Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America.
PLoS One. 2011;6(7):e22226. doi: 10.1371/journal.pone.0022226. Epub 2011 Jul 11.
Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing ∼100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution.
甲基化 CpG 结合域蛋白测序（MBD-seq）广泛用于检测 DNA 甲基化模式。然而，MBD-seq 的最佳实验参数仍不清楚，数据分析仍然具有挑战性。在这项研究中，我们在 MCF-7 细胞中生成了高深度的 MBD-seq 数据，并开发了一种双不对称拉普拉斯模型（BALM）来进行数据分析。我们发现，通过在 MCF-7 细胞中使用 500mM 和 1000mM 盐浓度洗脱的组合测序约 1 亿个独特映射标签，可以实现 MBD-seq 实验的最佳效率。克隆亚硫酸氢盐测序结果表明，使用所提出的模型可以以高分辨率准确检测测试区域中每个 CpG 二核苷酸的甲基化状态。这些结果表明，由于其低成本、高特异性、效率和分辨率，MBD-seq 和 BALM 的组合可以作为一种有用的工具来研究 DNA 甲基组。
