ArticleGenome biology2020
AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 49 citations in OpenAlex.
- Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance.Nature plants · 2026Article
- Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus.bioRxiv : the preprint server for biology · 2026Article
- Branching architecture limits the number of fixed somatic mutations in trees.G3 (Bethesda, Md.) · 2025Article
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Accelerated growth increases the somatic epimutation rate in trees.Nature communications · 2025Article
- Somatic Evolution of Stem Cell Mutations in Long-Lived Plants.Molecular biology and evolution · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Article
- Transgenerational increases in DNA methylation in Arabidopsis plants defective in active DNA demethylation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza.G3 (Bethesda, Md.) · 2024Article
- An evolutionary epigenetic clock in plants.bioRxiv : the preprint server for biology · 2023Article
- Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda).Molecular ecology resources · 2023Article
- Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits.Biochemical Society transactions · 2022Article
- Molecular properties of epimutation hotspots.Nature plants · 2022Article
- Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet.NAR genomics and bioinformatics · 2021Article
- Heterochromatin is a quantitative trait associated with spontaneous epiallele formation.Nature communications · 2021Article
- Epimutations Define a Fast-Ticking Molecular Clock in Plants.Trends in genetics : TIG · 2021Review
- Evolutionary and functional genomics of DNA methylation in maize domestication and improvement.Nature communications · 2020Article
Corrections and comments
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Authors and funding
12 authors at 7 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be employed to study transgenerationally heritable epimutations in clonal or sexually derived mutation accumulation lines, as well as somatic epimutations in long-lived perennials. Application of our method to published and new data reveals that spontaneous epimutations accumulate neutrally at the genome-wide scale, originate mainly during somatic development and that they can be used as a molecular clock for age-dating trees.
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