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

被引：26

作者：

Shahryary, Yadollah ^{[1
,2
]}

Symeonidi, Aikaterini ^{[1
]}

Hazarika, Rashmi R. ^{[1
,2
]}

Denkena, Johanna ^{[3
]}

Mubeen, Talha ^{[1
,2
]}

Hofmeister, Brigitte ^{[4
]}

van Gurp, Thomas ^{[7
]}

Colome-Tatch, Maria ^{[3
,5
,6
]}

Verhoeven, Koen J. F. ^{[7
]}

Tuskan, Gerald ^{[8
]}

Schmitz, Robert J. ^{[2
,9
]}

Johannes, Frank ^{[1
,2
]}

机构：

[1] Tech Univ Munich, Dept Plant Sci, Liesel Beckmann Str 2, D-85354 Freising Weihenstephan, Germany

[2] Tech Univ Munich, Inst Adv Study, Lichtenbergstr 2a, D-85748 Garching, Germany

[3] Helmholtz Zentrum Munchen, Inst Computat Biol, Ingolstadter Landstr 1, D-85764 Neuherberg, Germany

[4] Inst Bioinformat, 120 East Green St, Athens, GA 30602 USA

[5] Univ Groningen, Univ Med Ctr Groningen, European Res Inst Biol Ageing, A Deusinglaan 1, NL-9713 AV Groningen, Netherlands

[6] Tech Univ Munich, TUM Sch Life Sci Weihenstephan, Emil Erlenmeyer Forum 2, D-85354 Freising Weihenstephan, Germany

[7] Netherlands Inst Ecol N100 KNAW, Dept Terr Ecol, Wageningen, Netherlands

[8] Oak Ridge Natl Lab, Ctr Bioenergy Innovat, Oak Ridge, TN USA

[9] Univ Georgia, Dept Genet, 120 East Green St, Athens, GA 30602 USA

来源：

GENOME BIOLOGY | 2020年 / 21卷 / 01期

基金：

美国国家科学基金会;

关键词：

Epimutation; DNA methylation; Plants; Trees; Epigenetics; Epimutation rate; Evolution; Molecular clock; Epigenetic clock; Bioinformatics software tool; R; Bioconductor package; MUTATIONS; PATTERNS; EPIGENOME; MEIOSIS; MAPS;

D O I：

10.1186/s13059-020-02161-6

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：22

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