DOI: 10.5061/dryad.40gd6
title: Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

description: 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.
description: Figure 1-source data
 1Figure 1-source data 1:
 FPKM and fold change of all genes in rice roots and shoots upon Pi
 treatments.Figure 2-source data
 1Figure 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
 2Figure 2-source data 2:
 Transcription levels of TEs overlapping PSI DMRS after 7 d and 21 d of Pi
 deprivation.Figure 2-source data
 3Figure 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
 1Figure 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
 1Figure 4-source data 1:
 List of 14 root persisting PSI DMRs, despite 31 d of Pi
 resupply.Figure 4-source data
 2Figure 4-source data 2:
 List of 36 panicle PSI DMRs.Figure 4-source data
 3Figure 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
 1Figure 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 &lt; 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 &lt; 0.05).Figure 5-source data
 2Figure 5-source data 2:
 11 DCL3a-dependant PSI DMRs, with methylation levels and associated gene
 transcription.Figure 6-source data
 1Figure 6-source data 1:
 FPKM and fold change of all genes in Arabidopsis roots upon Pi
 starvation.Figure 5-source data
 3409
 PSI DMRs in the DCL3a RNAi line, and 88 PSI DMRs in the DCL3a RNAi line,
 associated with significant changes in nearby gene
 expression