Research Horizons, July 09 - Everyone has fragile sites on their chromosomes that are particularly prone to breaking, making them hot spots for rearrangements that can lead to hereditary diseases and cancer. Georgia Tech School of Biology associate professor Kirill Lobachev is trying to understand what's special about these regions, the consequences of the breaks, and the pathways that are involved in promoting and repairing these breaks.

"It is becoming clear that the fragile sites often contain unstable repetitive sequences that can adopt unusual DNA structures," says Lobachev. "We think that everyone is probably a carrier of these unstable motifs that can cause chromosomes to break anytime, so we ultimately want to be able to predict where a chromosome is going to break and how frequently this break will occur, and determine if we can prevent it."

Determining whether a particular chromosomal region is predisposed to breakage requires knowledge about the structural parameters of the unstable sequences that make chromosomes fragile, such as their size or composition of the genetic sequences they contain. Using the yeast Saccharomyces cerevisiae as a model organism, Lobachev's laboratory has been able to mimic some of the structural instability that cancer cell chromosomes exhibit.

In a recent study, Lobachev and colleagues demonstrated that DNA replication machinery sometimes stalls when it reaches a long sequence of palindromes - sequences that read the same way backward and forward. Further analysis has shown that chromosomes break when DNA replication is slowed or altered.

"Long palindromes were known to change the shape of DNA from a double helix into a hairpin or cruciform structure, but this was one of the first studies to show that these changes could affect DNA integrity," explains Lobachev.

In addition, Lobachev and postdoctoral fellow Vidhya Narayanan determined that palindromic sequences induce a particular type of DNA break that is a precursor to a process involved in cancer called gene amplification. Amplification of genes involved in metabolism or inactivation of drugs can lead to chemotherapy resistance, and amplification of genes that turn normal cells into cancer cells are known to occur in several late-stage cancers.

They showed that gene amplification depends on the location of an oncogene relative to the break - called a hairpin-capped double strand break - and the end of the chromosome. The study indicated that restricting breakage of the unstable sequences may be a promising strategy for pharmaceutical cancer prevention and treatment.

In the future, knowing what genetic sequences are more likely to lead to chromosomal fragility and being able to explore genetic pathways involved in this process may help researchers identify persons who might be prone to developing cancer, adds Lobachev.

By Abby Vogel
Photos By Gary Meek