Studying the role of DNA methylation in moss development

Epigenetic modifications such as DNA methylation and histone modifications are a means of regulating gene expression and maintaining genome integrity in eukaryotes. DNA methylation occurs on the fifth carbon of a Cytosine and is usually regarded as a repressive mark as it may block the transcriptional machinery. In plants, DNA methylation occurs in three contexts; CG, CHG and CHH (where H is any nucleotide but G), and is targeted to genes and transposons. DNA methylation in plants carries a role of both the silencing of transposable elements and controlling gene expression. Despite the long-established role of DNA methylation in development in various flowering plants, such a connection in early land plants is yet to be shown. Here we aimed to identify genes regulated by DNA methylation that are involved in moss morphology and development. To that end we quantified developmental phenotypes of moss plants hypomethylated in CG, CHG or CHH methylation mutants and correlated them with whole transcriptome profiles. Differential expression analyses show enrichment for particular gene ontologies associated with morphological changes. Correlation between differentially expressed genes to differentially methylated ones, identified genes that could potentially regulated directly DNA methylation. Overall, our study substantiates the role of DNA methylation in gene regulation and development in plants.