Functional Consequences of Methylating the Unmethylated Yeast Genome*

Cytosine methylation in DNA is an important epigenetic mark in many higher eukaryotes, established in vivo by a variety of DNA methyltransferase enzymes (DNMTs). The genome-wide methylation patterns these enzymes establish have complex relations with gene transcription, chromatin architecture and histone modifications, only some of which may be attributable to direct cellular response to information contained in methylation patterns. To disentangle fundamental causes and consequences of DNA methylation from secondary correlations, we profiled the transcriptomes and methylomes produced by combinatorial knock-in of DNMT genes in Pichia pastoris, a yeast species lacking DNA methylation machinery. We find that all active DNMTs preferentially methylate the linker DNA separating nucleosomes along the chromatin fiber and produce distinct methylation patterns at differentially expressed genes. We study variations in methylation patterns established by different DNMTs and use a time-course experiment to capture adaptation of the yeast cells to de novo methylation distinguishing changes in gene expression directly caused by DNA methylation from those caused by stress response.