Halder Rashi, Halder Kangkan, Sharma Priyanka, Garg Gaurav, Sengupta Shantanu, Chowdhury Shantanu
G.N.R. Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India.
Mol Biosyst. 2010 Dec;6(12):2439-47. doi: 10.1039/c0mb00009d. Epub 2010 Sep 29.
Cytosine methylation in mammals is important for epigenetic control of the transcriptome. Although altered methylation is frequently encountered in disease situations, particularly cancer, the relationship between genome-wide methylation and DNA structure is poorly understood. It is now evident that alternative DNA forms are functionally relevant in replication, recombination and transcription. Herein, we researched the role of alternative DNA structure in cytosine methylation using quadruplex DNA as a case study. Our findings from analysis of 2.1 million CpGs in humans, across 12 tissues from the Human Epigenome Project (HEP), revealed a striking correlation within each tissue: CpGs with low methylation were enriched (P = 5.24E(-20)) whereas CpGs with high methylation were relatively depleted (P = 9.28E(-15)), within quadruplex-forming regions. This was further substantiated on considering 1.07E(8) methylcytosines from genome-wide sequencing within embryonic stem cells and differentiated fibroblasts. To further test the predictions we experimentally determined methylation in >600,000 CpGs across 18 individuals using bisulfite mapping and found significantly low methylation of CpGs within quadruplex-forming regions (P = 1.36E(-08)). Together, these suggest the role of guanine-quadruplexes in CpG methylation and directly impact our understanding of the inter-relationship between DNA conformation and global cytosine methylation.
哺乳动物中的胞嘧啶甲基化对于转录组的表观遗传控制至关重要。尽管在疾病状态尤其是癌症中经常会遇到甲基化改变的情况，但全基因组甲基化与DNA结构之间的关系却知之甚少。现在很明显，替代性DNA形式在复制、重组和转录中具有功能相关性。在此，我们以四链体DNA为例，研究了替代性DNA结构在胞嘧啶甲基化中的作用。我们对来自人类表观基因组计划（HEP）的12个组织中的210万个CpG进行分析，结果显示每个组织内都存在显著的相关性：在四链体形成区域内，低甲基化的CpG富集（P = 5.24E(-20)），而高甲基化的CpG相对减少（P = 9.28E(-15)）。考虑到胚胎干细胞和分化成纤维细胞中全基因组测序得到的1.07E(8)个甲基胞嘧啶，这一结果得到了进一步证实。为了进一步验证这些预测，我们使用亚硫酸氢盐定位法对18个个体中的60多万个CpG进行了实验性甲基化测定，发现四链体形成区域内的CpG甲基化水平显著较低（P = 1.36E(-08)）。这些结果共同表明了鸟嘌呤四链体在CpG甲基化中的作用，并直接影响我们对DNA构象与全基因组胞嘧啶甲基化之间相互关系的理解。
