Comparative WGBS identifies genes that influence non-ripe phenotype in tomato epimutant Colourless non-ripening
Comparative WGBS identifies genes that influence non-ripe phenotype in tomato epimutant Colourless non-ripening
复制标题
比较 WGBS 鉴定了影响番茄表突变体中不成熟表型的基因 无色不成熟
DOI：
10.1007/s11427-017-9206-5
复制
发表时间：
2018-02-01
影响因子：
9.1
通讯作者：
Hong, Yiguo
中科院分区：
文献类型：
--
作者：
Chen, Weiwei;Yu, Zhiming;Hong, Yiguo
全基因组亚硫酸氢盐测序 (WGBS) 可对植物和动物中的 DNA 甲基化进行单碱基分辨率和全基因组分析。该技术提供了一个强大的工具来识别可能受 DNA 甲基化和去甲基化动态变化控制的基因。然而，自然发生的表观突变体很少见，表观遗传调控下的基因及其生物学相关性通常很难定义。在番茄中，果实发育和成熟是一个涉及表观遗传控制的复杂过程。我们利用了番茄表观突变体 Colorless non-ripening (Cnr) 的优势，并对 Cnr 和 SlCMT3 沉默的 Cnr 果实的 WGBS 数据集进行了比较挖掘。我们比较了紧邻 20 个基因的编码区上游约 5,000 bp 的启动子序列的 DNA 甲基化谱。其中一些基因发现了差异甲基化区域。差异甲基化基因 SlDET1 或 SlPDS 的病毒诱导基因沉默 (VIGS) 导致 Cnr 果实出现异常的棕色色素沉着。这些结果表明，比较 WGBS 与 VIGS 结合可用于鉴定可能有助于 Cnr 表突变体中果实无色未成熟表型的基因。
Whole-genome bisulfite sequencing (WGBS) allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals. This technology provides a powerful tool to identify genes that are potentially controlled by dynamic changes of DNA methylation and demethylation. However, naturally occurring epimutants are rare and genes under epigenetic regulation as well as their biological relevances are often difficult to define. In tomato, fruit development and ripening are a complex process that involves epigenetic control. We have taken the advantage of the tomato epimutant Colourless non-ripening (Cnr) and performed comparative mining of the WGBS datasets for the Cnr and SlCMT3-silenced Cnr fruits. We compared DNA methylation profiles for the promoter sequences of approximately 5,000 bp immediately upstream of the coding region of a list of 20 genes. Differentially methylated regions were found for some of these genes. Virus-induced gene silencing (VIGS) of differentially methylated gene SlDET1 or SlPDS resulted in unusual brown pigmentation in Cnr fruits. These results suggest that comparative WGBS coupled with VIGS can be used to identify genes that may contribute to the colourless unripe phenotype of fruit in the Cnr epimutant.