Researchers report that non-coding “junk” DNA, far from being harmless and inert, could potentially contribute to the development of cancer. Their study “The mechanism of replication stalling and recovery within repetitive DNA,” which appears in Nature Communications, has shown how non-coding DNA can get in the way of the replication and repair of the genome, potentially allowing mutations to accumulate.
“Accurate chromosomal DNA replication is essential to maintain genomic stability. Genetic evidence suggests that certain repetitive sequences impair replication, yet the underlying mechanism is poorly defined. Replication could be directly inhibited by the DNA template or indirectly, for example by DNA-bound proteins,” wrote the investigators.
“Here, we reconstitute replication of mono-, di- and trinucleotide repeats in vitro using eukaryotic replisomes assembled from purified proteins. We find that structure-prone repeats are sufficient to impair replication. Whilst template unwinding is unaffected, leading strand synthesis is inhibited, leading to fork uncoupling.
“Synthesis through hairpin-forming repeats is rescued by replisome-intrinsic mechanisms, whereas synthesis of quadruplex-forming repeats requires an extrinsic accessory helicase. DNA-induced fork stalling is mechanistically similar to that induced by leading strand DNA lesions, highlighting structure-prone repeats as an important potential source of replication stress.
“Thus, we propose that our understanding of the cellular response to replication stress may also be applied to DNA-induced replication stalling.”
Disrupting the replication of the genome
It has been previously found that non-coding or repetitive patterns of DNA, which make up around half of our genome, could disrupt the replication of the genome.
But until now scientists have not understood the underlying mechanism, or how it could contribute to cancer’s development. In the new study, scientists at The Institute of Cancer Research 0ICR), London, reconstituted the entire process of DNA replication in a test tube in order to understand it more completely.
The researchers were able to describe how repetitive patterns of DNA are copied during replication and how they are able to stall replication entirely—increasing the risk of errors that can be an early driver of cancer. The team says this knowledge may eventually lead to better drugs and treatments.
The researchers also believe the work could also help to improve the diagnosis and monitoring of some cancers, such as bowel cancer, where common errors in copying the repetitive sequences of DNA indicate whether cancer is progressing.
Scientists at the ICR found that when the DNA replication machinery encountered repetitive DNA, it was able to unwind the DNA strands, but it sometimes failed to copy the opposite DNA strand. This error could cause replication to stall, resulting in collapse of the replication machinery in a manner similar to that induced by DNA damage.
The findings lead scientists to believe that repetitive DNA sequences could trigger a damage response signal indicating that errors in DNA replication have occurred and require repair.
DNA damage and ensuing genome instability are known to promote cancer formation and progression, so the research strengthens the link between junk DNA and cancer.
It was scientists at the ICR who, in the 1960s, provided the first conclusive evidence that DNA damage is the fundamental cause of cancer. In the early 2000s, ICR researchers then showed that drugs called PARP inhibitors could be genetically targeted against cancers with DNA repair mutations.
The researchers now hope that improved understanding of DNA replication, and how it can go wrong, might lead to new ways of treating the disease.
“We wanted to understand why it seems more difficult for cells to copy repetitive DNA sequences than other parts of the genome,” says Gideon Coster, PhD, team leader in genome replication at the ICR. “Our study suggests that so-called junk DNA is actually playing an important and potentially damaging role in cells, by blocking DNA replication and potentially opening the door to cancerous mutations.
“We now believe that repetitive DNA sequences trigger a response that is similar to the one induced by DNA damage, which we know can lead to cancer. Our study therefore fundamentally advances our understanding of cancer, and I’m hopeful it will help us come up with new treatments in the future.”