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

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^* (Corresponding author), Frank Johannes (Corresponding author)

^*Corresponding author for this work

NIOO - Terrestrial Ecology (TE)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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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.

Original language	English
Article number	260
Journal	Genome Biology
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s13059-020-02161-6
Publication status	Published - 06 Oct 2020

Keywords

Bioinformatics software tool
DNA methylation
Epigenetic clock
Epigenetics
Epimutation
Epimutation rate
Evolution
Molecular clock
Plants
R/Bioconductor package
Trees
international
Plan_S-Compliant_OA

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10.1186/s13059-020-02161-6

7113_ShahryaryFinal published version, 1.73 MBLicence: CC BY

Taraxacum officinale cultivar:A34, H72
Shahryary, Y. (Creator), Symeonidi, A. (Creator), Hazarika, R. R. (Creator), Denkena, J. (Creator), Mubeen, T. (Creator), Hofmeister, B. (Creator), Van Gurp, T. (Creator), Colomé-Tatché, M. (Creator), Verhoeven, K. (Creator), Tuskan, E. (Creator), Schmitz, R. J. (Creator) & Johannes, F. (Creator), NCBI, 24 Feb 2020
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA608438
Dataset

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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. (2020). AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biology, 21(1), Article 260. https://doi.org/10.1186/s13059-020-02161-6

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

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, international, Plan_S-Compliant_OA",

author = "Yadollah Shahryary and Aikaterini Symeonidi and Hazarika, {Rashmi R.} and Johanna Denkena and Talha Mubeen and Brigitte Hofmeister and {Van Gurp}, Thomas and Maria Colom{\'e}-Tatch{\'e} and Verhoeven, {Koen J.F.} and Gerald Tuskan and Schmitz, {Robert J.} and Frank Johannes",

note = "7113, TE; Data archiving: data archived in NCBI (PRJNA608438), software in GitHub (not NIOO software)",

year = "2020",

month = oct,

day = "6",

doi = "10.1186/s13059-020-02161-6",

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Shahryary, Y, Symeonidi, A, Hazarika, RR, Denkena, J, Mubeen, T, Hofmeister, B, Van Gurp, T, Colomé-Tatché, M, Verhoeven, KJF, Tuskan, G, Schmitz, RJ & Johannes, F 2020, 'AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants', Genome Biology, vol. 21, no. 1, 260. https://doi.org/10.1186/s13059-020-02161-6

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T2 - Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

AU - Shahryary, Yadollah

AU - Symeonidi, Aikaterini

AU - Hazarika, Rashmi R.

AU - Denkena, Johanna

AU - Mubeen, Talha

AU - Hofmeister, Brigitte

AU - Van Gurp, Thomas

AU - Colomé-Tatché, Maria

AU - Verhoeven, Koen J.F.

AU - Tuskan, Gerald

AU - Schmitz, Robert J.

AU - Johannes, Frank

N1 - 7113, TE; Data archiving: data archived in NCBI (PRJNA608438), software in GitHub (not NIOO software)

PY - 2020/10/6

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N2 - 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.

AB - 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.

KW - Bioinformatics software tool

KW - DNA methylation

KW - Epigenetic clock

KW - Epigenetics

KW - Epimutation

KW - Epimutation rate

KW - Evolution

KW - Molecular clock

KW - Plants

KW - R/Bioconductor package

KW - Trees

KW - international

KW - Plan_S-Compliant_OA

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DO - 10.1186/s13059-020-02161-6

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AN - SCOPUS:85092414939

SN - 1474-7596

VL - 21

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 260

ER -

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

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Taraxacum officinale cultivar:A34, H72

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