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Black Truffle Methylome Reveals Regulation of Transposable Elements

NEW YORK (GenomeWeb) – Using epigenetic regulation, the black truffle genome is able to control the transposable elements that make up a large portion of its DNA, an international team of investigators reported in Genome Biology.

Researchers led by the University of California, Los Angeles' Matteo Pellegrini examined the methylome of the black truffle, Tuber melanosporum, at various stages of its lifecycle. Through this, he and his colleagues found that transposable elements are far more likely than other parts of the genome to be methylated and silenced. That silencing, the researchers noted, occurs through a reversible process.

"This reversible methylation may increase the plasticity of the truffle genome, allowing it to adapt to its surroundings," Pellegrini said in a statement. "Because the truffle lives underground and doesn't have an active spore dispersal system, it might need this plasticity to adapt to sudden environmental changes."

More than 45,000 repeated elements are incorporated into the T. melanosporum genome where they make up nearly 60 percent of its 125 megabase genome. Epigenetic regulation, the researchers said, could help the truffle cope with such a large portion of transposable elements.

Pellegrini and his colleagues performed whole-genome bisulfite sequencing on black truffle samples from different developmental stages, including the fruit body and free-living mycelium stages. They aligned these reads against the T. melanosporum genome and estimated methylation levels for each cytosine covered by at least four reads, which they said covered some 90 percent of the cytosines in the truffle genome.

Generally, fruit body and free-living mycelium samples had similar methylation levels. For the fruit body and free-living mycelium stages, 44 percent and 41 percent of the cytosines they examined were methylated, respectively. The methylation level for CG sites was, on average, some 30 percent and 10 percent for non-CG sites.

DNA methylation, the researchers noted, was more common in regions containing transposable elements and less common in gene-rich regions. For instance, in fruit bodies, the researchers reported that genes and exons are weakly methylated, about 1 percent, while transposable elements are highly methylated at CG and non-CG sites, about 80 percent and 30 percent, respectively.

The researchers further reported that DNA methylation is negatively associated with transposon expression, in both fruit body and free-living mycelium, indicating that the methylation silences the elements.

"In Tuber, DNA methylation targets TEs in a nearly exclusive manner," Pellegrini and his colleagues wrote in their paper. "The functional consequence of this preferential targeting is that transposable element, but not gene, expression is largely repressed and that the extent of such repression is proportional to methylation levels."

Pellegrini and his colleagues also found a correlation between methylation and transposon size — the bigger the transposon, the more likely it was to be methylated — and between transposon methylation and nearby gene expression — cytosines of transposable elements close to highly expressed genes tended not to be methylated.

In filamentous fungi, two methylation-dependent transposable element silencing mechanisms have been reported, the researchers said, though one is reversible while the other is not.

By treating free-living black truffle mycelium with 5-azacytidine, a demethylating agent, and then subjecting them to bisulfite and RNA sequencing, the researchers found that the methylation-induced silencing of transposable elements was reversible and likely occurred through a process like Methylation Induced Premeiotically, or MIP.

"Instead of the methylated gene body or promoters that we usually see in plants and animals, the black truffle has very little gene body methylation and it appears that the methylation is occurring in the transposon," co-author Pao-Yang Chen from UCLA said in a statement. "All this means the truffle has a very unique pattern of DNA methylation which may play a role in the gene regulation."

Such regulation, Simone Ottonello from the University of Parma noted, may also affect commercially relevant traits like smell and color.

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