Expanding the DNA alphabet: ‘extra’ DNA base found to be stable in mammals
A team of scientists, including Cancer Research at Bath researcher Dr Adele Murrell, has found that a rare ‘extra’ DNA base is present in the DNA of many mammalian tissues, possibly representing an expansion of the functional DNA alphabet. This discovery could give scientists a clearer understanding of how the activity of genes is regulated in the body.
The genetic code is normally made up of four bases: adenine, thymine, cytosine and guanine, (A, T, C and G). The combination of these bases in the strands of DNA instructs the cell how to make proteins, the molecular machines of the cell.
In addition to A, T, C and G, there are also small chemical modifications, ‘epigenetic marks’, which affect how the DNA sequence is interpreted and control how certain genes are switched on or off.
The new study, led by the University of Cambridge, is published in the prestigious journal Nature Chemical Biology. It found that an epigenetic mark called 5-formylcytosine (5fC), previously thought to be a temporary modification, is stable in living mouse tissues. This suggests that it plays a key role in cellular function.
5fC is an epigenetic mark, 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, this 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.
While its exact function is yet to be determined, 5fC’s physical position in the genome makes it likely that it plays a key role in gene activity.
Dr Murrell, currently a reader in the Department of Biology & Biochemistry, collaborated on the study whilst at the Cancer Research UK Cambridge Institute. She explained: “It was previously thought that 5fC was only a short-lived base, but our study shows that it is present in living tissues, suggesting it has an important role in how gene activity is regulated.
“Since the structure of DNA was discovered more than 60 years ago, scientists have believed the genetic code was made of just four bases, however this research suggests that the picture is more complex than that.”
“This modification to DNA is found in very specific positions in the genome – the places which regulate genes,” said the paper’s lead author Dr Martin Bachman, who conducted the research while at Cambridge’s Department of Chemistry. “In addition, it’s been found in every tissue in the body – albeit in very low levels.”
Altering DNA recognition by proteins
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 – the body’s master cells which can become almost any cell type in the body.
They found that 5fC is present in all tissues, but is very rare, making it difficult to detect. Even in the brain, where it is most common, 5fC is only present at around 10 parts per million or less. In other tissues throughout the body, it is present at between one and five parts per million.
The researchers believe that 5fC might alter the way DNA is recognised by proteins. “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,” said Bachman. “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,” said Professor Shankar Balasubramanian of the Department of Chemistry and the Cancer Research UK Cambridge Institute, who led the research. “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.”
The research was supported by Cancer Research UK, the Wellcome Trust and the Biotechnology and Biological Sciences Research Council UK.
According to the latest Research Excellence Framework (REF) 2014, 85 per cent of Bath research in this area was assessed to be either 'world-leading' or 'internationally excellent'.
To access the latest paper, 5-Formylcytosine can be a stable DNA modification in mammals, in Nature Chemical Biology see http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1848.html. For more information on Cancer Research at Bath see http://www.bath.ac.uk/science/research/cancer-research/.
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