Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.胞嘧啶DNA甲基化（mC）是一类可调控编码与非编码遗传元件表达的基因组修饰方式。目前对于mC参与环境应答过程的机制仍所知甚少。本研究采用全基因组亚硫酸氢盐测序（whole genome bisulfite sequencing）技术，对磷酸盐饥饿及恢复培养条件下水稻体内mC的时空动态特征展开分析，鉴定出大量由磷酸盐饥饿诱导的mC变化，此类变化优先定位于高诱导基因邻近的转座因子（TEs）区域。上述mC变化发生于邻近基因转录改变之后，且大多不依赖DCL3a途径，可通过有丝分裂实现部分传递，但未观察到减数分裂传递的相关证据。在拟南芥中开展的类似分析显示，磷酸盐饥饿对mC的影响极为有限，这表明该调控过程存在物种特异性机制。综上，本研究提示环境诱导基因附近的转座因子可通过高甲基化途径被沉默，并明确了胁迫响应过程中转录与表观基因组变化的时间层级关系。