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 demonstrat...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-10-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02161-6 |
| _version_ | 1831836045358923776 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Yadollah Shahryary |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-23T04:48:53Z |
| format | Article |
| id | doaj.art-61ed9b5876c743479bc2eb35c96c2191 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-23T04:48:53Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-61ed9b5876c743479bc2eb35c96c21912022-12-21T17:59:32ZengBMCGenome Biology1474-760X2020-10-0121112210.1186/s13059-020-02161-6AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plantsYadollah Shahryary0Aikaterini Symeonidi1Rashmi R. Hazarika2Johanna Denkena3Talha Mubeen4Brigitte Hofmeister5Thomas van Gurp6Maria Colomé-Tatché7Koen J.F. Verhoeven8Gerald Tuskan9Robert J. Schmitz10Frank Johannes11Technical University of Munich, Department of Plant SciencesTechnical University of Munich, Department of Plant SciencesTechnical University of Munich, Department of Plant SciencesInstitute of Computational Biology, Helmholtz Zentrum MünchenTechnical University of Munich, Department of Plant SciencesInstitute of BioinformaticsNetherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial EcologyInstitute of Computational Biology, Helmholtz Zentrum MünchenNetherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial EcologyThe Center for Bioenergy Innovation, Oak Ridge National LaboratoryTechnical University of Munich, Institute for Advanced StudyTechnical University of Munich, Department of Plant SciencesAbstract 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.http://link.springer.com/article/10.1186/s13059-020-02161-6EpimutationDNA methylationPlantsTreesEpigeneticsEpimutation rate |
| spellingShingle | 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 AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants Genome Biology Epimutation DNA methylation Plants Trees Epigenetics Epimutation rate |
| title | AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants |
| title_full | AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants |
| title_fullStr | AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants |
| title_full_unstemmed | AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants |
| title_short | AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants |
| title_sort | alphabeta computational inference of epimutation rates and spectra from high throughput dna methylation data in plants |
| topic | Epimutation DNA methylation Plants Trees Epigenetics Epimutation rate |
| url | http://link.springer.com/article/10.1186/s13059-020-02161-6 |
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