‘DNA makes RNA makes protein’ is a fundamental principle in molecular biology. The process of gene expression, namely creating RNA from a specific DNA sequence, is tightly regulated in different ways. The DNA itself carries a reversible chemical modification – called methylation – that can influence gene expression.
Scientists at EMBL Rome, in collaboration with Tim Bestor at Columbia University in New York and John Edwards at Washington University in St. Louis, Missouri, now show for the first time how DNA methylation instructs cells to repress parts of their genome by inducing the assembly of a silencing complex. Their work was published in Proceedings of the National Academy of Sciences (PNAS).
DNA methylation is the only epigenetic modification known to be inherited when cells divide, meaning once a specific DNA sequence is methylated it remains in that state throughout the lifespan of an organism. Methylation acts like a mark on the DNA that inactivates some genes in a manner that is dependent on the parental origin. DNA methylation also acts as a cellular defense mechanism against parasitic pieces of DNA that can move within the genome and threaten its integrity. The modification instructs cells to repress these so-called transposons.
Despite four decades of research, the precise mechanism by which DNA methylation represses gene expression has remained unknown. The scientists in Mathieu Boulard’s group found that the protein TRIM28, which is a known silencing factor that had not been previously linked to DNA methylation, is required for the repression of methylated genes. However, TRIM28 does not directly interact with DNA, which meant that other proteins must be involved in the process.
Using a combination of genetic and biochemical analyses they showed that in the presence of DNA methylation, TRIM28 binds to the enzyme OGT, which modifies other proteins by adding sugar groups (a process known as glycosylation). They also show that methylation-directed glycosylation of specific DNA binding proteins prevents methylated genes from being expressed.
“Our study reveals that protein glycosylation plays a central role in DNA methylation, thereby unveiling the mechanism behind the most studied epigenetic modification,” explains Matthieu Boulard, Group Leader at EMBL Rome.
The first evidence that glycosylation plays a major function in gene regulation came from another study at EMBL, which showed that glycosylation represses developmental genes in certain cells during the development of the fruit fly Drosophila. However, gene repression in this case does not involve DNA methylation.
Boulard says: “We show that DNA methylation in mammals induces gene silencing by activating a process that induces glycosylation of regulatory factors. These findings address one of the core questions in the field of epigenetics, which is the nature of the mechanism that represses methylated promoters.”
M. Boulard et al. PNAS, published online 09 June 2020. Methylation-directed glycosylation of chromatin factors represses retrotransposon promoters. DOI: https://doi.org/10.1073/pnas.1912074117
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