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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq MEFs)

ABSTRACT: We have mapped binding sites for the histone demethylase, Jmjd2c/Kdm4c/Gasc1, in mouse embryonic fibroblasts (MEFs) and the impact of Jmjd2c depletion on H3K9me3 and H3K36me3 distributions. ChIP-seq was performed using antibodies recognizing Jmjd2c, H3K9me3 or H3K36me3. Chromatin was obtained from conditional Jmjd2c knockout MEFs cultured in the absence or presence of OHT to induce activation of Cre recombinase and loss of Jmjd2c expression.

ORGANISM(S): Mus musculus

SUBMITTER: Marianne Pedersen

PROVIDER: E-GEOD-53939 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The demethylase JMJD2C localizes to H3K4me3-positive transcription start sites and is dispensable for embryonic development.

Pedersen Marianne Terndrup MT Agger Karl K Laugesen Anne A Johansen Jens V JV Cloos Paul A C PA Christensen Jesper J Helin Kristian K

Molecular and cellular biology 20140106 6

The histone demethylase JMJD2C, also known as KDM4C/GASC1, has activity against methylated H3K9 and H3K36 and is amplified and/or overexpressed in human cancers. By the generation of Jmjd2c knockout mice, we demonstrate that loss of Jmjd2c is compatible with cellular proliferation, embryonic stem cell (ESC) self-renewal, and embryonic development. Moreover, we report that JMJD2C localizes to H3K4me3-positive transcription start sites in both primary cells and in the human carcinoma KYSE150 cell ...[more]

PMID: 24396064

Similar Datasets

The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq KYSE150 cell line)

Project description:We have mapped binding sites for the histone demethylase, JMJD2C/KDM4C/GASC1, and the effect of JMJD2C depletion on H3K9me3 and H3K36me3 distributions in KYSE150 cells. The human esophageal carcinoma cell line, KYSE150, contains an amplification of the JMJD2C locus. ChIP-seq was performed using chromatin from control or JMJD2C-depleted KYSE150 cells and antibodies recognizing JMJD2C, H3K4me3, H3K9me3 or H3K36me3.

2014-01-09 | E-GEOD-53938 | biostudies-arrayexpress

The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq ESCs)

Project description:We have mapped binding sites for the histone demethylase, Jmjd2c/Kdm4c/Gasc1, in mouse embryonic stem cells (ESCs). ChIP-seq was performed using an antibody recognizing Jmjd2c. Chromatin was obtained from conditional Jmjd2c knockout ESCs cultured in the absence or presence of OHT to induce activation of Cre recombinase and loss of Jmjd2c expression.

2014-01-09 | E-GEOD-53936 | biostudies-arrayexpress

The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq MEFs)

Project description:We have mapped binding sites for the histone demethylase, Jmjd2c/Kdm4c/Gasc1, in mouse embryonic fibroblasts (MEFs) and the impact of Jmjd2c depletion on H3K9me3 and H3K36me3 distributions.

2014-01-09 | GSE53939 | GEO

The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq KYSE150 cell line)

2014-01-09 | GSE53938 | GEO

Jmjd2a and Jmjd2c regulate H3K9me3 and H3K36me3 at H3K4me3 positive transcription start sites being essential for ESC self-renewal and embryogenesis (ChIP-Seq)

Project description:We have characterized the role of the Jmjd2/Kdm4 proteins in embryonic stem cell (ESC) biology, histone methylation and gene regulation. The Jmjd2 proteins are H3K9/H3K36 histone demethylases and three Jmjd2 family members are expressed in ESCs: Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c/Gasc1. We find that specifically Jmjd2a and Jmjd2c exert redundant functions, which are essential for ESC self-renewal and early embryonic development. ChIP-seq studies show that Jmjd2a and Jmjd2c both localize to H3K4me3 marked regions, where they have general and widespread roles preventing the accumulation of especially H3K9me3, but also H3K36me3. Jmjd2 catalytic activity is required for ESC maintenance, and increased H3K9me3 levels in knockout ESCs compromise the expression of several Jmjd2a/c targets, including genes that are important for ESC self-renewal. Thus, continual removal of H3K9 promoter methylation by Jmjd2 demethylases represents a novel mechanism ensuring transcriptional competence and stability of the pluripotent cell identity.

2016-05-09 | GSE64252 | GEO

Jmjd2a and Jmjd2c regulate H3K9me3 and H3K36me3 at H3K4me3 positive TSSs being essential for ESC self-renewal and embryogenesis (microarray)

2016-05-09 | GSE64251 | GEO

Cooperative Epigenetic Modulation by Cancer Amplicon Genes

Project description:Amplification of a ~2.5 megabase region on chromosome 9p24 is frequent in both primary mediastinal B-cell lymphoma (PMBL) and Hodgkin's lymphoma (HL). To identify the oncogenic genes in this interval, we created a RNA interference library targeting amplicon genes. A genetic screen using this library identified three genes that are essential for the proliferation and survival of PMBL and HL lines with this amplicon, which encode the kinase JAK2, the histone demethylase JMJD2C and a gene of unknown function, RANBP6. Inhibition of JAK2 and JMJD2C cooperated in killing these lymphomas and in remodeling their chromatin by globally increasing trimethylation of lysine 9 on histone H3 (H3K9me3) and heterochromatin formation. JAK2 and JMJD2C inhibition silenced MYC and its target genes, which coincided with an increase in H3K9me3 and the heterochromatin protein HP1alpha at the MYC locus. We conclude that amplification of JAK2 and JMJD2C cooperatively reprograms the PMBL and HL epigenome, sustaining their survival and proliferation. Signal from untreated shRNA cells or DMSO control cells (Cy3) was compared to 4 dox-treated JAK2 shRNA cells, 4 dox-treated JMJD2C shRNA cells, or 8 JAK2 inhibitor-treated cells (Cy5).

2011-01-04 | E-GEOD-20988 | biostudies-arrayexpress

Cooperative Epigenetic Modulation by Cancer Amplicon Genes

2011-01-04 | GSE20988 | GEO

Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription

Project description:This SuperSeries is composed of the following subset Series: GSE26018: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st] GSE26019: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuGene-1_0-st] GSE26038: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st, transcript] GSE26040: Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks Refer to individual Series

2011-03-31 | E-GEOD-26020 | biostudies-arrayexpress

Mus musculus

Project description:Jmjd2a and Jmjd2c regulate H3K9me3 and H3K36me3 at H3K4me3 positive TSSs being essential for ESC self-renewal and embryogenesis (microarray)

| PRJNA320657 | ENA

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