A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects
A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects
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DOI：
10.1093/hmg/ddt511
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发表时间：
2014-03-01
影响因子：
3.5
通讯作者：
Van den Oord, Edwin J. C. G.
中科院分区：
文献类型：
--
作者：
McClay, Joseph L.;Aberg, Karolina A.;Van den Oord, Edwin J. C. G.
表观遗传学对衰老过程的核心重要性越来越被认识到。在这里，我们对718名年龄在25-92岁（平均= 55）的个体的全血DNA进行了甲基化全关联研究（MWAS）。我们对甲基-CpG富集的基因组DNA部分进行测序，平均每个受试者6730万个读数，以获得人类基因组中类似于2700万个常染色体CpG的甲基化测量值。在广泛的质量控制之后，我们自适应地将相邻的高度相关的CpG的甲基化测量组合成4 344 016个CpG块，我们使用这些块进行关联测试。11个与年龄相关的差异甲基化区域（DMR）通过了Bonferroni校正（P值< 1.15 x 10（-8））。使用亚硫酸氢盐转化的DNA的焦磷酸测序，在558名受试者的独立样本集中复制了最佳结果（最小P值< 10（-30））。为了检查生物主题，我们选择了70个错误发现率< 0.1的DMR。其中，42例显示低甲基化，28例显示高甲基化。高甲基化的DMR更可能与CpG岛和海岸重叠。低甲基化DMR更可能位于与多梳/调节蛋白相关的区域（例如，G. EZH 2）或组蛋白修饰H3 K27 ac、H3 K4 m1、H3 K4 m2、H3 K4 m3和H3 K9 ac。与最常见的DMR相关的基因包括原钙粘蛋白、同源盒基因、MAPK和兰尼碱受体。我们的几个DMR是与年龄相关疾病潜在相关的基因。这项研究成功地证明了下一代测序在MWAS中的应用，除了使用微阵列复制先前研究中涉及的几个基因座之外，还通过询问大部分甲基化组并返回潜在的新年龄DMR。
The central importance of epigenetics to the aging process is increasingly being recognized. Here we perform a methylome-wide association study (MWAS) of aging in whole blood DNA from 718 individuals, aged 25-92 years (mean = 55). We sequenced the methyl-CpG-enriched genomic DNA fraction, averaging 67.3 million reads per subject, to obtain methylation measurements for the similar to 27 million autosomal CpGs in the human genome. Following extensive quality control, we adaptively combined methylation measures for neighboring, highly-correlated CpGs into 4 344 016 CpG blocks with which we performed association testing. Eleven age-associated differentially methylated regions (DMRs) passed Bonferroni correction (P-value < 1.15 x 10(-8)). Top findings replicated in an independent sample set of 558 subjects using pyrosequencing of bisulfite-converted DNA (min P-value < 10(-30)). To examine biological themes, we selected 70 DMRs with false discovery rate of < 0.1. Of these, 42 showed hypomethylation and 28 showed hypermethylation with age. Hypermethylated DMRs were more likely to overlap with CpG islands and shores. Hypomethylated DMRs were more likely to be in regions associated with polycomb/regulatory proteins (e. g. EZH2) or histone modifications H3K27ac, H3K4m1, H3K4m2, H3K4m3 and H3K9ac. Among genes implicated by the top DMRs were protocadherins, homeobox genes, MAPKs and ryanodine receptors. Several of our DMRs are at genes with potential relevance for age-related disease. This study successfully demonstrates the application of next-generation sequencing to MWAS, by interrogating a large proportion of the methylome and returning potentially novel age DMRs, in addition to replicating several loci implicated in previous studies using microarrays.