One feature of organisms is the ability to adapt to the environment. Thanks to this ability, organisms could survive on the earth in changeable conditions. Such an ability is supported by flexibility of the genome. On the other hand, the genome determines the design of life. Therefore, changing of genomic information, if it occurs randomly, is likely to be toxic for organisms. Indeed, it is known that instability causes cancer and premature senescence. We are studying how cells change their genome safely. One attractive mechanism for this change is gene amplification. Gene amplification makes it possible to create new genes and modify them without destroying the original one.

The ribosomal RNA gene repeats (rDNA) are one of the most characteristic amplified genes in eukaryotic chromosomes. The repeats consist of more than 100 tandem units occupying large regions of the chromosome(s) in most organisms. Cells are known to deal with this “unusual domain” in a unique manner. In particular, repeated gene families such as the rDNA are one of the most fragile sites for deletional recombination. Even though the rDNA is susceptible to this kind of instability, each organism is known to maintain a specific copy number of rDNA repeat, thereby indicating the presence of a mechanism for maintenance of copy number. We have been studying this mechanism and found a unique amplification system that uses replication fork blocking activity. The replication fork barrier site (RFB) inhibits the replication fork and causes DNA double strand breaks (DSBs). These DSBs are then repaired by recombination. If the broken end recombines with an unequal sister-chromatid, some copies are replicated twice and the copy number increases. In this way, amplification takes place (see Fig.1).

We have been analyzing amplification of the rDNA as a model system to understand how the rDNA is stabilized (Fig.1). Interestingly, manipulation of the mechanism to change rDNA stability also changes the lifespan of the cell and induces other unusual phenotypes (Fig.2). These features suggest that the rDNA has some extra-coding functions that are not yet identified. Research into these extra-coding functions of the rDNA is going on now.

Repeating genes within genomes are maintained with similar sequences by an unusual type of evolution called “concerted evolution”, where repeats in an array evolve “in concert” via continual turnover of repeats by recombination. In concerted evolution, a mutation that occurs in one of the repeating genes can spread to all of the repeats. We have shown the absolute levels of sequence variation within the rDNA, and this work demonstrates that the rDNA is evolving via concerted evolution.