An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.
An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.
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改进的基因组宽DNA甲基化分析的方法与两种乳腺癌细胞系中的转录和基因组不稳定性相关。
DOI：
10.1186/1471-2164-10-223
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发表时间：
2009-05-13
期刊：
影响因子：
4.4
通讯作者：
Bolund L
中科院分区：
文献类型：
--
作者：
Li J;Gao F;Li N;Li S;Yin G;Tian G;Jia S;Wang K;Zhang X;Yang H;Nielsen AL;Bolund L
DNA甲基化是一种广泛研究的表观遗传机制，已知与基因阻遏和基因组稳定性相关。开发用于DNA甲基化事件的全局检测的灵敏方法是特别重要的。我们在这里描述了一种技术，称为改良甲基化特异性数字核型分析（MMSDK）的基础上甲基化特异性数字核型分析（MSDK）与一种新的测序方法。简言之，在用甲基化敏感性作图酶和片段化酶串联消化基因组DNA后，获得短序列标签。扩增这些标签，然后进行直接、大规模平行测序（Solexa 1G基因组分析仪）。该方法允许高通量和低成本的全基因组DNA甲基化作图。我们应用这种方法来研究广泛使用的乳腺癌细胞系MCF-7和MDA-MB-231的全局DNA甲基化谱，这两种细胞系分别代表管腔样和间充质样癌症类型。通过比较，揭示了两种细胞系的高度相似的总体DNA甲基化模式。然而，鉴定了在两个细胞系之间具有显著不同的DNA甲基化状态的单个基因组基因座的群组。此外，我们揭示了基因表达与两种癌细胞系中具有CpG岛（CGI）的基因启动子甲基化状态之间的全基因组显著相关性，以及MCF-7细胞中基因表达与无CGI的启动子甲基化状态之间的相关性。MMSDK方法将是一个有价值的工具，以增加目前的知识全基因组DNA甲基化谱。
DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of particular importance. We here describe a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach. Briefly, after a tandem digestion of genomic DNA with a methylation-sensitive mapping enzyme and a fragmenting enzyme, short sequence tags are obtained. These tags are amplified, followed by direct, massively parallel sequencing (Solexa 1G Genome Analyzer). This method allows high-throughput and low-cost genome-wide DNA methylation mapping. We applied this method to investigate global DNA methylation profiles for widely used breast cancer cell lines, MCF-7 and MDA-MB-231, which are representatives for luminal-like and mesenchymal-like cancer types, respectively. By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines. However a cohort of individual genomic loci with significantly different DNA methylation status between two cell lines was identified. Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells. The MMSDK method will be a valuable tool to increase the current knowledge of genome wide DNA methylation profiles.
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影响因子：
64.5
作者：
Casper, AM;Nghiem, P;Glover, TW
通讯作者：
Glover, TW
影响因子：
64.5
作者：
Gilbert, N;Lutz-Prigge, S;Moran, JV
通讯作者：
Moran, JV
影响因子：
3.7
作者：
Rivenbark, Ashley G.;Jones, Wendell D.;Coleman, William B.
通讯作者：
Coleman, William B.
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard
DOI：
10.1073/pnas.0712251105
发表时间：
2008-03-25
影响因子：
11.1
作者：
Ehrich, Mathias;Turner, Julia;van den Boom, Dirk
通讯作者：
van den Boom, Dirk