Recognition of H3K9me1 by Maize RNA-directed DNA methylation factor SHH2.

RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation pathway, which has extensive crosstalk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2 (SHH2) is an H3K9me1 reader. Our structural studies reveal that H3K9me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt bridge interactions with the free protons of the mono-methyllysine. The di- and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a mono-methyllysine recognition mechanism which potentially links RdDM to H3K9me1 in maize. This article is protected by copyright. All rights reserved.