Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells

In this study, we analyzed the DNA methylation levels of 4799 IAP LTRs in three murine cell types: AB2.2 ES cells, somatic cells and a neuroblastoma cell line Neuro2A. According to the results, half of the IAP LTR retrotransposons show constant methylation patterns between the three cell types whereas the remaining half display variable levels of methylation. About half of the variably methylated IAP LTRs tend to be hypomethylated in ES cells, and nearly all of this group are hypomethylated in Neuro2A cells. Interestingly, the observed hypomethylation in both cell types occur in a non-uniform, locus-specific manner and to various degrees of severity, with some of them being easily detectible by COBRA. Overall, this study demonstrates the feasibility of HT-TREBS to study alterations in DNA methylation at retrotransposons in a locus-specific manner in multiple cell types and further suggests the potential utility of this technique in developing epigenetic biomarkers for tracking disease progression. HT-TREBS has been used with the Ion Torrent PGM platform to analyze the DNA methylation of 4799 IAP LTRs in a locus-specific manner in 3 cell types: somatic cells (previously submitted under GEO Accession GSE49222), AB2.2 ES cells and Neuro2A cells

本研究对三种小鼠细胞类型中的4799个内含子A型病毒长末端重复序列（IAP LTRs）的DNA甲基化（DNA methylation）水平展开分析，所涉细胞类型包括AB2.2胚胎干细胞（ES cells）、体细胞以及神经母细胞瘤细胞系Neuro2A。分析结果显示，半数IAP LTR逆转录转座子（retrotransposons）在三类细胞中呈现恒定的甲基化模式，剩余半数则表现出可变的甲基化水平。在可变甲基化的IAP LTRs中，约有半数在胚胎干细胞中呈低甲基化状态，且该亚群中的几乎所有成员在Neuro2A细胞中均为低甲基化。值得注意的是，上述两种细胞中观察到的低甲基化均以非均匀、位点特异性的方式发生，且严重程度各异，其中部分位点可通过结合亚硫酸氢盐限制性分析（Combined Bisulfite Restriction Analysis, COBRA）轻松检出。总体而言，本研究证实HT-TREBS技术可通过位点特异性的方式，在多种细胞类型中分析逆转录转座子的DNA甲基化改变，并进一步提示该技术在开发用于追踪疾病进展的表观遗传生物标志物方面具备潜在应用价值。本研究依托Ion Torrent PGM测序平台开展HT-TREBS实验，对三类细胞中的4799个IAP LTRs进行了位点特异性的DNA甲基化分析，其中体细胞数据此前已提交至基因表达综合数据库（Gene Expression Omnibus, GEO），登录号为GSE49222，其余两种细胞类型为AB2.2胚胎干细胞与Neuro2A细胞。