Checkpoint protein blocks chromosome breaks at fragile sites

With 46 chromosomes and six feet of DNA to copy every time most human cells divide, it’s not surprising that gaps or breaks sometimes show up in the finished product – especially when the cell is under stress or dividing rapidly, as in cancer.

But what is surprising – according to Thomas Glover, Ph.D., a geneticist at the University of Michigan Medical School – is that the breaks don’t always occur at random. They happen at a few specific locations on chromosomes, when cells are under stress, during the stages in the cell cycle where DNA is copied, or replicated, and the cell splits into two identical daughter cells.

Scientists call them fragile sites, but the reasons for their inherent instability have remained a mystery. Now Glover and colleagues at the U-M Medical School and the Howard Hughes Medical Institute have discovered that a protein called ATR protects fragile sites from breaking during DNA replication. Results of their research will be published in the Dec.13 issue of Cell.

The discovery is significant because it is the first evidence of a major molecular pathway that regulates genome stability at chromosomal fragile sites. Since fragile site breaks are very common in some tumor cells and often occur near genes associated with tumors, defects in the ATR protein pathway may be involved in the progression of cancer.

Seventy-five fragile sites have been identified in the human genome, but most are rarely seen, according to Glover, a U-M professor of human genetics and of pediatrics, who directed the study. “Twenty sites account for 80 percent of all chromosome breaks, and five sites are responsible for nearly half the breaks,” says Glover.

Fragile sites are large and can extend over hundreds of thousands of DNA base pairs. “The most common fragile site, FRA3B, spans at least 500 kilobases,” says Anne M. Casper, a U-M graduate student in human genetics and first author on the Cell paper. “In different metaphases – the stage in the cell cycle when a cell divides into two identical cells – FRA3B breaks at different points throughout this 500-kilobase region, which contains a possible tumor suppressor gene called FHIT.”

Glover credits Casper with the discovery that ATR is the key to damage control at fragile sites. When she started her study, however, Casper was more interested in a related protein called ATM, which recognizes a specific type of DNA damage in replicating chromosomes.

“ATM responds to DNA double-strand breaks by signaling cells to stop replicating until the damage is repaired,” says Casper. “But when we studied cells without ATM, we found no difference in fragile site instability as compared to normal cells.”

“It turns out there is a parallel pathway, controlled by the ATR gene, which recognizes DNA damage at fragile sites,” Casper adds. “Instead of double-strand breaks, ATR recognizes stalled replication forks where DNA replication is blocked. For reasons we don’t understand, fragile sites seem to be difficult to copy. When replication starts to stall, ATR sends out a chemical signal telling the cell to shut down replication until it can fix the problem.”

To find out what happens during DNA replication in the absence of ATR protein, Casper used three different techniques to inactivate or disable ATR expression in human cell cultures used in the U-M study. To put cells under stress, she treated the cell cultures with aphidicolin, a substance that makes it harder for cells to make new DNA. Casper discovered that fragile site breaks were 5- to 10-times more common in cell lines without ATR as compared to normal cell controls.

“If you complete the cell cycle without replicating the fragile site and the cell continues into metaphase, our hypothesis is that the cell goes into metaphase with a gap in the chromosome,” says Glover. “That can lead to double-strand breaks, chromatid recombination and all sorts of things that aren’t supposed to occur.”

Casper found that increasing the amount of aphidicolin in cell cultures without ATR produced more fragile site breaks. She emphasized, however, that future research will be necessary to know whether stressed cells in living organisms have more chromosomal breaks during DNA replication and what the effects of those breaks could be.

“ATR regulates the activity of several important proteins in the chain of signals that controls cell replication, ” says Casper. “One of its primary targets is BRCA1. Mutations in the BRCA1 gene increase the risk of breast cancer. It is widely known that cells deficient in BRCA1 protein have a lot of chromosomal instability.”

Glover has studied fragile sites for more than 20 years and was the first scientist to characterize the most common sites. He first noticed these sites on all chromosomes during his post-doctoral fellowship at the University of Hawaii, while studying how folic acid deficiency is responsible for the chromosomal break in a rare condition called Fragile X Syndrome. Males with this syndrome have profound mental retardation. Glover also has shown that cell cultures exposed to very high doses of caffeine have more fragile site breaks.

One of the most intriguing things about fragile sites, says Glover, is that they are found in humans, primates, mice and possibly even yeast. “These are regions of DNA that are prone to breakage and difficult to replicate, so why have they been conserved by evolution for millions of years? Evolution should have blocked them out long ago, unless there was a good reason to keep them. At this point, we can only guess at the reason.”

The U-M research study was funded by the National Institutes of Health. Anne Casper is supported by a Predoctoral Fellowship from the National Science Foundation. Martin F. Arlt, Ph.D., a U-M post-doctoral fellow in human genetics, and Paul Nghiem, Ph.D., a Howard Hughes Medical Institute post-doctoral fellow at Harvard University and the Dana-Farber Cancer Institute, were collaborators on the study.