A histone methylation-dependent DNA methylation pathway is uniquely impaired by deficiency in S-adenosylhomocysteine hydrolase

S-adenosylhomocysteine hydrolase (SAH) is a key enzyme in the maintenance of methylation homeostasis in eukaryotes because it is needed to metabolize the by-product of transmethylation reactions, S-adenosylhomocysteine (AdoHcy), which causes by-product inhibition of methyltransferases (MTases). Complete loss of SAH function is lethal. Partial loss of SAH function causes pleiotropic effects including reduced cytosine methylation. Here we describe a novel allele of the Arabidopsis SAH1 gene that specifically causes loss of cytosine methylation in non-CG contexts controlled by the CMT3 DNA MTase without other obvious phenotypic consequences. The CMT3 methylation pathway depends on histone H3 lysine 9 methylation (H3 mK9) to guide DNA methylation. Chromatin immunoprecipitation (ChIP) analysis shows that the weak sah1 mutant is not significantly depleted for H3 mK9 relative to control strains. This result indicates that preferential inhibition of H3 K9 MTases by AdoHcy is not the basis for preferential inhibition of the CMT3 pathway. Instead, it is likely that simultaneous slight downregulation of H3 K9 MTases and the CMT3 DNA MTase have a synergistic effect on the DNA methylation output of this pathway. By extension, controlled SAH downregulation could provide a powerful tool in understanding the relationship between histone methylation and DNA methylation in other organisms that contain multiple DNA methylation pathways.