Pe'rigord black truffle (Tuber melanosporum Vittad.) is a gastronomic delicacy produced in southern Europe. The 125-megabase (Mb) genome of T. melanosporum is the largest sequenced fungal genome to date. In this project, we performed... more
Pe'rigord black truffle (Tuber melanosporum Vittad.) is a gastronomic delicacy produced in southern Europe. The 125-megabase (Mb) genome of T. melanosporum is the largest sequenced fungal genome to date. In this project, we performed whole bisulfite sequencing on the fruit body and the free-living mycelium, and observed a mosaic pattern of DNA methylation across the genome. The methylation is mainly in transposons but absent in genes, indicating that the fungal DNA methylation system appears to be very different from plant and mammalian ones. We examined whether DNA methylation of transposons upstream of transcription start sites (TSS) affects the transcription of the associated genes. As a preliminary result, we found that transposons are less methylated in the vicinity of highly expressed genes compared to poorly expressed genes. This association is even stronger in LTR-transposons. While the methylation patterns are very similar in fruit body and mycelium, we identified sever...
Methylation of cytosines (5(me)C) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation... more
Methylation of cytosines (5(me)C) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 show an increase of relative 5(me)C levels at the TSS and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methyl...
Research Interests:
Research Interests:
Research Interests:
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... more
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. 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 fre...
Research Interests:
Tuber melanosporum, also known in the gastronomic community as "truffle", features one of the largest fungal genomes (125 Mb) with an exceptionally high transposable element (TE) and repetitive DNA content (>58%). The main... more
Tuber melanosporum, also known in the gastronomic community as "truffle", features one of the largest fungal genomes (125 Mb) with an exceptionally high transposable element (TE) and repetitive DNA content (>58%). The main purpose of DNA methylation in fungi is TE silencing. As obligate outcrossing organisms, truffles are bound to a sexual mode of propagation, which together with TEs is thought to represent a major force driving the evolution of DNA methylation. Thus, it was of interest to examine if and how T. melanosporum exploits DNA methylation to maintain genome integrity. We performed whole-genome DNA bisulfite sequencing and mRNA sequencing on different developmental stages of T. melanosporum; namely, fruitbody ("truffle"), free-living mycelium and ectomycorrhiza. The data revealed a high rate of cytosine methylation (>44%), selectively targeting TEs rather than genes with a strong preference for CpG sites. Whole genome DNA sequencing uncovered multi...
Research Interests:
A novel protein family homologous to the sugar-binding antiviral protein cyanovirin-N (CVN) is described. CVN, an 11-kDa protein that, by binding to the high-mannose moiety of certain viral surface glycoproteins, blocks virus entry into... more
A novel protein family homologous to the sugar-binding antiviral protein cyanovirin-N (CVN) is described. CVN, an 11-kDa protein that, by binding to the high-mannose moiety of certain viral surface glycoproteins, blocks virus entry into target cells, has thus far been identified only in the cyanobacterium Nostoc ellipsosporum. Here we show that CVN belongs to a protein family identified by analysis of transcript sequences deriving from a gene expression profiling study conducted in the truffle Tuber borchii. Members of this family (named CyanoVirin-N Homology) are found in filamentous ascomycetes and in the fern Ceratopteris richardii. As revealed by 3D structure-based searches, all CVNH proteins have a predicted fold that matches the so far unique fold of the cyanobacterial polypeptide. The CVNH domain is a versatile protein module. In ferns and cyanobacteria it is found in secretory proteins. In filamentous ascomycetes it is found in nonsecretory monodomain proteins as well as part of multidomain proteins bearing functionally related modules such as the peptidoglycan and chitin-binding domain LysM. Transcript abundance data further indicate that the expression of different CVNH forms is modulated in response to nutrient availability. These findings have implications for the understanding of protein-oligosaccharide interaction in fungi and plants, and provide candidate polypeptides to be tested and exploited as antiviral agents.