Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA.
Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA, USA.
Sci Rep. 2023 Feb 27;13(1):3307. doi: 10.1038/s41598-023-30422-4.
Cytosine methylation is an epigenetic mark that participates in regulation of gene expression and chromatin stability in plants. Advancements in whole genome sequencing technologies have enabled investigation of methylome dynamics under different conditions. However, the computational methods for analyzing bisulfite sequence data have not been unified. Contention remains in the correlation of differentially methylated positions with the investigated treatment and exclusion of noise, inherent to these stochastic datasets. The prevalent approaches apply Fisher's exact test, logistic, or beta regression, followed by an arbitrary cut-off for differences in methylation levels. A different strategy, the MethylIT pipeline, utilizes signal detection to determine cut-off based on a fitted generalized gamma probability distribution of methylation divergence. Re-analysis of publicly available BS-seq data from two epigenetic studies in Arabidopsis and applying MethylIT revealed additional, previously unreported results. Methylome repatterning in response to phosphate starvation was confirmed to be tissue-specific and included phosphate assimilation genes in addition to sulfate metabolism genes not implicated in the original study. During seed germination plants undergo major methylome reprogramming and use of MethylIT allowed us to identify stage-specific gene networks. We surmise from these comparative studies that robust methylome experiments must account for data stochasticity to achieve meaningful functional analyses.
胞嘧啶甲基化是一种表观遗传标记，参与植物基因表达和染色质稳定性的调控。全基因组测序技术的进步使得人们能够在不同条件下研究甲基组动力学。然而，用于分析亚硫酸氢盐测序数据的计算方法尚未统一。在将差异甲基化位置与所研究的处理相关联以及排除这些随机数据集固有的噪声方面，仍然存在争议。流行的方法应用 Fisher 精确检验、逻辑回归或贝塔回归，然后根据甲基化水平差异的任意截止值进行分析。一种不同的策略，MethylIT 管道，利用信号检测来确定基于拟合广义伽马甲基化离散概率分布的截止值。对来自拟南芥中两个表观遗传学研究的公开可用 BS-seq 数据的重新分析以及应用 MethylIT 揭示了以前未报告的其他结果。对磷酸盐饥饿的响应导致甲基组重新模式化，这是组织特异性的，除了在原始研究中未涉及的硫酸盐代谢基因外，还包括磷酸盐同化基因。在种子萌发过程中，植物经历主要的甲基组重编程，使用 MethylIT 使我们能够鉴定特定阶段的基因网络。通过这些比较研究，我们推测稳健的甲基组实验必须考虑数据随机性，以实现有意义的功能分析。
