Unusual Epigenetic Finding Explained by Mycoplasma Contamination

A new study shows that the epigenetic mark 6mdA is not present in humans or other mammals, and its previously reported detection in animals was probably the result of limitations of the technology used and bacterial contamination of samples.

A few years ago, numerous research groups reported that they had found 6mdA in various animal species, and even in human cells. These findings stimulated not only major interest among the research community, but also some questions. One of these concerned the levels of 6mdA detected, which were so low that scientists wondered whether such a rare epigenetic signal could truly have a function.

Colm Nestor's group at Linköping University tried to replicate the studies and was unable to detect 6mdA in human or mouse cells. Eventually, they detected 6mdA in two samples of human cells, but it turned out that both of the samples were contaminated with mycoplasma bacteria. The researchers suspected that the epigenetic mark came from the bacteria and not the human cells. They treated the cells with antibiotics against mycoplasma and saw the 6mdA signal disappear.

The LiU researchers believe that contamination with mycoplasma bacteria is an underestimated problem in epigenetic research. Since mycoplasma bacteria can exist not only outside cells but also inside cells in the body, it may be that this bacterium is present, but undetected, in human samples. For most types of bacteria, researchers can easily detect if cells cultured in the laboratory are contaminated. However, this is not the case for mycoplasma contamination, which requires special testing.

The LiU researchers soon discovered that it is not only mycoplasma bacteria that cause problems for researchers studying the 6mdA mark. They also found problems with several methods used to detect this epigenetic modification. "We realised that the 6mdA 'signals' detected by these techniques were simply noise. However, as a consequence of several complex technical problems the background noise in several of the methods was not random, but appeared to be a true signal. Now we can say without a doubt that 6mdA is not present in mammals," explained Colm Nestor, senior author of a paper published in Science Advances today.

"When we analyse very rare phenomena, we must be extremely careful and consider whether we truly can measure them using the methods we have chosen. With respect to 6mdA, a lot of time and money can be saved, and a lot of disappointment avoided, if researchers stop studying something that is simply not there," Nestor added.