Adusumalli Swarnaseetha, Mohd Omar Mohd Feroz, Soong Richie, Benoukraf Touati
Brief Bioinform. 2015 May;16(3):369-79. doi: 10.1093/bib/bbu016. Epub 2014 May 27.
The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation beyond CpG sites and CpG islands. These technologies have opened new avenues to understand the interplay between epigenetic events, chromatin plasticity and gene regulation. However, the processing, managing and mining of this huge volume of data require specialized computational tools and statistical methods that are yet to be standardized. Here, we describe a complete bisulfite sequencing analysis workflow, including recently developed programs, highlighting each of the crucial analysis steps required, i.e. sequencing quality control, reads alignment, methylation scoring, methylation heterogeneity assessment, genomic features annotation, data visualization and determination of differentially methylated cytosines. Moreover, we discuss the limitations of these technologies and considerations to perform suitable analyses.
DNA亚硫酸氢盐处理与高通量测序技术的结合，使得对CpG位点和CpG岛以外的全基因组DNA甲基化进行研究成为可能。这些技术为理解表观遗传事件、染色质可塑性和基因调控之间的相互作用开辟了新途径。然而，处理、管理和挖掘如此大量的数据需要专门的计算工具和统计方法，而这些方法尚未标准化。在此，我们描述了一个完整的亚硫酸氢盐测序分析工作流程，包括最近开发的程序，突出了所需的每个关键分析步骤，即测序质量控制、读段比对、甲基化评分、甲基化异质性评估、基因组特征注释、数据可视化以及差异甲基化胞嘧啶的确定。此外，我们还讨论了这些技术的局限性以及进行合适分析时的注意事项。
