Abstract
DNA methylation is found throughout all domains of life, yet the extent and function of DNA methylation differ among eukaryotes. Strains of the plant pathogenic fungus Zymoseptoria tritici appeared to lack cytosine DNA methylation (5mC) because gene amplification followed by Repeat-Induced Point mutation (RIP) resulted in the inactivation of the dim2 DNA methyltransferase gene. 5mC is, however, present in closely related sister species. We demonstrate that inactivation of dim2 occurred recently as some Z. tritici isolates carry a functional dim2 gene. Moreover, we show that dim2 inactivation occurred by a different path than previously hypothesized. We mapped the genome-wide distribution of 5mC in strains with or without functional dim2 alleles. Presence of functional dim2 correlates with high levels of 5mC in transposable elements (TEs), suggesting a role in genome defense. We identified low levels of 5mC in strains carrying non-functional dim2 alleles, suggesting that 5mC is maintained over time, presumably by an active Dnmt5 DNA methyltransferase. Integration of a functional dim2 allele in strains with mutated dim2 restored normal 5mC levels, demonstrating de novo cytosine methylation activity of Dim2. To assess the importance of 5mC for genome evolution, we performed an evolution experiment, comparing genomes of strains with high levels of 5mC to genomes of strains lacking functional dim2. We found that presence of a functional dim2 allele alters nucleotide composition by promoting C to T transitions (C→T) specifically at CpA (CA) sites during mitosis, likely contributing to TE inactivation. Our results show that 5mC density at TEs is a polymorphic trait in Z. tritici populations that can impact genome evolution.
Highlights
DNA methylation is an important process for epigenetic regulation, and functions range from dynamic control of gene expression to transposon silencing and the maintenance of genome integrity [1,2]
We show extensive differences of 5mC levels within a single species of an important wheat pathogen. These differences were caused by inactivation of the DNA methyltransferase Dim2 in the majority of studied isolates
The mutation pattern is dependent on the presence of Dim2 and resembles a mitotic version of Repeat-Induced Point mutation (RIP)
Summary
DNA methylation is an important process for epigenetic regulation, and functions range from dynamic control of gene expression to transposon silencing and the maintenance of genome integrity [1,2]. DNA methylation has been detected on both cytosines and adenines in eukaryotes, cytosine DNA methylation (5mC) has been the focus of most studies so far. Various DNA methyltransferases (DNMTs) are involved in the establishment and maintenance of DNA methylation but the distribution and number of enzymes involved is highly variable in different kingdoms [5]. Enzymes of the DNMT1/MET1 class are maintenance methyltransferases that detect hemi-methylated DNA sequences, for example after replication [6,7,8]. Like DNMT3a and DNMT3b in mammals [9] and DRM in plants [10] act on sequences that are free of methylation, presumably by recognition of specific motifs or patterns [9,11]. DNMTs are often classified as maintenance or de novo enzymes their function is not necessarily limited to one or the other [12,13]
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.