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Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8OE]

ABSTRACT: Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8OE]

PROVIDER: PRJNA1067611 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27682345_1.fastq.gz	Fastqsanger.gz
	SRR27682345_2.fastq.gz	Fastqsanger.gz
	SRR27682346_1.fastq.gz	Fastqsanger.gz
	SRR27682346_2.fastq.gz	Fastqsanger.gz
	SRR27682347_1.fastq.gz	Fastqsanger.gz

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Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8KO]

Project description:To identify target genes of the histone demethylase Phf8 in oligodendroglial cells in a genome-wide and unbiased approach, RNA-sequencing studies were performed on wildtype CG4 cells and CRISPR/Cas9-edited Phf8 knockout cell lines. We compared three wildtype and one CRISPR/Cas9-treated clone without genome editing with four CRISPR/Cas9 Phf8-knockout clones. Among others we detected substantial changes in the expression of genes associated with cell cycle and replication of DNA.

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Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8OE]

Project description:To identify target genes of the histone demethylase Phf8 in oligodendroglial cells in a genome-wide and unbiased approach, RNA-sequencing studies were performed on CG4 cells transduced with control or Phf8-overexpressing retroviruses. Transduced, GFP-expressing cells underwent fluorescence-activated cell-sorting, were expanded and then differentiated for three days. Two biological replicates were used for each condition. Gene expression analysis revealed an increase in oligodendrocyte progenitor proliferation and a general decrease in cell differentiation.

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Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8KO]

Project description:Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8KO]

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The histone demethylase PHF8 is essential for cytoskeleton dynamics

Project description:PHF8 is a histone demethylase associated with X-linked mental retardation (XLMR). It has been described as a transcriptional coactivator involved in cell cycle progression, but its physiological role is still poorly understood. Here we show that PHF8 controls the expression of genes involved in cell adhesion and cytoskeleton organization such as RhoA, Rac1 and GSK3M-NM-2. A lack of PHF8 not only results in a cell cycle delay but also in a disorganized actin cytoskeleton and impaired cell adhesion. Our data demonstrate that PHF8 directly regulates the expression of these genes by demethylating H4K20me1 at promoters. Moreover, c-Myc transcription factor interacts with PHF8 and binds to the analyzed promoters, suggesting that c-Myc is involved on PHF8 recruitment to these promoters. Further analysis in the neuroblastoma cell line SH-SY5Y and in cortical neurons shows that depletion of PHF8 results in deficient neurite elongation. Overall, our results suggest that the mental retardation phenotype associated with loss of function of PHF8 could be due to abnormal neuronal connections as a result of alterations in cytoskeleton function. HeLa cells were transfected with either control or PHF8 siRNAs. Experiments were performed in biological triplicates. RNA were extracted and sujected to microarray analysis.

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Genome-wide identification of target genes for the transcription factors Nkx2.2 and Zfp488 in differentiating CG4 cells as a model for differentiating oligodendrocytes

Project description:In an attempt to validate the CG4 cell line as a model for oligodendrocytes, we determined the expression profiles in both cell types and the alterations during differentiation and found a striking overlap. Using CG4 cells as a model system for oligodendroglial cells, we generated several Nkx2.2 and Zfp488 overexpressing CG4 lines and compared their expression profile under differentiating conditions to regular CG4 cells to identify target genes of the two transcription factors in a genome-wide and unbiased approach. Several target genes were shared between Nkx2.2 and Zfp488, among them Gpr37.

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The histone demethylase PHF8 is essential for cytoskeleton dynamics

Project description:PHF8 is a histone demethylase associated with X-linked mental retardation (XLMR). It has been described as a transcriptional coactivator involved in cell cycle progression, but its physiological role is still poorly understood. Here we show that PHF8 controls the expression of genes involved in cell adhesion and cytoskeleton organization such as RhoA, Rac1 and GSK3β. A lack of PHF8 not only results in a cell cycle delay but also in a disorganized actin cytoskeleton and impaired cell adhesion. Our data demonstrate that PHF8 directly regulates the expression of these genes by demethylating H4K20me1 at promoters. Moreover, c-Myc transcription factor interacts with PHF8 and binds to the analyzed promoters, suggesting that c-Myc is involved on PHF8 recruitment to these promoters. Further analysis in the neuroblastoma cell line SH-SY5Y and in cortical neurons shows that depletion of PHF8 results in deficient neurite elongation. Overall, our results suggest that the mental retardation phenotype associated with loss of function of PHF8 could be due to abnormal neuronal connections as a result of alterations in cytoskeleton function.

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The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis [ChIP-seq]

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Project description:To identify the downstream targets of transcription factor Ascl1, transcriptional profiling of rat glial cell line, CG4 cell, transfected with either Ascl1 or mock control was performed. Comparison was performed between Ascl1 overexpressing CG4 cell and mock control transduced cell on 3D-Gene rat mRNA oligo 12k chip. Biological replication was not prepared. The results were confirmed by real time RT-PCR in several genes.

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