DNA Replication, Not Chemical Reaction, Primary Cause of Common Mutation

A new study by a Ludwig Cancer Research team challenges long-held beliefs about the origin of the most prevalent type of DNA mutation seen in the genome. The team, led by Marketa Tomkova, discovered that the common cytosine (C) to thymine (T) mutation at CpG sites is primarily caused by errors during DNA replication rather than a spontaneous chemical reaction with water.

"It has long been assumed that C to T mutations are caused by a random chemical reaction," said Tomkova. “Our study demonstrates that this is not entirely correct. Rather, the mutation is primarily produced when the cell copies its genome to divide and is mainly caused by the tendency of a key component of the cell's DNA-copying machinery to make editing mistakes when it encounters methylated cytosines."

The study, published in Nature Genetics, utilized a novel DNA sequencing technology called Polymerase Error Rate Sequencing (PER-seq) to analyze over 28 billion bases across more than 130 million DNA molecules. This method allowed researchers to distinguish between genuine replication errors and experimental artifacts.

Results showed that DNA polymerase ε (Pol ε), a key component of the cell's DNA-copying machinery, is more prone to making mistakes when encountering methylated cytosines. Even normal Pol ε produced mutations at methylcytosine sites at seven times the rate observed for nonmethylated cytosines.

This discovery has significant implications for cancer biology, risk assessment of environmental carcinogens, and understanding drug resistance in cancer therapy. It explains why CpG to TpG mutations accumulate with age and vary in frequency across tissues and tumors, as different cell types proliferate at different rates.

The findings also suggest that the accumulation of these mutations could be used as a cellular "clock" to determine cell age and potentially track cancer growth rates before drug resistance develops.