Brewer, B. J.; Martin, R.; Ramage, E.; Payen, C.; Di Rienzi, S. C.; Zhao, Y.; Zane, K.; Verhey, J.; Galey, M.; Miller, D. E.; Ong, G. T.; McKee, J. L.; Alvino, G. M.; Dunham, M. J.; Raghuraman, M. K.

Gene amplification is a potent driver of evolution and is thought to contribute to genetic diseases, including cancer. The yeast Saccharomyces cerevisiae is a powerful organism for understanding amplification mechanisms. When yeast is grown long term in sulfate-limiting chemostats, amplification of the gene that encodes the primary sulfate transporter, SUL1, is a common outcome. Here we describe a form of SUL1 amplification in which multiple copies of the right terminal region of chromosome II are appended in tandem to a native telomere. We find this form of amplicon when we delete the origin of replication next to SUL1 or delete a variety of genes involved in DNA metabolism. It is the only form of amplification found in a yku70{triangleup} mutant suggesting that unprotected telomeres are involved. We propose that these terminal addition events occur when the unprotected 3' G1-3T telomeric sequence invades a short (~7 bp) internal telomere sequence (ITS) to begin a form of microhomology-mediated break-induced replication (mmBIR) that has been documented in type-I survivors of telomerase mutants. In addition to amplification of the right end of chromosome II we also find that telomeres containing the sub-telomeric repeat Y' experience similar tandem amplification events and show that their formation is reduced in a pol32{triangleup} mutant, a gene required for mmBIR. Within individual amplicons the ITSs and Y's are nearly identical, suggesting that the multiple copies of the amplified region are generated in a single mmBIR event that we describe as pseudo-rolling circle mmBIR. A similar amplification event at the P-telomere of human chromosome 18 has four copies of a ~54 kb region separated by ITSs of nearly identical size. This finding suggests that these additional copies of the terminal fragment of human chromosome 18 arose by the same pseudo-rolling circle mechanism, perhaps during a period of telomeric stress.