Insight into DNA’s "Weakest Links" May Yield Clues to Cancer Biology

The chromosomes of mammals, including humans, contain regions that are particularly prone to breaking under conditions of stress and in cancer. Now, new research by geneticists at Duke University Medical Center finds that yeast cells also contain such weak links in DNA and begins to reveal the molecular characteristics of these links that might help to explain them.

The findings, published in the March 11, 2005, issue of Cell, suggest that yeast may offer a useful model system for studying the fundamental properties of so-called DNA fragile sites, providing new insight into the chromosomal instability found in cancer cells, said the researchers. “If you look at solid tumors in humans, you see that the chromosomes of cancer cells exhibit incredible instability,” said Thomas Petes, Ph.D., chair of genetics and microbiology at Duke. “Now, we have been able to mimic some of that instability in yeast cells and can begin to ask whether there is anything special that defines those places where chromosomes tend to break.”

Organisms normally exhibit extremely low rates of mutation and chromosomal rearrangements. Conditions that elevate genomic instability lead to an increase in cell death and, in some cases, an increased incidence of cancer, Petes said. Earlier work by other researchers had shown that mammalian chromosomes break at particular sites under certain types of stress or upon exposure to particular drugs, he said. Evidence has suggested that chromosomes break when DNA replication – the process by which DNA copies itself before cell division – slows or stalls. However, the DNA characteristics that make particular sites vulnerable to breakage had remained unclear, he said.

The researchers slowed DNA replication in yeast cells by reducing the availability of one form of DNA polymerase, which are enzymes critical in DNA duplication. Yeast with abnormally low levels of DNA polymerase exhibited higher frequencies of chromosomal loss and aberrations than normal, resulting when broken chromosomes re-joined with others to form novel arrangements, the researchers reported. Through further examination of breakpoints in a small region of one chromosome, the researchers found that the fragile sites occurred at locations along the DNA containing “retrotransposons” called Ty elements. Retrotransposons are mobile gene segments that duplicate themselves and insert the new copies back into other sites in the genome.

The most common breakpoint involved two Ty elements in an inverted, head-to-head orientation, they reported. That finding led the researchers to suggest one possible mechanism for chromosomal breaks and rearrangements. A delay in DNA synthesis leads to an increase in single-stranded DNA, the researchers explained. While DNA is in a single-stranded form, multiple copies of retrotransposons are more likely to interact, forming a kink in the DNA. Rearrangements may occur when those kinks are improperly excised and repaired by rejoining with retrotransposons on other chromosomes. “The current findings offer the first indication that yeast have fragile sites,” said Francene Lemoine, Ph.D., of Duke, first author of the study. “The finding will allow us to develop a simple model to study fragile sites in a way that can’t be done in more complex organisms.”

The findings suggest that mammalian and yeast fragile sites may have common features, an indication that a common mechanism may underlie their occurrence, Petes said. Fragile sites in mammalian cells tend to duplicate late and also include sequences prone to forming kinks, or hairpin structures, like those observed in yeast. “The findings may ultimately help us better understand what goes wrong in cancer cells, an important step in developing a better plan of attack against the disease,” Petes added.

Collaborators on the study include Natasha Degtyareva, of Emory University, and Kirill Lobachev, of the Georgia Institute of Technology. The work was supported by the National Institutes of Health, the National Cancer Institute and the National Science Foundation.