Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nonlinear DNA methylation trajectories in aging mice [RRBS]

ABSTRACT: Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigated the methylation trajectories in DNA from 82 male mouse (C57BL/6J/Ukj) colons at five different time points (3, 9, 15, 24, 28 months). Our study indicates the existence of linear and nonlinear DNA methylation changes during aging. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 mo) and mid-to-late-life (15-24 mo) transitions, separating the rodents' life into three major stages. The results were validated with samples from an independent mouse cohort of 20 male C57BL6/J mice at four different ages (3, 7, 12, 27 months).

ORGANISM(S): Mus musculus

PROVIDER: GSE233734 | GEO | 2023/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Nonlinear DNA methylation trajectories in aging male mice [RNA-seq]

Project description:Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.

2024-01-15 | GSE248002 | GEO

Nonlinear DNA methylation trajectories in aging mice [RRBS]

Project description:Nonlinear DNA methylation trajectories in aging mice [RRBS]

| PRJNA977677 | ENA

Nonlinear DNA methylation trajectories in aging male mice [RNA-seq]

Project description:Nonlinear DNA methylation trajectories in aging male mice [RNA-seq]

| PRJNA1041390 | ENA

X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription

Project description:Dosage compensation in mammals occurs at two levels. In addition to balancing X-chromosome dosage between males and females via X-inactivation, mammals also balance dosage of Xs and autosomes. It has been proposed that X-autosome equalization occurs by upregulation of Xa (active X). To investigate the mechanism, we perform allele-specific ChIP-seq for chromatin epitopes and analyze RNA-seq data (SRA010053). The hypertranscribed Xa demonstrates enrichment of active chromatin marks relative to autosomes. We derive predictive models for relationships among Pol II, active mark densities and gene expression, and we suggest that Xa upregulation involves increased transcription initiation and elongation. Enrichment of active marks on Xa does not scale proportionally with transcription output, a disparity explained by nonlinear quantitative dependencies among active histone marks, Pol II occupancy and transcription. Notably, the trend of nonlinear upregulation also occurs on autosomes. Thus, Xa upregulation involves combined increases of active histone marks and Pol II occupancy, without invoking X-specific dependencies between chromatin states and transcription. Examination of 4 marks of active transcription (H3K4me3, H3K36me3, POL-II-S2P, POL-II-S5P) in a transformed female mouse embryonic fibroblast cell line (EY.T4).

2012-01-06 | E-GEOD-33823 | biostudies-arrayexpress

Nonlinear control of transcription through promoter-enhancer interactions

Project description:Nonlinear control of transcription through promoter-enhancer interactions

| PRJNA722525 | ENA

X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription

2012-01-06 | GSE33823 | GEO

Interspecies commensal interactions have nonlinear impacts on host immunity

Project description:Interspecies commensal interactions have nonlinear impacts on host immunity

| PRJNA742544 | ENA

Nonlinear control of transcription through promoter-enhancer interactions [Nanopore]

Project description:Nonlinear control of transcription through promoter-enhancer interactions [Nanopore]

| PRJNA722529 | ENA