CyMATE: a new tool for methylation analysis of plant genornic DNA after bisulphite sequencing
CyMATE: a new tool for methylation analysis of plant genornic DNA after bisulphite sequencing
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DOI：
10.1111/j.1365-313x.2007.03152.x
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发表时间：
2007-08-01
期刊：
影响因子：
7.2
通讯作者：
Scheid, Ortrun Mittelsten
中科院分区：
文献类型：
--
作者：
Hetzl, Jennifer;Foerster, Andrea M.;Scheid, Ortrun Mittelsten
胞嘧啶甲基化是许多真菌、脊椎动物和植物DNA表观遗传信息的标志。亚硫酸氢盐基因组测序技术揭示了序列中每个胞嘧啶的甲基化状态，从而提供了关于表观遗传多样性的高分辨率数据；然而，手动评估和记录大量数据是费力和容易出错的。虽然有一些软件可用于促进哺乳动物DNA甲基化的分析，这几乎只在CG位点发现，但没有软件最适合于来自具有显著非CG甲基化的DNA的数据。我们描述了CyMATE(Cytosine甲基化分析工具for Everyone)，用于对植物DNA亚硫酸氢盐转化后的DNA序列进行电子计算机分析，其中甲基化在序列背景和生物相关性方面更具差异性。从比对的序列中，CyMATE包括并区分CG、CHG和CHH(其中H=A、C或T)的甲基化，并可以提取关于每个序列和每个位置的一般和模式特定甲基化的定量和定性数据，即序列中单个位置的数据和样品中表观遗传差异的数据。此外，它可以提供图形输出的路线，无论是在一个概述或‘放大’视图作为pdf文件。详细信息，包括测序数据的质量控制，以文本格式提供。我们应用CyMATE对二倍体和多倍体拟南芥转录沉默启动子的DNA甲基化进行了分析，发现存在显著的超甲基化，甲基化状态的高度稳定与染色体数目无关，以及C-m分布的非冗余模式。CyMATE可在以下网址免费获得：ht-tp：//www.gmi.oeaw.ac.at/CyMATE。
Cytosine methylation is a hallmark of epigenetic information in the DNA of many fungi, vertebrates and plants. The technique of bisulphite genomic sequencing reveals the methylation state of every individual cytosine in a sequence, and thereby provides high-resolution data on epigenetic diversity; however, the manual evaluation and documentation of large amounts of data is laborious and error-prone. While some software is available for facilitating the analysis of mammalian DNA methylation, which is found nearly exclusively at CG sites, there is no software optimally suited for data from DNA with significant non-CG methylation. We describe CyMATE (Cytosine Methylation Analysis Tool for Everyone) for in silico analysis of DNA sequences after bisulphite conversion of plant DNA, in which methylation is more divergent with respect to sequence context and biological relevance. From aligned sequences, CyMATE includes and distinguishes methylation at CG, CHG and CHH (where H = A, C or T), and can extract both quantitative and qualitative data regarding general and pattern-specific methylation per sequence and per position, i.e. data for individual sites in a sequence and the epigenetic divergence within a sample. In addition, it can provide graphical output from alignments in either an overview or a 'zoom-in' view as pdf files. Detailed information, including a quality control of the sequencing data, is provided in text format. We applied CyMATE to the analysis of DNA methylation at transcriptionally silenced promoters in diploid and polyploid Arabiclopsis and found significant hypermethylation, high stability of the methylated state independent of chromosome number, and non-redundant patterns of C-m distribution. CyMATE is freely available for non-commercial use at ht-tp://www.gmi.oeaw.ac.at/CyMATE.