Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
Genetics. 2018 Aug;209(4):983-995. doi: 10.1534/genetics.118.300987. Epub 2018 May 30.
DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. To investigate heritable epigenetic changes as a consequence of tissue culture, a sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ∼15 Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines, suggesting that some loci are either targeted or hotspots for epigenetic variation. The consistent changes inherited following tissue culture include both gains and losses of DNA methylation and can affect CG, CHG, or both contexts within a region. Only a subset of the tissue culture changes observed in callus plants are observed in the primary regenerants, but the majority of DNA methylation changes present in primary regenerants are passed onto offspring. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.
DNA 甲基化有助于维持基因组的完整性和基因表达的调控。在大多数情况下，DNA 甲基化模式是相当稳定地遗传的。然而，由于组织培养，一些基因座的 DNA 甲基化会发生变化，从而导致体细胞变异。为了研究组织培养导致的可遗传的表观遗传变化，我们采用了一种序列捕获亚硫酸氢盐测序方法，监测来自组织培养再生植物群体的约 15 Mb 玉米基因组中特定位置的 DNA 甲基化模式。从组织培养中再生的植物在一组基因组区域中表现出 DNA 甲基化的获得和丢失。有证据表明，在多个独立的组织培养系中，DNA 甲基化水平的纯合变化发生的频率很高，这表明一些基因座是表观遗传变异的靶标或热点。组织培养后遗传的一致变化包括 DNA 甲基化的获得和丢失，并且可以影响一个区域内的 CG、CHG 或两者的情况。在愈伤组织植物中观察到的组织培养变化只有一部分在原再生体中观察到，但原再生体中存在的大多数 DNA 甲基化变化都会传递给后代。这项研究为一些基因座的易感性和可能导致组织培养过程中发生的 DNA 甲基化和表观遗传状态改变的潜在机制提供了新的认识。
