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Mus musculus

ABSTRACT: ChIP-seq analysis of PHF20 and Wdr5 binding sites in ESCs

PROVIDER: PRJNA185142 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR643442.fastq.gz	Fastqsanger.gz
	SRR643443.fastq.gz	Fastqsanger.gz
	SRR643444.fastq.gz	Fastqsanger.gz
	SRR643445.fastq.gz	Fastqsanger.gz
	SRR643446.fastq.gz	Fastqsanger.gz

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ChIP-seq analysis of PHF20 and Wdr5 binding sites in ESCs

Project description:Although reprogramming of somatic cells to generate inducible pluripotent stem cells (iPSCs) is associated with remarkable epigenetic changes, the role and mechanisms of epigenetic factors in this process remains poorly understood. Here we describe identification of Jmjd3 as a potent negative regulator of reprogramming. Jmjd3-deficient MEFs produced significantly more iPSC colonies than did wild-type cells, while ectopic expression of Jmjd3 markedly inhibited reprogramming. We further show that the inhibitory effects of Jmjd3 are produced through both histone demethylase-dependent and -independent pathways acting in concert. The latter pathway is entirely novel and involved Jmjd3 targeting of PHF20 for ubiquitination and degradation by recruiting an E3 ligase Trim26. Importantly, PHF20-deficient MEFs could not be converted to fully reprogrammed iPSCs, even with knockdown of Jmjd3, Ink4a or p21, indicating dominant effects of this protein on reprogramming. Our findings identify a previously unrecognized role of Jmjd3 in reprogramming and provide molecular insight into the mechanisms by which the Jmjd3-PHF20 axis controls the reprogramming process. This study was an examination of phf20 and wdr5 binding patterns in embryonic stem cells, using a ChIP-Sequencing methodology with antibodies for each of these factors in the cell lines indicated.

2013-12-06 | E-GEOD-43247 | biostudies-arrayexpress

The histone H3 lysine 4 presenter WDR5 induces N-Myc target gene transcription and promotes neuroblastoma [ChIP-Seq]

Project description:WDR5 is an important co-factor for N-Myc-regulated transcriptional activation and tumorigenesis Using ChIP-Seq, We profiled key epigenetic marks H3K4 trimethylation in BE(2)-C neuroblastoma cells transfected with control siRNA or WDR5 siRNA-1 at N-Myc target gene promoters The results showed knockdown WDR5 significantly reduced H3K4me3 at 93.2% of N-Myc binding promoters, but only at 53.5% of N-Myc non-binding promoters. Identification of Histone H3K4 trimethylation and N-Myc binding sites in BE(2)-C cells transfected with control siRNA or WDR5 siRNA-1.

2015-12-31 | E-GEOD-70098 | biostudies-arrayexpress

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Project description:ChIP-seq analysis of CTCF binding sites in lymphocyte subsets [DN thymocytes]

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Project description:ChIP-seq analysis of CTCF binding sites in lymphocyte subsets [DP thymocytes]

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Project description:ChIP-seq analysis of CTCF binding sites in lymphocyte subsets [pro-B cells]

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Project description:Genome-wide maps of Tbx3 binding sites in mouse ESCs

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Loss of PHF20 does not negatively affect deposition of H4K16 acetylation, but does impact the expression of MOF targets

Project description:Protein post-translational modifications transmit signals in part by creating binding sites for effector molecules. This is especially true in epigenetic pathways where histone tails are heavily modified, resulting in the recruitment of molecules that can affect transcription. One such molecule, plant homeodomain finger protein 20 (PHF20), uses a Tudor domain to read dimethyl-lysine residues and is a known component of the MOF histone acetyltransferase protein complex, suggesting it plays a role in the crosstalk between lysine methylation and histone acetylation. We sought to investigate the biological role of PHF20 by generating a knockout mouse. Without PHF20, mice die shortly after birth and display a wide variety of phenotypes within the skeletal and hematopoietic systems. Mechanistically, PHF20 is not required for maintaining the global H4K16 acetylation levels, but instead works downstream in transcriptional regulation of MOF target genes. ChIP sequencing of H4K16ace ChIP DNA from PHF20 knockout and wild type cells using Illumina Solexa Genome Analyzer II single end sequencing protocol.

2012-02-27 | E-GEOD-29306 | biostudies-arrayexpress

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Project description:Genome-wide ChIP-seq analysis of Nr4a1 binding sites in regulatory T (Treg) cells

| PRJNA288579 | ENA

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Project description:Genome-wide analysis of Nrdc-binding sites by ChIP-seq in mouse embryonic fibroblasts

| PRJNA354481 | ENA

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

| PRJNA234002 | ENA