Comparative characterization of chromatin-targeting mechanisms across seven H3K4 methyltransferases in Arabidopsis

Methylation of histone H3 at lysine 4 (H3K4me) marks transcribed elements of the eukaryotic genome, and its distribution changes dynamically across developmental stages and in response to environmental factors. These dynamic regulatory changes are mediated by the combinatorial action of H3K4me methyltransferases, and multicellular organisms carry multiple copies of these enzymes. The model plant Arabidopsis has at least seven H3K4 methyltransferase genes. Here, we comparatively analyze these seven enzymes using epigenomic and biochemical approaches to better understand the mechanisms underlying their target specificity. Our findings, in combination with previous work, show that ATX1-ATX5 (Trx/Trr-type methyltransferases) localize to genomic regions with distinct sets of chromatin modifications and DNA motifs, which vary among the ATX proteins. Notably, ATX3 localizes to the binding motifs of the ASR3 and RAP2.11 transcription factors (TFs) and directly interacts with these TFs. ATXR7 (a Set1-type H3K4 methyltransferase) and ATXR3 (a non-canonical H3K4 methyltransferase) co-localize with the transcriptional machinery, suggesting co-transcriptional mechanisms of action for these enzymes. Interestingly, ATXR3, the primary H3K4 trimethylation (H3K4me3) methyltransferase in Arabidopsis, appears to form a protein complex independent of the Complex Proteins Associated with Set1 (COMPASS), which indicates that the regulatory mechanisms governing H3K4me3 have diverged between plants and animals. Our work provides a foundation for understanding the chromatin targeting of H3K4 methyltransferases in plants and highlights significant differences in H3K4me3 regulation between plants and other eukaryotes.