Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.
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DOI：
10.1101/gr.143008.112
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发表时间：
2012-12
期刊：
影响因子：
7
通讯作者：
Jones PA
中科院分区：
文献类型：
--
作者：
Kelly TK;Liu Y;Lay FD;Liang G;Berman BP;Jones PA
DNA甲基化和核小体定位共同作用产生调节基因表达的染色质结构。核小体通常使用核酸酶消化来定位，这需要大量的材料和不同的酶浓度。我们开发了一种方法（NOMe - seq），该方法使用GpC甲基转移酶（M.CviPI）和新一代测序技术，使用不到100万个细胞就能在全基因组范围内产生高分辨率的核小体定位足迹，同时保留来自同一DNA链的内源性DNA甲基化信息。使用一种新的生物信息学流程，我们发现在CTCF区域核小体占据率和DNA甲基化之间存在显著的反相关，而在启动子区域则不存在这种情况。我们进一步表明，启动子处核小体缺失的程度与表达水平直接相关，并且可以容纳多个核小体，还提供了全基因组证据表明表达的非CpG岛启动子处核小体缺失。重要的是，NOMe - seq从同一DNA分子获取DNA甲基化和核小体定位信息，首次在单分子以及单细胞水平上给出了全基因组的DNA甲基化和核小体定位相关性，可用于监测疾病进展和对治疗的反应。
DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome-depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule, and thus, single cell level, that can be used to monitor disease progression and response to therapy.
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