Histone H3K4 methyltransferases SDG25 and ATX1 maintain heat‐stress gene expression during recovery in Arabidopsis

Summary Plants have short‐term stress memory that enables them to maintain the expression state of a substantial subset of heat‐inducible genes during stress recovery after heat stress. Little is known about the molecular mechanisms controlling stress‐responsive gene expression at the recovery stage in plants, however. In this article, we demonstrate that histone H3K4 methyltransferases SDG25 and ATX1 are required for heat‐stress tolerance in Arabidopsis. SDG25 and ATX1 are not only important for stress‐responsive gene expression during heat stress, but also for maintaining stress‐responsive gene expression during stress recovery. A combination of whole‐genome bisulfite sequencing, RNA‐sequencing and ChIP‐qPCR demonstrated that mutations of SDG25 and ATX1 decrease histone H3K4me3 levels, increase DNA cytosine methylation and inhibit the expression of a subset of heat stress‐responsive genes during stress recovery in Arabidopsis. ChIP‐qPCR results confirm that ATX1 binds to chromatins associated with these target genes. Our results reveal that histone H3K4me3 affects DNA methylation at regions in the loci associated with heat stress‐responsive gene expression during stress recovery, providing insights into heat‐stress transcriptional memory in plants. Significance Statement This article reveals that histone H3K4 methyltransferases, SDG25 and ATX1, prevent DNA methylation at loci associated with heat‐stress gene expression during stress recovery in Arabidopsis.