A 'hidden' modification of DNA plays a key role in liverwort

DNA is often seen as the blueprint of life—carrying the code to govern the development and traits of an organism—but “there are things beyond the DNA sequence,” says Xiaoqi Feng, a plant geneticist at the Institute of Science and Technology Austria (ISTA).

Through a mechanism called epigenetics, the instructions in DNA can be edited without changing the underlying code. Chemical modification is one way this can be done. For example, enzymes like methyltransferases can attach methyl groups to certain parts of DNA, typically on cytosine or adenine bases. Such chemical modifications can change how genes are expressed.

Depending on where a methyl group appears, scientists give these modifications different names, such as 5-methylcytosine (5mC), 6-methyladenine (6mA), or 4-methylcytosine (4mC). While 5mC and 6mA are widely studied and have been found across many organisms, 4mC has been known mainly in prokaryotes, organisms without a separate nucleus.

That’s now changing. In a recent study, Feng and her team discovered functionally important 4mC modifications in the plant kingdom (Cell 2025, DOI: 10.1016/j.cell.2025.03.014). The researchers found that 4mC plays a crucial role in sperm development in the plant Marchantia polymorpha, a liverwort often called a “living fossil.” Marchantia represents one of the earliest plant lineages to colonize land, and it still relies on water-based fertilization, where sperm swim through rain droplets to fertilize female plants.

“If you look at Marchantia’s leaves, you won’t find any 4mC,” Feng says. Her group found that 4mC appears only during sperm development, when methyltransferase genes switch on in a narrow developmental window and install 4mC specifically onto sperm DNA.

What’s more, 4mC isn’t just present—it’s functionally important. “If you don’t have 4mC,” Feng says, “the sperm swim much slower.”

Irina Arkhipova, a molecular evolutionary geneticist at the Marine Biological Laboratory whose work has helped show functional 4mC in microscopic freshwater animals called rotifers, praises the new Marchantia findings.

Both Arkhipova and Feng think that the use of 4mC modifications in plants and animals likely originated from bacteria, where such marks are widespread. “It speaks to the potential of horizontal gene transfer to reshape genome function in eukaryotes,” Arkhipova says.

In bacteria, 4mC functions as a self-defense mechanism, marking the bacteria’s own DNA so that it can be distinguished from any invading viral DNA, which lacks these methyl tags and can be destroyed by restriction enzymes. For bacteria, it’s a tightly regulated immune-like system —one that plants and animals appear to have co-opted and adapted for their own gene regulation.

“Though acquired independently, both plant and animal systems have evolved distinct ways of putting the bacterial methyl mark to different use,” Arkhipova says.

Until recently, 4mC had not been convincingly shown to function in eukaryotes. This finding in Marchantia —and others, like Arkhipova’s rotifers —suggests that 4mC, long thought to be exclusive to bacteria, can be co-opted by eukaryotes and used in essential developmental processes. Feng believes the developmental specificity that she found in the little liverwort raises a provocative question: Are there more such “hidden” epigenetic modifications that occur in short-lived stages or specialized cells that scientists have overlooked?