The Role of Histone Methyltransferase SDG8 in Nitrate Signaling

SET Domain-containing Group 8 (SDG8) is a histone methyltransferase that mediates H3K36 methylation and affects gene expression level. Our study uncovered that SDG8 is required for plant responses to nitrate, a major form of nitrogen available to plants, across multiple scales ranging from genome-wide histone modification, transcriptome, RNA processing, root development, nitrate uptake, to primary metabolism. In response to nitrate level changes, plants change the H3K36me3 modifications at functionally relevant genomic loci, in a SDG8-dependent manner. Nitrate also induces preferential expression of gene isoforms, and the isoform shift is more prominent in the sdg8 mutant, indicating that SDG8 is required for canonical RNA processing. We showed that SDG8 regulates the isoform-specific expression of a putative transcription factor CCT101 in response to nitrate, and that CCT101 isoforms encode different proteins with distinct functions in transcriptional control. On a broad term, our study provides a framework to understand how chromatin modifications contribute towards effecting plant responses to environmental changes.