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

Yadollah Shahryary; Aikaterini Symeonidi; Rashmi R Hazarika; Johanna Denkena; Talha Mubeen; Brigitte Hofmeister; Thomas van Gurp; Maria Colomé-Tatché; Koen J F Verhoeven; Gerald Tuskan; Robert J Schmitz; Frank Johannes

doi:10.1186/s13059-020-02161-6

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

Genome Biol. 2020 Oct 6;21(1):260. doi: 10.1186/s13059-020-02161-6.

Authors

Yadollah Shahryary^{1

2}, Aikaterini Symeonidi¹, Rashmi R Hazarika^{1

2}, Johanna Denkena³, Talha Mubeen^{1

2}, Brigitte Hofmeister⁴, Thomas van Gurp⁵, Maria Colomé-Tatché^{3

6

7}, Koen J F Verhoeven⁵, Gerald Tuskan⁸, Robert J Schmitz^{9

10}, Frank Johannes^{11

12}

Affiliations

¹ Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354, Germany.
² Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748, Germany.
³ Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany.
⁴ Institute of Bioinformatics, 120 East Green Street, Athens, 30602, USA.
⁵ Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, Wageningen, The Netherlands.
⁶ European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, Groningen, 9713 AV, Netherlands.
⁷ TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Erlenmeyer-Forum 2, Freising, 85354, Germany.
⁸ The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, USA.
⁹ Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748, Germany. [email protected].
¹⁰ Department of Genetics, The University of Georgia, 120 East Green Street, Athens, 30602, USA. [email protected].
¹¹ Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354, Germany. [email protected].
¹² Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748, Germany. [email protected].

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.

Keywords: Bioinformatics software tool; DNA methylation; Epigenetic clock; Epigenetics; Epimutation; Epimutation rate; Evolution; Molecular clock; Plants; R/Bioconductor package; Trees.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Arabidopsis
DNA Methylation*
Epigenome*
Genome, Plant*
Genomics / methods*
Populus
Software*
Taraxacum