A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation

Abstract

In plants, RNA-directed DNA methylation (RdDM) is a well-known de novo DNA methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized an RdDM factor, RDM15. Through DNA methylome and genome-wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monomethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported monomethyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone H3K4me1-specific binding protein as an RdDM component, and structural analysis of RDM15 revealed a chemical feature-based lower methyllysine recognition mechanism.

The H3K4me1 histone mark recruits DNA repair to functionally constrained genomic regions in plants

“…We found evidence of mutation bias caused by H3K4me1-mediated DNA repair in rice, and examined potential mechanisms. Our findings here, derived from reanalyses of data generated by independent research groups (G. Li et al 2017; Niu et al 2021; Xie et al 2021), are consistent with our previous observations of mutation biases in A. thaliana (Monroe et al 2022). They are aligned with evolutionary models of evolved mutation bias and provide a higher resolution mechanistic model of gene body and essential genes hypomutation in plants, motivating experimental investigations into the several DNA repair pathways with potential to target active and constrained genes.…”

“… A , Results from blastp of PCDS5C Tudor domain, which has confirmed H3K4me1 binding specificity (Niu et al 2021) identified 29 genes. Nine of these are annotated as having DNA repair function (significant enrichment by gene ontology analysis).…”

“… A , ChlP-seq analysis of PDS5C in A thaliana , cohesion cofactor involved in HDR and possibly NER confirms enrichment in features in gene bodies. Raw data from Niu et al 2021. Letters represent TukeyHSD contrast at p=0.…”

“…ATX1, ATX2, ATXR7 are responsible for the enrichment of H3K4me1 in the gene bodies of active genes (Oya et al 2021). Tudor domain of PDS5C binds H3K4me1 (Niu et al 2021). Other repair genes with Tudor domains, such as PDS paralogs and MSH6 may also target H3K4me1 via Tudor domain binding.…”

“…We confirmed the structures from Alphafold's own database for A. thaliana genes. We used blastp on Phytozome (Goodstein et al 2012) to search the rice proteome for PDS5C and MHS6 orthologs, and to search the A. thaliana proteome for genes containing Tudor domains similar to that of PDS5C, which was validated experimentally to bind H3K4me1 (Niu et al 2021). We submitted the resulting list of 29 genes with putative Tudor domains to gene ontology analysis with ShinyGO (bioinformatics.sdstate.edu/go/) (Ge, Jung, and Yao 2019).…”