June 8, 2017  |  General

Widespread Methylation in Earliest Fungi Offers Clue to Expression of Essential Genes

The Joint Genome Institute recently announced results from a project that used SMRT Sequencing to generate high-quality genome assemblies and detect epigenetic modifications for fungal species that represent the earliest branches of that kingdom’s phylogeny. The work was done as part of the 1000 Fungal Genomes Project, which aims to better characterize a diverse range of fungal species.
Published in Nature Genetics, “Widespread adenine N6-methylation of active genes in fungi” comes from lead author Stephen Mondo, senior author Igor Grigoriev, and collaborators at JGI and other institutions. The major finding is that N6-methyldeoxyadenine (6mA) is seen at the earliest stages of fungal evolution, in groups that have not been studied much in genomics. “By and large, early-diverging fungi are very poorly understood compared to other lineages. However, many of these fungi turn out to be important in a variety of ways,” Mondo said.
The study involved analyzing 16 fungal genomes with SMRT Sequencing, which generates genome-wide epigenetic data while it sequences the DNA. Scientists discovered that 6mA, which is present at low levels in many plant and animal species, was much more common in these early-diverging fungi. As many as 2.8% of adenine bases were methylated, “far exceeding levels observed in other eukaryotes and more derived fungi,” they report in the paper. The previous highest 6mA rate was observed in Chlamydomonas reinhardtii, an alga with 0.4% of its adenines methylated.
The team also found that the presence of 6mA and 5-methylcytosine (5mC) is inversely correlated, and that 6mA appears to boost gene expression while 5mC suppresses it. “Our analysis has shown that 6mA modifications are associated with expressed genes and is preferentially deposited based on gene function and conservation, revealing 6mA as a marker of expression for important functionally-relevant genes,” Grigoriev said.
In the paper, the authors write, “Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.”
To learn more, watch this presentation from Mondo on 6mA in fungal genomes.

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