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AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

ABSTRACT: AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

PROVIDER: PRJNA641352 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12075109.fastq.gz	Fastqsanger.gz
	SRR12075110.fastq.gz	Fastqsanger.gz
	SRR12075111.fastq.gz	Fastqsanger.gz
	SRR12075112.fastq.gz	Fastqsanger.gz
	SRR12075113.fastq.gz	Fastqsanger.gz

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Similar Datasets

AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Project description:Heritable changes in cytosine methylation can arise stochastically in plant genomes independently of DNA sequence alterations. These so-called ‘spontaneous epimutations’ appear to be abyproduct of imperfect DNA methylation maintenance during mitotic or meitotic cell divisions. Accurate estimates of the rate and spectrum of these stochastic events are necessary to be able to quantify how epimutational processes shape methylome diversity in the context of plant evolution, development and aging.

2020-08-21 | GSE153055 | GEO

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.

Project description: Not available

| S-EPMC7539454 | biostudies-literature

Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance [WGBS]

Project description:Spontaneous epimutations—stochastic changes in cytosine methylation—can persist across generations in plants and are thought to contribute to phenotypic variation. Although epimutations are increasingly studied for their potential long-term effects, it remains unclear why their accumulation varies across genotypes. Here, we tracked DNA methylation across nine generations in ~400 mutation accumulation lineages derived from ~70 Arabidopsis Ler × Cvi recombinant inbred lines. Treating epimutation rates as quantitative molecular traits, we mapped a major QTL to a Cvi-derived deletion near VIM2 and VIM4, two genes involved in CG methylation (mCG) maintenance. We show that this deletion rapidly reduces genome-wide methylation to a lower steady-state and compromises mCG maintenance fidelity across generations, resulting in a ~1.5-fold increase in epimutation rates. Genotypes with elevated rates exhibited accelerated epigenetic drift and phenotypic divergence. Our findings support a punctuated-equilibrium model of mCG evolution, in which sudden disruptions to methylation homeostasis can destabilize epigenetic inheritance over longer time-scales.

2026-07-18 | GSE296957 | GEO

Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance [ATAC-seq]

2026-07-18 | GSE297077 | GEO

Molecular properties of epimutation hotspots

Project description:Mistakes in the maintenance of CG methylation is a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harboring localized “epimutation hotspots”. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states (CS) that map to sub-regions of gene body methylation genes. Although these regions comprise only ~12% of all CGs in the genome, they account for ~63% of all epimutation events per unit time. Molecular profiling revealed that these regions contain unique sequence features, harbor steady-state intermediate methylation levels, and act as putative targets of antagonistic DNA methylation pathways. We further demonstrate that experimentally-induced shifts in steady-state methylation in these hotspot regions are sufficient to significantly alter local epimutation intensities. Our work thus lays foundation for dissecting the molecular mechanisms of epimutation hotspots in plants.

2021-12-02 | GSE178684 | GEO

Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance

Project description:Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance

| PRJNA1262718 | ENA

Molecular properties of epimutation hotspots

Project description:Molecular properties of epimutation hotspots

| PRJNA740019 | ENA

Blood cells genome-wide methylation profiles of BRCA1 mutation and epimutation carries, women with neither BRCA1 mutation nor epimutation prior BC diagnosis and healthy women with neither BRCA1 mutation nor epimutation (Controls)

Project description:Genome-wide DNA methylation patterns were quantified in peripheral blood samples collected from 112 individuals (with determined BRCA1 mutation and epimutation status) using the Illumina Infinium HumanMethylationEPIC BeadChip

2025-11-27 | GSE272644 | GEO

Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance [WGBS]

Project description:Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance [WGBS]

| PRJNA1262514 | ENA

Dietary folate and cofactors accelerate age-dependent p16 epimutation to promote intestinal tumorigenesis

Project description:We use a mouse model of age-dependent p16 epimutation, in which the p16 gene activity is directly controlled by promoter DNA methylation. We show p16 epimutation is modulated by folate and cofactors in dietary supplementation, which leads to increased colon cancer risk. Importantly, our findings provide functional evidence concerning the safety of folate fortification in the general population.

2024-08-19 | GSE243762 | GEO

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