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ChIP-seq analysis of H3K4me1 and H3K27ac in TFAM-depleted HepG2 cells

ABSTRACT: ChIP-seq analysis of H3K4me1 and H3K27ac in TFAM-depleted HepG2 cells

PROVIDER: PRJNA809415 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18105003.fastq.gz	Fastqsanger.gz
	SRR18105004.fastq.gz	Fastqsanger.gz
	SRR18105005.fastq.gz	Fastqsanger.gz
	SRR18105006.fastq.gz	Fastqsanger.gz
	SRR18105007.fastq.gz	Fastqsanger.gz

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ChIP-seq analysis of H3K4me1 and H3K27ac in TFAM-depleted HepG2 cells

Project description:ChIP-seq analyses were used to examine the effect of TFAM inhibition on mono-methylated H3K4 (H3K4me1) and acetylated H3K27 (H3K27ac), which are histone marks characteristic of enhancer activity. Our study revealed that c-JUN-mediated enhancer activation shapes the mitochondrial stress-associated secretory phenotype.

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Transcriptome analysis of TFAM-depleted HepG2 cells and HeLa cells

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Project description:Transcriptome analysis of LSD2-depleted HepG2 cells revealed that many of the target genes were related to lipid metabolism. We found that LSD2 is an important epigenetic regulator of hepatic lipid metabolism. We depleted LSD2 in HepG2 human hepatic cells using three different siRNAs, and then carried out an expression microarray experiment.

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Role of H3K4me1 and H3K27ac histone marks in aging Drosophila

Project description:Temporal and spatial gene expression patterns are regulated by enhancer-specific histone modifications H3K4me1 and H3K27ac. To better understand age-dependent alteration of these enhancer marks, we analysed their genome-wide profiles and compared against changes in gene expression in the head tissues harvested from young Day 10 and D50 male Drosophila. The genome-wide binding patterns of H3K4me1 and H3K27ac remain highly similar (>85%) during ageing with marginally higher signals for both marks in older Day 50 flies. Signals were significantly higher in Day 50 flies near the transcription start sites for H3K4me1 whereas for H3K27ac, signals were significantly higher in Day 50 flies globally. Interestingly, analysis using MACS bdgdiff identified “x” H3K4me1 and “y” H3K27ac differential peaks that correlated with distinct sets of age-dependent differential expressed genes (DEG). Most of the H3K4me1 differential peaks (percentage of x) are located within the gene body of DEGs that are associated with RNA and metabolic processes. On the other hand, majority of differential H3K27ac peaks (percentage of y) are located 5 kb upstream of TSS of DEG enriched for various immune responses. Our results suggest that while both enhancer marks do not undergo significant global reconfiguration during aging, they are likely to be involved in activating independent sets of genes through distinct transcription activators.

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