Pezone Antonio, Tramontano Alfonso, Scala Giovanni, Cuomo Mariella, Riccio Patrizia, De Nicola Sergio, Porcellini Antonio, Chiariotti Lorenzo, Avvedimento Enrico V
Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy.
Department of Precision Medicine, University of Campania 'L. Vanvitelli', 80138 Naples, Italy.
NAR Genom Bioinform. 2020 Nov 16;2(4):lqaa096. doi: 10.1093/nargab/lqaa096. eCollection 2020 Dec.
DNA methylation is a stable epigenetic modification, extremely polymorphic and driven by stochastic and deterministic events. Most of the current techniques used to analyse methylated sequences identify methylated cytosines (mCpGs) at a single-nucleotide level and compute the average methylation of CpGs in the population of molecules. Stable epialleles, i.e. CpG strings with the same DNA sequence containing a discrete linear succession of phased methylated/non-methylated CpGs in the same DNA molecule, cannot be identified due to the heterogeneity of the 5'-3' ends of the molecules. Moreover, these are diluted by random unstable methylated CpGs and escape detection. We present here MethCoresProfiler, an R-based tool that provides a simple method to extract and identify combinations of methylated phased CpGs shared by all components of epiallele families in complex DNA populations. The methylated cores are stable over time, evolve by acquiring or losing new methyl sites and, ultimately, display high information content and low stochasticity. We have validated this method by identifying and tracing rare epialleles and their families in synthetic or complex cell populations derived from mouse brain areas and cells during postnatal differentiation. MethCoresProfiler is written in R language. The software is freely available at https://github.com/84AP/MethCoresProfiler/.
DNA甲基化是一种稳定的表观遗传修饰，具有高度多态性，由随机和确定性事件驱动。目前用于分析甲基化序列的大多数技术在单核苷酸水平上识别甲基化胞嘧啶（mCpG），并计算分子群体中CpG的平均甲基化水平。由于分子5'-3'末端的异质性，无法识别稳定的表观等位基因，即同一DNA分子中具有相同DNA序列且包含连续线性排列的阶段性甲基化/非甲基化CpG的CpG串。此外，这些会被随机不稳定的甲基化CpG稀释并逃避检测。我们在此展示MethCoresProfiler，这是一种基于R的工具，它提供了一种简单的方法来提取和识别复杂DNA群体中表观等位基因家族所有组分共有的甲基化阶段性CpG组合。甲基化核心随时间稳定，通过获得或失去新的甲基位点而进化，最终显示出高信息含量和低随机性。我们通过在合成或源自小鼠脑区和出生后分化过程中的细胞的复杂细胞群体中识别和追踪罕见的表观等位基因及其家族，验证了该方法。MethCoresProfiler用R语言编写。该软件可在https://github.com/84AP/MethCoresProfiler/免费获取。
