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。然而，目前对于mC在环境应答过程中的参与机制仍知之甚少。本研究采用全基因组亚硫酸氢盐测序（whole genome bisulfite sequencing）技术，对磷酸盐饥饿及复养条件下水稻中mC的时空动态特征展开分析，鉴定出大量磷酸盐饥饿诱导的mC变化，此类变化优先富集于高诱导表达基因邻近的转座因子（transposable elements, TEs）区域。此类mC变化发生于邻近基因转录改变之后，且大多不依赖DCL3a，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。对拟南芥开展的同类分析显示，磷酸盐饥饿对mC的影响极为有限，提示该调控机制具有物种特异性。综上，本研究表明环境诱导基因附近的转座因子可通过高甲基化途径实现沉默，并明确了胁迫应答过程中转录与表观基因组变化的时间层级关系。