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Shahryary, Y.* ; Symeonidi, A.* ; Hazarika, R.R.* ; Denkena, J. ; Mubeen, T.* ; Hofmeister, B.* ; Van Gurp, T.* ; Colomé-Tatché, M. ; Verhoeven, K.J.F.* ; Tuskan, G.* ; Schmitz, R.J.* ; Johannes, F.*

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

Genome Biol. 21:33023650 (2020)

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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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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Epimutation ; Dna Methylation ; Plants ; Trees ; Epigenetics ; Epimutation Rate ; Evolution ; Molecular Clock ; Epigenetic Clock ; Bioinformatics Software Tool ; R ; Bioconductor Package; Mutations; Patterns; Epigenome; Meiosis; Maps

ISSN (print) / ISBN 1474-760X

e-ISSN 1465-6906

Journal Genome Biology

Quellenangaben Volume: 21, Issue: 1, Article Number: 33023650

Publisher BioMed Central

Publishing Place Campus, 4 Crinan St, London N1 9xw, England

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Institute of Computational Biology (ICB)

Grants Projekt DEAL
Deutsche Forschungsgemeinschaft (DFG)
Pew Charitable Trusts
National Science Foundation
European Seventh Framework Programme
Technical University of Munich-Institute for Advanced Study - German Excellent Initiative