Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354, Germany.
Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748, Germany.
Genome Biol. 2020 Oct 6;21(1):260. doi: 10.1186/s13059-020-02161-6.
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.
DNA 甲基化的随机变化（即自发的表观突变）导致了植物中甲基组的多样性。在这里，我们描述了 AlphaBeta，这是一种使用基于谱系的 DNA 甲基化数据作为输入来估计这种随机事件的确切速率的计算方法。我们展示了如何使用 AlphaBeta 来研究克隆或性衍生的突变积累系中的跨代遗传的表观突变，以及在长寿多年生植物中的体细胞表观突变。我们的方法在已发表和新数据中的应用表明，自发的表观突变在全基因组范围内中性积累，主要发生在体细胞发育过程中，并且可以作为树木年龄测定的分子钟。
