Portions of newly copied DNA that grow piece by piece may be imperfectly stitched together, which is seldom a problem, since poor genomic needlework is usually redone as necessary. Copied DNA, however, is often folded and tucked away quickly, which means that some ragged seams may remain, causing snags down the line.
Hasty tailoring of this sort, say University of Edinburgh researchers, may cause mutations to occur in bunches at regulatory elements. These researchers noticed that the 5′ ends of Okazaki fragments have significantly increased levels of nucleotide substitution. The Okazaki fragments, which form along the lagging strand of replicating DNA, typically undergo processing to form continuous, error-free stretches of DNA. But the processing may be incomplete if DNA’s error-correcting machinery cannot reach all the errors. Hence mistakes that occur during replication may remain uncorrected, giving rise to mutations.
To explore this sort of mutational mechanism, the scientists, led by Martin Taylor, Ph.D., and Andrew Jackson, Ph.D., devised a technique to track where DNA-copying errors were likely to occur. The technique, which was used for studies conducted at the Medical Research Council's Human Genetics Unit, was described January 26 in Nature, in an article entitled, “Lagging-strand replication shapes the mutational landscape of the genome.”
“Using a novel method, emRiboSeq, we map the genome-wide contribution of polymerases, and show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-α (Pol-α) is retained in vivo, comprising approximately 1.5% of the mature genome,” wrote the authors. “We propose that DNA-binding proteins that rapidly re-associate post-replication act as partial barriers to Pol-δ-mediated displacement of Pol-α-synthesized DNA, resulting in incorporation of such Pol-α tracts and increased mutation rates at specific sites.”
The scientists emphasized that the mutations they studied tended to occur at points in the important regulatory switches that often control when genes are switched on and off. These sites are therefore more likely than other regions to have trapped scaffold DNA and its associated errors.
Mistakes in these crucial genetic sequences can change or destroy the regulatory switch, which can lead to genetic diseases, alter susceptibility to common diseases, or contribute to the development of cancer. The researchers hope that this knowledge will aid in the hunt for disease causing mutations, particularly in the difficult to interpret regions of the genome that do not code for proteins.
“We have been aware of striking patterns in how DNA changes for several years but couldn't explain why the patterns were there,” said Dr. Taylor. “This new work gives us a mechanism and revealed previously unseen patterns that are probably the most important finding, as they point to sites in our DNA that are likely to have a high rate of damaging mutations.”
“Our research groups are very proud to have devised an important new method to track polymerase enzymes that copy our genome within the cell itself,” added Dr. Jackson. “This shows us that despite DNA replication being an amazingly accurate process, errors do occur that cluster at important sites in the genome.”
The authors of the Nature paper concluded that there is “a mutational cost to chromatin and regulatory protein binding, resulting in mutation hotspots at regulatory elements, with signatures of this process detectable in both yeast and humans.”