Genome-Wide Quantitative Identification of DNA Differentially Methylated Sites in Arabidopsis Seedlings Growing at Different Water Potential

BACKGROUND: In eukaryotes, the combinatorial usage of cis-regulatory elements enables the assembly of composite genetic switches to integrate multifarious, convergent signals within a single promoter. Plants as sessile organisms, incapable of seeking for optimal conditions, rely on the use of this resource to adapt to changing environments. Emerging evidence suggests that the transcriptional responses of plants to stress are associated with epigenetic processes that govern chromatin accessibility. However, the extent at which specific chromatin modifications contribute to gene regulation has not been assessed. METHODOLOGY/PRINCIPAL FINDINGS: In the present work, we combined methyl-sensitive-cut counting and RNA-seq to follow the transcriptional and epigenetic response of plants to simulated drought. Comprehensive genome wide evidence supports the notion that the methylome is widely reactive to water potential. The predominant changes in methylomes were loci in the promoters of genes encoding for proteins suited to cope with the environmental challenge. CONCLUSION/SIGNIFICANCE: These selective changes in the methylome with corresponding changes in gene transcription suggest drought sets in motion an instructive mechanism guiding epigenetic machinery toward specific effectors genes.