UCLA

Chemical modifications to histones and DNA regulate various biological processes including transcriptional silencing and DNA replication. One of the most well studied chromatin modifications in Arabidopsis thaliana is DNA methylation and its role in silencing transposable elements (TEs) and genes. In Arabidopsis, certain DNA methylation pathways are controlled by histone H3 lysine 9 methylation, a histone modification associated with heterochromatin. A much less characterized heterochromatic mark is histone H3 lysine 27 monomethylation (H3K27me1). Two SET domain proteins, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, were found to catalyze H3K27me1. In atxr5 atxr6 double mutants, transcriptional reactivation of TEs was observed without global defects in DNA methylation levels. Thus, unlike H3K9 methylation, H3K27me1 appeared to be involved in a silencing system independent of DNA methylation.

In addition to transcriptional reactivation of TEs, we found that atxr5 atxr6 mutants show increased copies of heterochromatic DNA, suggesting that ATXR5 and ATXR6 are involved in a pathway that prevents heterochromatin from over-replicating.

To gain better understanding about DNA methylation and H3K27me1, we performed genome-wide mapping of these chromatin marks. We profiled DNA methylation in a comprehensive list of mutants and characterized locations different DNA methylation pathways act in the genome. We also profiled H3K27me1 and found that it is enriched at sites heavily DNA methylated. Sites of over-replication in atxr5 atxr6 mutants correlated with sites normally enriched with H3K27me1, consistent with the fact that ATXR5 and ATXR6 catalyze this mark.

Given the overlap between H3K27me1 and DNA methylation across the genome, we explored the relationships between ATXR5 ATXR6 and DNA methylation in regulating gene silencing and DNA replication. We found that ATXR5 ATXR6 and DNA methylation cooperatively silence TEs through independent pathways, indicating that multiple pathways redundantly silence many TEs across the Arabidopsis genome. In contrast, we found that ATXR5 ATXR6 and DNA methylation antagonistically regulate heterochromatic DNA replication, suggesting a complex relationship between these chromatin marks in regulating transcriptional silencing TEs and heterochromatic DNA replication.

Taken together, our results provide insight into the roles of epigenetic marks in regulating gene silencing and DNA replication.