Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping.
Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping.
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DOI：
10.1186/1471-2164-9-598
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发表时间：
2008-12-11
期刊：
影响因子：
4.4
通讯作者：
Schwartz DA
中科院分区：
文献类型：
--
作者：
Boon K;Tomfohr JK;Bailey NW;Garantziotis S;Li Z;Brass DM;Maruoka S;Hollingsworth JW;Schwartz DA
随着各种基于阵列的技术的发展，全基因组DNA甲基化变化的研究变得更加容易，尽管在研究人类以外的物种时，应用的选择有限，而且并不总是触手可及。在这项研究中，我们采用并测试了甲基化特异性数字染色体分型(MSDK)的适用性，这是一种基于非阵列的方法，用于前瞻性分析围产期营养改善后过敏性呼吸道疾病小鼠模型的表观遗传学变化。MSDK是一种基于测序的方法，允许进行全面和公正的甲基化分析。该方法从基因组中的特定位置产生21个碱基对的长序列标签。由此产生的标签频率以定量的方式确定相应基因座的甲基化水平。提取全肺基因组DNA，以甲基化敏感酶Not I为作图酶，Nla III为碎片酶，进行MSDK分析。在对生成的小鼠MSDK文库进行配对比较中，我们在小鼠模型中确定了围产期饮食改变后显着差异甲基化的158个基因座(P值=0.05)。定量甲基化特异性聚合酶链式反应和硫酸氢修饰基因组DNA的序列分析证实了特定位点甲基化的变化。选定的一组基因的基因组MSDK标签计数的差异，与实时荧光聚合酶链式反应(Real-time PCR)测量的转录水平的变化密切相关。此外，基因表达谱系列分析表明，暴露于围产期营养变化的小鼠的表达转录本存在显着差异。这项研究中应用的全基因组甲基化调查允许无偏见的甲基化图谱，揭示了母亲暴露于饮食中甲基供体含量变化的小鼠DNA甲基化的细微变化。MSDK方法适用于混合细胞群体中复杂人类疾病的小鼠模型，可能是确定环境暴露是否会导致表观遗传变化的一项有价值的技术。
The study of genome-wide DNA methylation changes has become more accessible with the development of various array-based technologies though when studying species other than human the choice of applications are limited and not always within reach. In this study, we adapted and tested the applicability of Methylation Specific Digital Karyotyping (MSDK), a non-array based method, for the prospective analysis of epigenetic changes after perinatal nutritional modifications in a mouse model of allergic airway disease. MSDK is a sequenced based method that allows a comprehensive and unbiased methylation profiling. The method generates 21 base pairs long sequence tags derived from specific locations in the genome. The resulting tag frequencies determine in a quantitative manner the methylation level of the corresponding loci. Genomic DNA from whole lung was isolated and subjected to MSDK analysis using the methylation-sensitive enzyme Not I as the mapping enzyme and Nla III as the fragmenting enzyme. In a pair wise comparison of the generated mouse MSDK libraries we identified 158 loci that are significantly differentially methylated (P-value = 0.05) after perinatal dietary changes in our mouse model. Quantitative methylation specific PCR and sequence analysis of bisulfate modified genomic DNA confirmed changes in methylation at specific loci. Differences in genomic MSDK tag counts for a selected set of genes, correlated well with changes in transcription levels as measured by real-time PCR. Furthermore serial analysis of gene expression profiling demonstrated a dramatic difference in expressed transcripts in mice exposed to perinatal nutritional changes. The genome-wide methylation survey applied in this study allowed for an unbiased methylation profiling revealing subtle changes in DNA methylation in mice maternally exposed to dietary changes in methyl-donor content. The MSDK method is applicable for mouse models of complex human diseases in a mixed cell population and might be a valuable technology to determine whether environmental exposures can lead to epigenetic changes.
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DOI：
10.1073/pnas.93.18.9821
发表时间：
1996-09-03
影响因子：
11.1
作者：
Herman, JG;Graff, JR;Baylin, SB
通讯作者：
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影响因子：
64.8
作者：
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影响因子：
30.8
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Polyak, K
影响因子：
4.4
作者：
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通讯作者：
Jirtle, RL