Adenine, guanine, cytosine, and thymine. How these four DNA bases are ordered determines the makeup of a genome. And now, researchers have discovered an extra DNA base, called 5-Formylcytosine, or 5fC. They’re not sure what it does just yet, but it’s stable in every living tissue in the bodies of mice. The findings were published in Nature Chemical Biology this week.
In addition to the familiar A, G, C, and T, there are also many small chemical modifications to DNA that affect how sequences are interpreted. These are known as epigenetic marks, and they can control when certain genes are switched on or off. For example, when methyl groups – a chemical tag with one carbon and two hydrogen atoms – were added to a particular gene in ants, researchers doubled their size. In humans, babies born to mothers who smoke show epigenetic changes that aren’t seen in the babies of nonsmokers.
First discovered in 2011, 5fC is one of these marks. It’s formed when enzymes add oxygen to methylated DNA, specifically DNA with methyl attached to cytosine. But at the time, researchers thought that 5fC was just a transitional state of cytosine, which was being removed by repair enzymes. As it turns out, 5fC isn’t temporary: It’s stable in living tissue, which means that it likely plays an important role.
A team led by University of Cambridge’s Shankar Balasubramanian used high-resolution mass spectrometry to examine the levels of 5fC in living adult and embryonic mouse tissues, as well as in mouse embryonic stem cells. 5fC, they discovered, is present in all tissues, though it was difficult to detect.
“This modification to DNA is found in very specific positions in the genome – the places which regulate genes,” first author Martin Bachman of Cambridge says in a statement. “In addition, it's been found in every tissue in the body – albeit in very low levels.” Balasubramanian adds: “If 5fC is present in the DNA of all tissues, it is probably there for a reason.” It’s the most common in the brain, but even there, 5fC is present at 10 parts per million or less; elsewhere, that number drops to between 1 and 5 parts per million.
The team measured the uptake of stable carbon and hydrogen isotopes to 5fC in the DNA of mouse cells. If 5fC were a transient molecule, the isotope uptake would be high. But instead, they saw a lack of uptake in the adult brain tissue, suggesting that 5fC is, in fact, a stable modification. “It had been thought this modification was solely a short-lived intermediate,” Balasubramanian says, “but the fact that we've demonstrated it can be stable in living tissue shows that it could regulate gene expression and potentially signal other events in cells.”
While its function is a mystery for now, the team thinks that 5fC may alter the way that DNA is recognized by proteins, which could result in changes to the way genes are expressed.