Tri-methylation of H3 Lysine 9 provides a biomarker to track histone methyltransferase targeting in Arabidopsis
In many eukaryotes including mammals and plants, histone H3 lysine 9 methylation (H3K9me) and cytosine methylation (5meC) are targeted to transposons and repeats to silence these sequences, thereby preventing deleterious consequences such as the expression of aberrant gene products and transposon mobilization. In Arabidopsis, H3K9me mediated by the SUVH4, SUVH5, and SUVH6 histone methyltransferases (MTases) is associated with 5meC mediated by the CMT3 cytosine MTase. In order to understand targeting of H3K9me, we developed a strategy to track hotspots of SUVH activity. Our strategy uses expression of SUVH active site mutants predicted to catalyze tri-methylation of H3 K9 (H3K9me3), rather than the mono- or di-methylation catalyzed by wild type SUVH enzymes. We focused on the SUVH6 MTase, which acts preferentially at a transcribed inverted repeat locus. We found that the SUVH6 active site mutant drives H3K9me3 specifically at this preferred target. In addition, the H3me3K9 modification results in enhanced 5meC at the preferred target through enhanced CMT3 activity. Because both H3K9me3 and enhanced 5meC are novel epigenetic signatures, the SUVH active site mutant strategy provides a means to track H3 K9 MTase activity genome-wide with high-throughput approaches.