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Genome-wide mapping of 5-hydroxymethylcytosine enrichment in a novel model of 'NAFLD in a Dish'

ABSTRACT: Genome-wide mapping of 5-hydroxymethylcytosine enrichment in a novel model of 'NAFLD in a Dish'

PROVIDER: PRJNA605438 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11041038.fastq.gz	Fastqsanger.gz
	SRR11041039.fastq.gz	Fastqsanger.gz
	SRR11041040.fastq.gz	Fastqsanger.gz
	SRR11041041.fastq.gz	Fastqsanger.gz
	SRR11041042.fastq.gz	Fastqsanger.gz

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Genome-wide mapping of 5-hydroxymethylcytosine enrichment in a novel model of 'NAFLD in a Dish'

Project description:Human pluriopotent H9 cells were differentiated to hepatocyte-like cells and exposed to a cocktail of lactate, pyruvate and octanoic acid (LPO) for 48 hours. This stimulated development of macrovesicular steatosis, which has previously been reported to impact on mitochondrial metabolism. Under our experimental conditions, we identified rewiring of the TCA cycle linked to macrovesicular steatosis. As key TCA cycle metabolites, alpha-ketoglutarate, succinate and fumarate impact on ten-eleven translocation (TET) enzyme activity, we hypothesised that this rewiring would impact on levels of 5-hydroxymethylcytosine (5hmC) enrichment across the genome. To this end, we performed DNA immunoprecipitation sequencing (DIPseq) to map any changes that occurred. Using IonTorrent, we sequenced our samples and generated bam files aligned to Homo sapiens Hg19. We used the MACS2 pipeline to compare our control and steatosis group, and identified a large number of changes in 5hmC enrichment in response to LPO exposure, indicating that TCA cycle wiring may impact on TET activity.

2020-12-03 | GSE144955 | GEO

mRNA sequencing analysis of a novel model of 'NAFLD in a Dish'

Project description:mRNA sequencing analysis of a novel model of 'NAFLD in a Dish'

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mRNA sequencing analysis of a novel model of 'NAFLD in a Dish'

Project description:The goal of this study was to determine the changes to cellular transcriptional programs following induction of intracellular lipid accumulation, with the aim of confirming the utility of this model for exploring mechanisms underlying the pathogenesis of NAFLD. Comparisons with other publically available data confirm that the alterations we observe in mRNA expression are similar to those observed in both humans and rodents.

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PRDM9 activity depends on HELLS and promotes 5-Hydroxymethylcytosine enrichment

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Project description:In this project, the gene expression profiles of commonly used murine models of NAFLD were compared to two publically available human datasets to assess proximity to human pathophysiology, focusing on differential expression and pathway enrichment. CCL4 was used as a positive control for fibrosis.

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Selective chemical labeling reveals intragenic enrichment of 5-hydroxymethylcytosine in mouse cerebellum

Project description:5-Methylcytosine (5-mC) is an important DNA modification found in eukaryotes that impacts gene regulation and disease pathogenesis. Recently, 5-hydroxymethylcytosine (5-hmC), another form of DNA modification, has been identified in substantial amounts in certain mammalian cell types; however, its roles as well as its distribution in mammalian genomes are unknown. Here we present a selective chemical labeling method for 5-hmC by utilizing T4 bacteriophage BGT-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC, which in turn can chemically incorporate a biotin group for detection, affinity enrichment, and sequencing of 5-hmC in mammalian genomes. Using this highly effective method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized. We also find a gene expression level-dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders Identification of 5hmC enriched genmoic regions in mouse cerebellum

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Environmental enrichment modulates 5-hydroxymethylcytosine dynamics in hippocampus

Project description:Gene-environment interactions mediated at the epigenetic level may provide an initial step in delivering an appropriate response to environmental changes. 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC), accounts for ~40% of modified cytosine in brain and has been implicated in DNA methylation-related plasticity. To identify the role of 5hmC in gene-environment interactions, we exposed both young (6-week-old) and aged (18-month-old) mice to both an enriched environment and a standard environment. Exposure to EE significantly improves learning and memory in aged mice and reduces 5hmC abundance in mouse hippocampus. Furthermore, we mapped the genome-wide distribution of 5hmC and found that the alteration of 5hmC modification occurred mainly at gene bodies. In particular, genes involved in axon guidance are enriched among the genes with altered 5hmC modification. These results together suggest that environmental enrichment could modulate the dynamics of 5hmC in hippocampus, which could potentially contribute to improved learning and memory in aged animals.

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2014-01-03 | E-GEOD-53381 | biostudies-arrayexpress

Selective chemical labeling reveals intragenic enrichment of 5-hydroxymethylcytosine in mouse cerebellum

2010-12-12 | GSE25398 | GEO