Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
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DOI：
10.1038/nature06745
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发表时间：
2008-03-13
期刊：
影响因子：
64.8
通讯作者：
Jacobsen, Steven E.
中科院分区：
文献类型：
--
作者：
Cokus, Shawn J.;Feng, Suhua;Jacobsen, Steven E.
胞嘧啶DNA甲基化在调节基因表达和沉默转座子和其他重复序列中很重要（1,2）。最近对拟南芥的基因组研究表明，许多内源基因在其启动子或转录区域内甲基化，并且基因甲基化与转录水平高度相关（3-5）。然而，植物具有由不同遗传途径控制的不同类型的甲基化，并且缺乏任何给定基因组中每种胞嘧啶甲基化状态的详细信息。为此，我们利用Illumina 1G基因组分析仪和Solexa测序技术，结合亚硫酸处理基因组DNA和超高通量测序，绘制了拟南芥甲基化胞嘧啶的单碱基对分辨率图谱(6)。这种方法被称为BS- Seq，与以前基于微阵列的方法不同，它允许人们在特定序列背景下在全基因组范围内敏感地测量胞嘧啶甲基化。在这里，我们描述了甲基化在以前难以接近的基因组成分和分析DNA甲基化序列的组成和分布。我们还描述了各种DNA甲基化突变对全基因组甲基化模式的影响，并证明了我们新开发的文库构建和计算方法可以应用于大基因组，如小鼠基因组。
Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences(1,2). Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels(3-5). However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single- base- pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra- high- throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology(6). This approach, termed BS- Seq, unlike previous microarray- based methods, allows one to sensitively measure cytosine methylation on a genome- wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome- wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.