direct Targeting of MYCN Gene Amplification by CRISPR/Cas9 in Neuroblastoma Cells (CHP-134)

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Determinants of H3K4me pattern establishment

Project description:A hallmark of genes transcribed by RNA polymerase II (RNApII) is a "gradient" of histone H3 lysine 4 (H3K4) methylation. Various factors differentially bind to H3K4me3 near promoters, H3K4me2 just downstream, and H3K4me1 further downstream to modulate gene expression. Set1/COMPASS, the single S. cerevisiae H3K4 methyltransferase, binds transcribing RNApII, but COMPASS may also be allosterically regulated by specific subunits and histone H2B ubiquitylation. To ask whether differential H3K4 methylation is determined by regulated activity at specific gene locations or by the amount of time COMPASS spends near the nucleosome, ChIP-Seq analyses was performed in cells with altered transcription elongation rates or with Set1 fused to RNApII. Our results support a simple model where higher H3K4 methylations result from both increased duration and frequency of COMPASS proximity to the nucleosome.

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Direct Targeting of MYCN Gene Amplification by Alkylating Pyrrole-Imidazole Polyamide in Neuroblastoma Cells (CHP-134)

Project description:Direct Targeting of MYCN Gene Amplification by Alkylating Pyrrole-Imidazole Polyamide in Neuroblastoma Cells (CHP-134)

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Integrated genome, transcriptome and translatome profiling of neuroblastoma cells

Project description:Microarray-based genome-wide measurements of copy number alterations and of transcriptome variations are proposed for neuroblastoma prognosis and possible treatment choice. Nonetheless, they lack to provide clues on a neglected layer of systems-level changes, the translatome, whose variations are defined by the activity of the translational regulatory machinery. Our study extends the conventional genome-wide approaches to translatome profiling in neuroblastoma, by means of polysomal sucrose gradient separation followed by microarray analysis. The panel of fourteen parental (not subcloned) neuroblastoma cell lines used in the study includes: CHP-134, SIMA, NB-69, LAN-1, KELLY, CHP-126, CHP-212, SK-N-BE(2), IMR-32, SK-N-AS, SK-N-SH, STA-NB-7, STA-NB-1, STA-NB-10 cells. Each cell line has been profiled with high resolution array CGH analysis for copy number changes, and for transcriptome and translatome variations. The integration of these three types of data sets obtained from the same cells can provide information on the impact in neuroblastoma of a defined pattern of genomic lesions on both transcriptional and translational alterations of gene expression.

2010-12-31 | GSE22785 | GEO

Regulation of chromatin structure by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase [H3K4me ChIP-seq]

Project description:Regulation of chromatin structure by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase [H3K4me ChIP-seq]

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Genome-wide Analysis of Mono-, Di- and Trimethylation of Histone H3 Lysine 4 in Arabidopsis thaliana

Project description:Background. Post-translational modifications of histones play important roles in regulating transcription by modulating the structural properties of the chromatin. In plants, methylation of histone H3 lysine4 (H3K4me) is associated with genes and required for normal plant development. Results. We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two thirds of Arabidopsis genes contain at least one type of H3K4me in seedlings. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5’ genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, a genome-wide preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to exist in plants, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, the relationship between H3K4me and DNA methylation was explored by comparing the genome-wide distribution patterns of H3K4me1, H3K4me2 and H3K4me3 in wild type plants and the met1 DNA methyltransferase mutant. Conclusions. H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.

2009-02-01 | GSE13613 | GEO

Direct Targeting of MYCN Gene Amplification by Alkylating Pyrrole-Imidazole Polyamide and CRISPR/Cas9 in Neuroblastoma Cells (CHP-134)

Project description:Direct Targeting of MYCN Gene Amplification by Alkylating Pyrrole-Imidazole Polyamide and CRISPR/Cas9 in Neuroblastoma Cells (CHP-134)

| PRJNA497575 | ENA

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