Corley Michael J, Zhang Wei, Zheng Xin, Lum-Jones Annette, Maunakea Alika K
a Department of Native Hawaiian Health; John A. Burns School of Medicine ; University of Hawaii ; Honolulu , HI USA.
Epigenetics. 2015;10(2):153-66. doi: 10.1080/15592294.2014.1003747.
Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we developed a MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is low cost, rapid, and scalable. We applied this protocol to demonstrate MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450 BeadChip array, and accurately identifies sites of differential DNA methylation. Furthermore, we applied an integrative approach to further investigate and confirm the role of DNA methylation in alternative splicing and to profile 5mC and 5hmC variants of DNA methylation in normal human brain tissue that is localized over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions.
甲基化DNA免疫沉淀测序（MeDIP-Seq）是一种广泛用于全基因组DNA甲基化研究的方法。在此，我们开发了一种与基于Ion Torrent半导体的测序平台兼容的MeDIP-Seq方案，该方案成本低、速度快且可扩展。我们应用此方案证明了在Ion Torrent平台上进行MeDIP-Seq能够对CpG胞嘧啶提供足够的覆盖，我们在Infinium HumanMethylation450 BeadChip阵列上以单碱基分辨率验证了其甲基化状态，并准确识别出差异DNA甲基化位点。此外，我们采用了一种综合方法来进一步研究和确认DNA甲基化在可变剪接中的作用，并对正常人脑组织中位于不同基因组区域的DNA甲基化的5mC和5hmC变体进行分析。MeDIP-Seq在Ion Torrent平台上的这些应用具有广泛的用途，并为当前在正常和疾病条件下分析全基因组DNA甲基化状态的方法增添了内容。
