Meissner Alexander, Mikkelsen Tarjei S, Gu Hongcang, Wernig Marius, Hanna Jacob, Sivachenko Andrey, Zhang Xiaolan, Bernstein Bradley E, Nusbaum Chad, Jaffe David B, Gnirke Andreas, Jaenisch Rudolf, Lander Eric S
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Nature. 2008 Aug 7;454(7205):766-70. doi: 10.1038/nature07107. Epub 2008 Jul 6.
DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.
DNA甲基化对于正常发育至关重要，并且与包括癌症在内的多种病理过程有关。我们对于DNA甲基化在全基因组范围内的分布、在细胞分化过程中的变化以及它与哺乳动物组蛋白甲基化和其他染色质修饰之间的关系的了解仍然有限。在此，我们报告了在哺乳动物细胞中以核苷酸分辨率生成和分析全基因组规模的DNA甲基化图谱。使用高通量简化代表性亚硫酸氢盐测序和基于单分子的测序技术，我们生成了覆盖大多数CpG岛以及保守非编码元件、转座子和其他基因组特征的代表性样本的DNA甲基化图谱，这些样本来自小鼠胚胎干细胞、胚胎干细胞衍生的神经细胞和原代神经细胞，以及其他八个原代组织。数据得出了几个关键发现。首先，DNA甲基化模式与组蛋白甲基化模式的相关性比与潜在的基因组序列背景的相关性更好。其次，CpG的甲基化是动态的表观遗传标记，在细胞分化过程中会发生广泛变化，尤其是在核心启动子以外的调控区域。第三，对胚胎干细胞衍生细胞和原代细胞的分析表明，与一组特定的发育调控基因相关的“弱”CpG岛在体外长期增殖过程中会发生异常的高甲基化，其模式类似于一些原发性肿瘤中报道的模式。更普遍地说，这些结果确立了简化代表性亚硫酸氢盐测序作为一种强大技术，可用于对与发育生物学、癌症和再生医学相关的细胞群体进行表观遗传分析。
