ArticleGenome biology2014
Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 92 citations in OpenAlex.
- 5mC and 6mA DNA Methylation in the Fungal Kingdom: From Genome Defense to Epigenetic Regulation.Epigenomes · 2026Review
- DNA methylation is associated with phenotypic divergence between the dermatophytes Trichophyton rubrum and Trichophyton violaceum.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Epigenetic regulation of mycorrhizal symbioses: from plastic responses to transgenerational legacies.The New phytologist · 2026Review
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- High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae.Genome research · 2025Article
- DNMT3L inhibits hepatocellular carcinoma progression through DNA methylation of CDO1: insights from big data to basic research.Journal of translational medicine · 2024Article
- Epigenetic regulation of nuclear processes in fungal plant pathogens.PLoS pathogens · 2023Review
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- The ectomycorrhizal fungusProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Epigenetic Modification: A Key Tool for Secondary Metabolite Production in Microorganisms.Frontiers in microbiology · 2022Review
- DNA methylation across the tree of life, from micro to macro-organism.Bioengineered · 2022Article
- Temporal genome-wide DNA methylation signature of post-smolt Pacific salmon challenged withEpigenetics · 2021Article
- Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae.Genome biology and evolution · 2021Article
- Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen.PLoS genetics · 2021Article
- Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes.The New phytologist · 2021Review
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- Comparative analysis of genome-wide DNA methylation inEpigenetics · 2020Article
- Evaluation of DNA Methylation Changes by CRED-RA Analysis Following Prednisone Treatment of Endophyte,Indian journal of microbiology · 2020Article
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Authors and funding
8 authors at 4 institutions in 5 countries.
Funding
Abstract
backgroundWe 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.
resultsWhole-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.
conclusionsEvidence 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.
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