Replication timing assays may allow much earlier cancer detection

Scientists have discovered a DNA sequence that is involved in controlling the timing of DNA replication. Because alterations in DNA replication timing are associated with cancer, this discovery may lead to improved methods for cancer detection.

The research appears as the "Paper of the Week" in the October 1 issue of the Journal of Biological Chemistry, an American Society for Biochemistry and Molecular Biology journal.

Before a cell can divide, it must duplicate its DNA. Duplication, which occurs during the S phase of the cell cycle, is initiated at many replication origins in the DNA molecule. These replication origins fire at specific times throughout S phase, causing each segment of the genome to replicate at a precise time.

"S phase lasts about 8 hours in human cells and about 40 minutes in cells of the fission yeast, Schizosaccharomyces pombe," explained Joel A. Huberman of Roswell Park Cancer Institute. "In both cases, some portions of DNA molecules are nearly always duplicated early in S phase while other portions are nearly always duplicated late."

Until recently, very little was known about how cells control replication timing. Studies in budding yeast (Saccharomyces cerevisiae) have suggested that, by default, replication origins fire early in S phase, but they can be forced to fire later by flanking and internal DNA sequences. Now, Huberman and Chulee Yompakdee have discovered a stretch of DNA that verifies this hypothesis.

To study DNA replication timing, Huberman and Yompakdee used fission yeast as a model organism because of its small size, rapid cell cycle, and convenient genetics. "Human beings have 46 large chromosomes, while cells of the tiny fission yeast contain three much smaller chromosomes," noted Huberman. "Despite these differences, the process of DNA replication is very similar in humans and fission yeast."

The scientists found that the DNA surrounding many late-firing origins contains repeats of a 10-basepair sequence that is rich in the nucleic acid component, guanine. Yompakdee and Huberman named these repeats "Late Consensus Sequences" (LCS). They found that one copy of an LCS produced no detectable effect on replication timing, two copies produced a partial effect, and three copies caused replication to occur in late S phase. The researchers confirmed this finding by removing the LCSs from a late-replicating origin to convert it to an early-replicating origin.

"Interestingly," noted Huberman, "in many cancer cells, the normal order of DNA replication is altered: regions that should replicate late sometimes replicate early and vice versa." As a result, tests for DNA replication timing may eventually become a method for the early detection of cancer.

"Replication timing assays are one of many promising techniques that are currently being studied that may, in the future, allow much earlier cancer detection than is possible today," concluded Huberman.