Epigenetic Regulation of Stress Response Genes in Drought-Exposed Maize
DOI:
https://doi.org/10.5281/zenodo.22688005Keywords:
DNA methylation, histone modification, drought stress, maize, epigenetics, stress memoryAbstract
Whether drought-induced changes in gene expression in crop plants are accompanied by stable, heritable
epigenetic marks, or instead reflect transient transcription factor activity that leaves no lasting chromatin signature,
has direct implications for whether a single stress exposure can prime a plant, or its progeny, for improved
performance under subsequent drought. We present a case study tracking DNA methylation (whole-genome
bisulfite sequencing) and two histone modifications (H3K4me3 and H3K27me3, by CUT&RUN) at 42
well-characterised drought-responsive loci in a single elite maize inbred line (B73) across a controlled progressive
drought and recovery cycle, followed by a second drought cycle imposed on both previously stressed and naive
plants to test for stress memory. During the first drought cycle, 34 of 42 target loci showed significant differential
DNA methylation relative to well-watered controls, predominantly hypomethylation in gene body and proximal
promoter regions of upregulated stress-response genes, and 29 loci showed a corresponding gain of the
active-chromatin mark H3K4me3. Following seven days of recovery under well-watered conditions, transcript
levels for all 42 loci returned to within twofold of pre-stress baseline, but DNA methylation at 18 of the 34 originally
affected loci remained significantly different from naive controls, and H3K4me3 enrichment persisted at 14 of 29
loci, indicating incomplete reversion of the epigenetic landscape despite transcriptional recovery. Under a second
drought cycle, previously stressed plants showed significantly faster transcriptional induction (reaching
half-maximal induction 1.8 days earlier on average) at the subset of loci retaining altered DNA methylation or
H3K4me3 enrichment after the first cycle, compared with naive plants experiencing drought for the first time, while
loci that had fully reverted showed no priming effect. These results provide direct locus-resolved evidence for
drought-associated epigenetic priming in a single well-characterised maize genotype, and identify persistent
chromatin marks at a defined subset of loci as a plausible molecular substrate for the faster stress response
observed on repeated drought exposure.
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