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.
Figure 1-source data 1
Figure 1-source data 1: FPKM and fold change of all genes in rice roots and shoots upon Pi treatments.
Figure 2-source data 1
Figure 2-source data 1: List of 175 PSI DMRs identified in the root, with DNA methylation levels and transcription levels of DMR-associated genes.
Figure 2-source data 2
Figure 2-source data 2: Transcription levels of TEs overlapping PSI DMRS after 7 d and 21 d of Pi deprivation.
Figure 2-source data 3
Figure 2-source data 3: List of 341 PSI DMRs identified in the shoots, with DNA methylation levels and transcription levels of DMR-associated genes.
Figure 3-source data 1
Figure 3-source data 1: Levels of DNA methylation and FDR values for the 100 PSI DMRs associated with changes in proximal gene transcription.
Figure 4-source data 1
Figure 4-source data 1: List of 14 root persisting PSI DMRs, despite 31 d of Pi resupply.
Figure 4-source data 2
Figure 4-source data 2: List of 36 panicle PSI DMRs.
Figure 4-source data 3
Figure 4-source data 3: Average methylation levels observed in the roots of the progeny of stressed- and non-stressed plants in all contexts and methylation levels for each replicate in CNN in the 175 root PSI DMRs.
Figure 5-source data 1
Figure 5-source data 1: FPKM and fold change of all genes between WT +Pi and DCL3a RNAi line +Pi as well as WT -Pi and DCL3a RNAi line -Pi (FDR < 0.05). List of DMRs identified between WT +Pi and DCL3a RNAi line +Pi as well as WT -Pi and DCL3a RNAi line -Pi is shown as well as the average methylation levels observed in all samples (FDR < 0.05).
Figure 5-source data 2
Figure 5-source data 2: 11 DCL3a-dependant PSI DMRs, with methylation levels and associated gene transcription.
Figure 6-source data 1
Figure 6-source data 1: FPKM and fold change of all genes in Arabidopsis roots upon Pi starvation.
Figure 5-source data 3
409 PSI DMRs in the DCL3a RNAi line, and 88 PSI DMRs in the DCL3a RNAi line, associated with significant changes in nearby gene expression
