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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)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter 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
Zeitschrift Genome Biology
Quellenangaben Band: 21, Heft: 1, Seiten: , Artikelnummer: 33023650 Supplement: ,
Verlag BioMed Central
Verlagsort Campus, 4 Crinan St, London N1 9xw, England
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
Förderungen 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