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DNA methylation entropy as a measure of stem cell replication and aging [BiSulfite-seq]

ABSTRACT: DNA methylation entropy as a measure of stem cell replication and aging [BiSulfite-seq]

PROVIDER: PRJNA882035 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21628000.fastq.gz	Fastqsanger.gz
	SRR21628100.fastq.gz	Fastqsanger.gz
	SRR21628001.fastq.gz	Fastqsanger.gz
	SRR21628101.fastq.gz	Fastqsanger.gz
	SRR21628002.fastq.gz	Fastqsanger.gz

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DNA methylation entropy as a measure of stem cell replication and aging

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Project description:The dynamic nature of epigenetic modifications has been leveraged to construct epigenetic clocks that accurately predict an individual’s age based on DNA methylation levels. Here we explore whether the accumulation of epimutations, which can be quantified by Shannon’s entropy, changes reproducibly with age. Using targeted bisulfite sequencing, we analyzed the associations between age, entropy, and methylation levels in human buccal swab samples. We find that epigenetic clocks based on the entropy of methylation states predict chronological age with similar accuracy as common approaches that are based on methylation levels of individual cytosines. Our approach suggests that across many genomic loci, methylation entropy changes reproducibly with age.

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DNA methylation entropy as a measure of stem cell replication and aging

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

2022-09-30 | GSE213723 | GEO

DNA methylation entropy as a measure of stem cell replication and aging.

Project description:BackgroundEpigenetic marks are encoded by DNA methylation and accumulate errors as organisms age. This drift correlates with lifespan, but the biology of how this occurs is still unexplained. We analyze DNA methylation with age in mouse intestinal stem cells and compare them to nonstem cells.ResultsAge-related changes in DNA methylation are identical in stem and nonstem cells, affect most prominently CpG islands and correlate weakly with gene expression. Age-related DNA methylation entropy, measured by the Jensen-Shannon Distribution, affects up to 25% of the detectable CpG sites and is a better measure of aging than individual CpG methylation. We analyze this entropy as a function of age in seven other tissues (heart, kidney, skeletal muscle, lung, liver, spleen, and blood) and it correlates strikingly with tissue-specific stem cell division rates. Thus, DNA methylation drift and increased entropy with age are primarily caused by and are sensors for, stem cell replication in adult tissues.ConclusionsThese data have implications for the mechanisms of tissue-specific functional declines with aging and for the development of DNA-methylation-based biological clocks.

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In vivo DNA replication dynamics unveil aging-dependent replication stress

Project description:In vivo DNA replication dynamics unveil aging-dependent replication stress

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