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RNA-Seq in Jurkat treated with either PBIT or DMSO

ABSTRACT: To assess whether genes associated with BH4Ds are more or less sensitive than genes associated with sharp H3K4me3 peaks to perturbation of H3K4me3 levels, we performed RNA-Seq experiment from Jurkat cells treated with DMSO or with 2-(4-methylphenyl)-1,2-benzisothiazol-3(2H)-one (PBIT), a specific inhibitor of JARID1 family of H3K4me3 demethylases, also known as KDM5 (Blair et al. 2011; Sayegh et al. 2013).

ORGANISM(S): Homo sapiens

PROVIDER: GSE164185 | GEO | 2021/04/16

REPOSITORIES: GEO

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ChIP-Seq H3K4me3 in Jurkat treated with either OICR-9429, PBIT or DMSO

Project description:To assess whether BH4Ds are more or less sensitive than sharp H3K4me3 peaks to perturbation of H3K4me3 levels, we performed H3K4me3 ChIP-seq experiments from Jurkat cells treated with DMSO or with either 2-(4-methylphenyl)-1,2-benzisothiazol-3(2H)-one (PBIT), a specific inhibitor of JARID1 family of H3K4me3 demethylases, also known as KDM5, or OICR-9429, an inhibitor of the MLL-WDR5, previously shown to decrease cellular levels of H3K4me3.

2021-04-16 | GSE164184 | GEO

Chemical reprogramming of human fibroblasts

Project description:The compound (O4I3) showed a remarkable OCT4 induction, which at least in part, is due to the inhibition of H3K4-specific lysine demethylase (KDM5, also known as JARID1). Experiments demonstrated that KDM5A, serves as a reprogramming barrier via interference with the enrichment of H3K4Me3 at the OCT4 promoter. Thus, our results introduce a new class of KDM5 chemical inhibitors and provide further insight into the pluripotency-related properties of KDM5-family members.

2018-12-12 | GSE123668 | GEO

RNA-seq analysis after the treatment with DMSO or dTAG-13 in TAL1-FKBP12 Jurkat cells

Project description:RNA-seq analysis was performed in a TAL1-FKBP12 Jurkat cell line to analyze gene expression changes after dTAG-13 treatmentat at various time points (1h, 2h, 4h, 6h, 8h, 16h, 24h, 48h and 72h).

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Genome-wide maps of KDM5 binding in drosophila adults

Project description:To determine which genes affected by loss of KDM5 in adults were direct targets, we carried out KDM5 ChIP-seq analyses. To valide this data, we utilized a previously generated fly strain in which the sole source of KDM5 is from a transgene expressing an HA tagged form of KDM5 expressed under the control of its endogenous promoter. Comparing genome-wide gene expression and KDM5 binding analyses in Drosophila adults, we demonstrate the primary function of KDM5 in adults is to activate gene expression KDM5. To investigate the link between KDM5 and H3K4me3, we carried out anti-H3K4me3 ChIP-seq from wildtype adults . Genome-wide, KDM5 and H3K4me3 peaks showed a similar distribution, with both peaking at the transcription start site (TSS) showed a striking overlap with the presence of H3K4me3. Examination of KDM5 binding and histone H3K4me3 modifications in drosophila adults

2015-12-22 | E-GEOD-70589 | biostudies-arrayexpress

H3K4me3 ChIP in multiple myeloma MM1S cells in the presence and absence of KDM5-C70

Project description:In this experiment we demonstrate the use of an inhibitor of the KDM5 family of histone demethylases, KDM5-C70, on H3K4me3 marks in the multiple myeloma cell line MM1S. KDM5-C70 increases H3K4me3 in a global fashion across the genome. Examination of H3K4me3 mark across MM1S cells treated with either KDM5-C70 or vehicle control

2016-04-05 | E-GEOD-78206 | biostudies-arrayexpress

SeaIce, Espegrend, Microscosm, Mnemi

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Genome-wide maps of KDM5 binding in drosophila adults

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H3K4me3 ChIP in multiple myeloma MM1S cells in the presence and absence of KDM5-C70

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Dissecting the effect of a long linker DNA on protein binding to di-nucleosomes decorated with promoter-associated PTMs

Project description:Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from around 35-55 bp in most eu- and heterochromatin domains (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 bp in nucleosome-depleted regions (NDRs) found at active enhancers and promoters (Schones et al, 2008; Hansen He et al, 2010). To investigate whether and how the nucleosome linker DNA affects chromatin recognition by nuclear proteins we performed a set of affinity purifications using di-nucleosomes incorporating different DNA linkers. Here, we investigated the effect of a 200 bp di-nucleosome linker DNA represented by scrambled DNA or SV40 promoter DNA sequence on the nuclear protein binding to di-nucleosome decorated with promoter-associated modifications, including H3K4me3K9acK14acK18acK23acK27ac, H4K5acK8acK12acK16acK20me2 and histone variant H2A.Z Below is a description (modifications and linker) of di-nucleosomes used in pull-downs with HeLa nuclear extracts followed by label-free MS: 1. H3K4me3-5ac,H4K20me2-4ac, H2AZ, 50bp linker 2. H3K4me3-5ac,H4K20me2-4ac, H2AZ, 200bp scrambled DNA linker 3. H3K4me3-5ac,H4K20me2-4ac, H2AZ, 200bp SV40 promoter DNA linker 4. Unmod. H3&H4, 50bp linker 5. Unmod. H3&H4, 200bp scrambled DNA linker 6. Unmod. H3&H4, 200bp SV40 promoter DNA linker

2023-12-10 | PXD041835 | Pride

Project description:Finn Et al.

| PRJNA433383 | ENA

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