'Extra' DNA base found to be stable in mammals

A study led by the University of Cambridge has discovered that a naturally occurring modified DNA base appears to be stably incorporated in the DNA of many mammalian tissues, possibly representing an expansion of the functional DNA alphabet. Published in the journal Nature Chemical Biology, the study determined that this rare ‘extra’ base, known as 5-formylcytosine (5fC), was found to be stable in living mouse tissues.

Since the structure of DNA was discovered more than 60 years ago, it’s been known that there are four DNA bases — G, C, A and T (guanine, cytosine, adenine and thymine) — whose structure determines the make-up of the genome. But in addition to G, C, A and T, there are also small chemical modifications, or epigenetic marks, which affect how the DNA sequence is interpreted and control how certain genes are switched on or off.

5fC is one of these marks, and it is formed when enzymes called TET enzymes add oxygen to methylated DNA — a DNA molecule with smaller molecules of methyl attached to the cytosine base. First discovered in 2011, it had been thought that 5fC was a ‘transitional’ state of the cytosine base which was then being removed from DNA by dedicated repair enzymes. However, the new research has found that 5fC can actually be stable in living tissue, making it likely that it plays a key role in the genome.

Using high-resolution mass spectrometry, the researchers examined levels of 5fC in living adult and embryonic mouse tissues, as well as in mouse embryonic stem cells. They found that 5fC is present in all tissues but is very rare, making it difficult to detect. Professor Shankar Balasubramanian, who led the research, noted, “If 5fC is present in the DNA of all tissues, it is probably there for a reason.”

The researchers fed cells and living mice with an amino acid called L-methionine, enriched for naturally occurring stable isotopes of carbon and hydrogen, and measured the uptake of these isotopes to 5fC in DNA. The lack of uptake in the non-dividing adult brain tissue pointed to the fact that 5fC can be a stable modification: if it was a transient molecule, this uptake of isotopes would be high.

“It had been thought this modification was solely a short-lived intermediate, 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,” said Professor Balasubramanian.

The researchers believe that 5fC might alter the way DNA is recognised by proteins. According to lead author Dr Martin Bachman, “Unmodified DNA interacts with a specific set of proteins, and the presence of 5fC could change these interactions either directly or indirectly by changing the shape of the DNA duplex. A different shape means that a DNA molecule could then attract different proteins and transcription factors, which could in turn change the way that genes are expressed.”

“This will alter the thinking of people in the study of development and the role that these modifications may play in the development of certain diseases,” added Professor Balasubramanian. “While work is continuing in determining the exact function of this ‘extra’ base, its position in the genome suggests that it has a key role in the regulation of gene expression.”

This article is a modified version of a news item published by the University of Cambridge under a Creative Commons Attribution 4.0 International licence.