Genome-wide high throughput analysis of DNA methylation in eukaryotes
Genome-wide high throughput analysis of DNA methylation in eukaryotes
复制标题
DOI：
10.1016/j.ymeth.2008.09.022
复制
发表时间：
2009-03-01
期刊：
影响因子：
4.8
通讯作者：
Freitag, Michael
中科院分区：
文献类型：
--
作者：
Pomraning, Kyle R.;Smith, Kristina M.;Freitag, Michael
胞嘧啶甲基化是典型的表观遗传标记。两种成熟的方法，亚硫酸氢盐测序和甲基DNA免疫沉淀（MeDIP），使自己的全基因组DNA甲基化分析的高通量测序。在这里，我们提供了这些方法的概述和简要回顾。我们总结了我们的经验与MeDIP其次是高通量Illumina/Solexa测序，举例说明了粗糙脉孢菌基因组的甲基化部分（“甲基化”）的分析。我们提供了用于Illumina/Solexa测序的DNA分离、处理和体外文库生成的详细方法。我们讨论了潜在的问题，在测序库的生成。最后，我们提供了一个概述的软件，是适合于分析的高通量测序数据所产生的Illumina/Solexa型测序合成，特别强调的方法和应用程序，可以产生更准确的序列读数，落在重复区域的选择参考基因组。(c)2008年爱思唯尔公司All rights reserved.
Cytosine methylation is the quintessential epigenetic mark. Two well-established methods, bisulfite sequencing and methyl-DNA immunoprecipitation (MeDIP) lend themselves to the genome-wide analysis of DNA methylation by high throughput sequencing. Here we provide an overview and brief review of these methods. We summarize our experience with MeDIP followed by high throughput Illumina/Solexa sequencing, exemplified by the analysis of the methylated fraction of the Neurospora crassa genome ("methylome"). We provide detailed methods for DNA isolation, processing and the generation of in vitro libraries for Illumina/Solexa sequencing. We discuss potential problems in the generation of sequencing libraries. Finally, we provide an overview of software that is appropriate for the analysis of high throughput sequencing data generated by Illumina/Solexa-type sequencing by synthesis, with a special emphasis on approaches and applications that can generate more accurate depictions of sequence reads that fall in repeated regions of a chosen reference genome. (c) 2008 Elsevier Inc. All rights reserved.