Data from: MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild growing species

Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cytosine methylation in genomic DNA obtained by HPLC analysis. A screening of literature revealed that methylation of cytosines at cleavage sites assayed by MSAP was greater than genome-wide estimates obtained by HPLC, and percentages of methylation at different nucleotide contexts varied within and across species. Concurrent HPLC and MSAP analyses of DNA from 200 individuals of the perennial herb Helleborus foetidus confirmed that methyl-cytosine was more frequent in CCGG contexts than in the genome as a whole. In this species, global methylation was unrelated to methylation at the inner CG site. We suggest that global HPLC and context-specific MSAP methylation estimates provide complementary information whose combination can improve our current understanding of methylation-based epigenetic processes in nonmodel plants.

DNA胞嘧啶的甲基化可调控转座子（transposons）的沉默与基因的表达，是植物响应环境变化的核心表观遗传机制。甲基化敏感扩增多态性（methylation-sensitive amplification polymorphism，MS-AFLP或MSAP）分析常被用于评估胁迫处理下的胞嘧啶甲基化变化，近年来亦逐步应用于野生植物种群的生态学研究。MSAP技术无需依赖已测序的参考基因组（sequenced reference genome），可随机扩增基因组中大量匿名位点并鉴定其甲基化状态。不过，MSAP数据的计分流程较为复杂，目前仍需开展标准化工作以充分区分不同核苷酸环境下的甲基化差异。此外，学界尚不清楚MSAP能否准确推断植物全基因组范围的胞嘧啶甲基化水平。
本研究分析了MSAP检测结果与高效液相色谱（High Performance Liquid Chromatography, HPLC）测定的基因组DNA总胞嘧啶甲基化百分比之间的相关性。文献筛查结果显示，MSAP检测的酶切位点处的胞嘧啶甲基化水平高于HPLC得到的全基因组甲基化估算值，且不同核苷酸环境下的甲基化百分比在物种内部及跨物种间均存在差异。我们对200份臭嚏根草（Helleborus foetidus）多年生草本个体的DNA同时开展了HPLC与MSAP分析，结果证实CCGG序列环境中的胞嘧啶甲基化频率高于全基因组整体水平。在该物种中，全基因组甲基化水平与内部CG位点的甲基化水平并无关联。我们认为，全基因组水平的HPLC甲基化估算值与特定核苷酸环境的MSAP甲基化估算值可提供互补信息，二者结合将有助于深化我们对非模式植物中基于甲基化的表观遗传过程的现有认知。