Lai Yun-Song, Zhang Xiaohui, Zhang Wei, Shen Di, Wang Haiping, Xia Yudong, Qiu Yang, Song Jiangping, Wang Chenchen, Li Xixiang
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611130, China.
J Exp Bot. 2017 May 17;68(11):2899-2912. doi: 10.1093/jxb/erx144.
Cucumber (Cucumis sativus L.) is characterized by its diverse and flexible sexual types. Here, we evaluated the effect of low temperature (LT) exposure on cucumber femaleness under short-day conditions. Shoot apices were subjected to whole-genome bisulfate sequencing (WGBS), mRNA-seq, and sRNA-seq. The results showed that temperature had a substantial and global impact on transposable element (TE)-related small RNA-directed DNA methylation (RdDM) mechanisms, resulting in large amounts of CHH-type cytosine demethylation. In the cucumber genome, TEs are common in regions near genes that are also subject to DNA demethylation. TE-gene interactions showed very strong reactions to LT treatment, as nearly 80% of the differentially methylated regions (DMRs) were distributed in genic regions. Demethylation near genes led to the co-ordinated expression of genes and TEs. More importantly, genome-wide de novo methylation changes also resulted in small amounts of CG- and CHG-type DMRs. Methylation changes in CG-DMRs located <600 bp from the transcription start and end sites (TSSs/TESs) negatively correlated with transcription changes in differentially expressed genes (DEGs), probably indicating epiregulation. Ethylene is called the 'sex hormone' of cucumbers. We observed the up-regulation of ethylene biosynthesis-related CsACO3 and the down-regulation of an Arabidopsis RAP2.4-like ethylene-responsive (AP2/ERF) transcription factor, demonstrating the inferred epiregulation. Our study characterized the response of the apex methylome to LT and predicted the possible epiregulation of temperature-dependent sex determination (TSD) in cucumber.
黄瓜（Cucumis sativus L.）具有多样且灵活的性型。在此，我们评估了短日照条件下低温暴露对黄瓜雌性化的影响。对茎尖进行了全基因组亚硫酸氢盐测序（WGBS）、mRNA测序和sRNA测序。结果表明，温度对转座元件（TE）相关的小RNA介导的DNA甲基化（RdDM）机制具有实质性的全局影响，导致大量CHH型胞嘧啶去甲基化。在黄瓜基因组中，TE在同样经历DNA去甲基化的基因附近区域很常见。TE与基因的相互作用对低温处理表现出非常强烈的反应，因为近80%的差异甲基化区域（DMR）分布在基因区域。基因附近的去甲基化导致基因和TE的协同表达。更重要的是，全基因组范围的从头甲基化变化也导致了少量CG型和CHG型DMR。位于转录起始和终止位点（TSS/TES）600 bp以内的CG-DMR中的甲基化变化与差异表达基因（DEG）的转录变化呈负相关，这可能表明存在表观调控。乙烯被称为黄瓜的“性激素”。我们观察到乙烯生物合成相关的CsACO3上调，以及拟南芥RAP2.4样乙烯响应（AP2/ERF）转录因子下调，证明了推断的表观调控。我们的研究表征了茎尖甲基化组对低温的响应，并预测了黄瓜中温度依赖性性别决定（TSD）可能的表观调控。
