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Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development [RRBS]

ABSTRACT: Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development [RRBS]

PROVIDER: PRJNA545107 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9136290.fastq.gz	Fastqsanger.gz
	SRR9136300.fastq.gz	Fastqsanger.gz
	SRR9136310.fastq.gz	Fastqsanger.gz
	SRR9136291.fastq.gz	Fastqsanger.gz
	SRR9136301.fastq.gz	Fastqsanger.gz

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Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development [RRBS]

Project description:Aim: Innate circadian rhythms are critical for optimal tissue-specific functions, including skeletal muscle, a major insulin-sensitive tissue responsible for glucose homeostasis. We determined whether transcriptional oscillations are associated with CpG methylation changes in skeletal muscle. Materials & methods: We performed rhythmicity analysis on the transcriptome and CpG methylome of circadian synchronized myotubes. Results: We identified several transcripts and CpG-sites displaying oscillatory behavior, which were enriched with GO terms related to metabolism and development. Oscillating CpG methylation was associated with rhythmic expression of 31 transcripts. Conclusion: Although circadian oscillations may be regulated by rhythmic DNA methylation, strong rhythmic associations between transcriptome and CpG methylation were not identified. This resource constitutes a transcriptomic/epigenomic atlas of skeletal muscle and regulation of circadian rhythms.

2020-03-11 | GSE131843 | GEO

Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development [RNA-Seq]

2020-03-11 | GSE131842 | GEO

Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development

Project description:Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development

| PRJNA545105 | ENA

Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development [RNA-Seq]

Project description:Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development [RNA-Seq]

| PRJNA545108 | ENA

Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-03-11 | GSE131844 | GEO

RRBS Profiling of Clonal Cell Lines with Different Circadian Period

Project description:Composed of negative feedback loops, circadian oscillations are thought to be noise-resistant. Yet, individual cells in culture are remarkably heterogenous, oscillating independently and with different period lengths. To assess whether differential methylation contributes to heritable heterogeneity of circadian periods, we used reduced representation bisulfite sequencing (RRBS) to explore DNA methylation profiles and their correlation with the transcriptome in the 10 clonal cell lines. To investigate the mechanisms underlying this heterogeneity, we generated and characterized hundreds of clonal cell lines from the same parent culture. By comparing clonal lines with different circadian periods, we identified a group of differentially methylated regions (DMRs).

2020-06-09 | GSE132665 | GEO

RRBS Profiling of Clonal Cell Lines with Different Circadian Period

Project description:RRBS Profiling of Clonal Cell Lines with Different Circadian Period

| PRJNA548678 | ENA

Glucocorticoid receptor (GR) target genes in C2C12 myotubes

Project description:Analysis of C2C12 myotubes treated with dexamethasone (Dex) for 6 or 24 hours. Dex is a synthetic glucorticoid receptor agonist. Results provide insight to the effect of glucocorticoids on myotubes.

2011-04-25 | GSE28840 | GEO

Saturated Fat Impairs Circadian Transcriptomics through Histone Modification of Enhancers

Project description:Aims/hypothesis: Obesity and elevated circulating lipids may impair metabolism by disrupting the molecular circadian clock. We tested the hypothesis that lipid-overload may interact with the circadian clock and alter the rhythmicity of gene expression through epigenetic mechanisms. Methods: We determined the effect of the saturated fatty acid palmitate on circadian transcriptomics and examined the impact on histone H3 lysine K27 acetylation (H3K27ac) and the regulation of circadian rhythms in primary human skeletal muscle myotubes. Total H3 abundance and histone H3K27ac was assessed in vastus lateralis muscle biopsies from men with either obesity or normal weight. Results: Palmitate reprogrammed the circadian transcriptome in myotubes without altering the mRNA rhythm of core clock genes. Genes with enhanced cycling in response to palmitate were associated with post-translational modification of histones. Cycling of histone 3 lysine 27 acetylation (H3K27ac), a marker of active gene enhancers, was modified by palmitate treatment in myotubes. Chromatin immunoprecipitation and sequencing confirmed that palmitate altered the cycling of DNA regions associated with H3K27ac. Overlap of mRNA and DNA regions associated with H3K27ac and pharmacological inhibition of histone acetyl transferases revealed novel cycling genes associated to lipid exposure in human myotubes. Conclusion/interpretation: Palmitate disrupts transcriptomic rhythmicity and modifies histone H3K27ac in circadian manner, suggesting acute lipid-overload alters the circadian chromatin landscape and reprograms circadian gene expression of skeletal muscle.

2022-09-27 | GSE205677 | GEO

Saturated Fat Impairs Circadian Transcriptomics through Histone Modification of Enhancers

2022-09-27 | GSE205424 | GEO