title: Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content.
abstract: BACKGROUND
  We investigated how an extremely transposon element (TE)-rich organism such as the plant-symbiotic ascomycete truffle Tuber melanosporum exploits DNA methylation to cope with the more than 45,000 repeated elements that populate its genome.
  
  
  RESULTS
  Whole-genome bisulfite sequencing performed on different developmental stages reveals a high fraction of methylated cytosines with a strong preference for CpG sites. The methylation pattern is highly similar among samples and selectively targets TEs rather than genes. A marked trend toward hypomethylation is observed for TEs located within a 1 kb distance from expressed genes, rather than segregated in TE-rich regions of the genome. Approximately 300 hypomethylated or unmethylated TEs are transcriptionally active, with higher expression levels in free-living mycelium compared to fruitbody. Indeed, multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs are found almost exclusively in free-living mycelium. A reduction of DNA methylation, restricted to non-CpG sites and accompanied by an increase in TE expression, is observed upon treatment of free-living mycelia with 5-azacytidine.
  
  
  CONCLUSIONS
  Evidence derived from analysis of the T. melanosporum methylome indicates that a non-exhaustive, partly reversible, methylation process operates in truffles. This allows for the existence of hypomethylated, transcriptionally active TEs that are associated with copy number variant regions of the genome. Non-exhaustive TE methylation may reflect a role of active TEs in promoting genome plasticity and the ability to adapt to sudden environmental changes.
authors.forename: Barbara
authors.initials: B
authors.lastname: Montanini
authors.forename: Pao-Yang
authors.initials: PY
authors.lastname: Chen
authors.forename: Marco
authors.initials: M
authors.lastname: Morselli
authors.forename: Artur
authors.initials: A
authors.lastname: Jaroszewicz
authors.forename: David
authors.initials: D
authors.lastname: Lopez
authors.forename: Francis
authors.initials: F
authors.lastname: Martin
authors.forename: Simone
authors.initials: S
authors.lastname: Ottonello
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
mesh_terms: D001203:Ascomycota / Q000235:genetics / Q000254:growth & development*; D001374:Azacitidine / Q000494:pharmacology; D056915:DNA Copy Number Variations; D019175:DNA Methylation / Q000187:drug effects; D004251:DNA Transposable Elements / Q000187:drug effects; D004271:DNA, Fungal / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects; D005800:Genes, Fungal; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D004271:DNA, Fungal; D001374:Azacitidine
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