Wardenaar René, Liu Haiyin, Colot Vincent, Colomé-Tatché Maria, Johannes Frank
Faculty of Mathematics and Natural Sciences, Groningen Bioinformatics Centre, University of Groningen, AG Groningen, The Netherlands.
Methods Mol Biol. 2013;1067:203-24. doi: 10.1007/978-1-62703-607-8_13.
Studies of DNA methylation in Arabidopsis have rapidly advanced from the analysis of a single reference accession to investigations of large populations. The goal of emerging population studies is to detect differentially methylated regions (DMRs) at the genome-wide scale, and to relate this variation to gene expression and phenotypic diversity.Whole-genome bisulfite sequencing (WGBS-seq) has established itself as a gold standard in DNA methylation analysis due to its high accuracy and single cytosine measurement resolution. However, scaling up the use of this technology for large population studies is currently not only cost prohibitive but also poses nontrivial bioinformatic challenges. If the end-point of the study is to detect DMRs at the level of several hundred base pairs rather than at the level of single cytosines, low-resolution array-based methods, such as MeDIP-chip, may be entirely sufficient. However, the trade-off between measurement accuracy and experimental/analytical practicality needs to be weighted carefully. To help make such experimental choices, we conducted a side-by-side comparison between the popular dual-channel MeDIP-chip Nimblegen technology and Illumina WGBS-seq in two independent Arabidopsis lines.Our analysis shows that MeDIP-chip performs reasonably well in detecting DNA methylation at probe-level resolution, yielding a genome-wide combined false-positive and false-negative rate of about 0.21. However, detection can be susceptible to strong signal distortions resulting from a combination of dye bias and the CG content of effectively unmethylated genomic regions. We show that these issues can be easily bypassed by taking appropriate data preparation steps and applying suitable analysis tools.We conclude that MeDIP-chip is a reasonable alternative to WGBS-seq in emerging Arabidopsis population epigenetic studies.
拟南芥DNA甲基化的研究已迅速从对单一参考种质的分析发展到对大量群体的研究。新兴群体研究的目标是在全基因组范围内检测差异甲基化区域（DMR），并将这种变异与基因表达和表型多样性联系起来。全基因组亚硫酸氢盐测序（WGBS-seq）因其高精度和单胞嘧啶测量分辨率，已成为DNA甲基化分析的金标准。然而，目前将该技术扩大用于大量群体研究不仅成本高昂，而且带来了不小的生物信息学挑战。如果研究的终点是在几百个碱基对水平而非单胞嘧啶水平检测DMR，基于阵列的低分辨率方法，如甲基化DNA免疫沉淀芯片（MeDIP-chip），可能就完全足够了。然而，测量准确性与实验/分析实用性之间的权衡需要仔细考量。为了有助于做出此类实验选择，我们在两个独立的拟南芥品系中对流行的双通道MeDIP-chip Nimblegen技术和Illumina WGBS-seq进行了并行比较。我们的分析表明，MeDIP-chip在探针水平分辨率下检测DNA甲基化方面表现相当不错，全基因组假阳性和假阴性率的综合约为0.21。然而，检测可能容易受到染料偏差和有效未甲基化基因组区域的CG含量共同导致的强烈信号失真影响。我们表明，通过采取适当的数据准备步骤并应用合适的分析工具，这些问题可以轻松规避。我们得出结论，在新兴的拟南芥群体表观遗传学研究中，MeDIP-chip是WGBS-seq的合理替代方法。
