WD40-protein-mediated crosstalk among three epigenetic marks regulates chromatin states and yield in rice

Although there is increasing understanding of the regulatory effects of particular epigenetic marks, much less is known about how crosstalk among multiple marks affects genetic regulation. Here, we show that Dwarf-related WD40 protein 1 (DRW1) is involved in DNA 6mA demethylation, H3K27 trimethylation, and RNA m⁵C methylation in rice through its respective recruitment of the DNA demethylase AlkB homolog 1 (OsALKBH1), the histone methyltransferase CURLY LEAF (OsCLF), and NOP2/Sun RNA methyltransferase family member 2 (OsNSUN2). Knockout of DRW1 significantly reduces the extent of chromatin occupancy by OsALKBH1, OsCLF, and OsNSUN2, resulting in increased chromatin accessibility and enhanced expression of genes associated with brassinosteroid biosynthesis and signaling. Gene editing at a CAAT-box (ATTGG→ATTGA) and a GATA motif (GATAGGG→GAT) in the DRW1 promoter leads to elevated DRW1 transcription and thereby enhanced rice grain yield and salt tolerance. In field trials, DRW1-overexpressing rice lines displayed yield increases of ∼30.2% (in both normal and saline soils), accompanied by decreases in DNA 6mA and increases in H3K27me3 and RNA m⁵C levels at target genes. Overall, our study uncovers DRW1-mediated crosstalk among three epigenetic marks (DNA 6mA, H3K27me3, and RNA m⁵C) and reveals how this crosstalk controls transcriptional and post-transcriptional regulation to affect rice yield and salt tolerance.