Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast

Abstract

We report here that a normal budding yeast chromosome (ChrVII) can undergo remarkable cycles of chromosome instability. The events associated with cycles of instability caused a distinctive "sectoring" of colonies on selective agar plates. We found that instability initiated at any of several sites on ChrVII, and was sharply increased by the disruption of DNA replication or by defects in checkpoint controls. We studied in detail the cycles of instability associated with one particular chromosomal site (the "403 site"). This site contained multiple tRNA genes known to stall replication forks, and when deleted, the overall frequency of sectoring was reduced. Instability of the 403 site involved multiple nonallelic recombination events that led to the formation of a monocentric translocation. This translocation remained unstable, frequently undergoing either loss or recombination events linked to the translocation junction. These results suggest a model in which instability initiates at specific chromosomal sites that stall replication forks. Forks not stabilized by checkpoint proteins break and undergo multiple rounds of nonallelic recombination to form translocations. Some translocations remain unstable because they join two "incompatible" chromosomal regions. Cycles of instability of this normal yeast chromosome may be relevant to chromosome instability of mammalian fragile sites and of chromosomes in cancer cells.[Keywords: Chromosome instability; checkpoints; fragile sites] Supplemental material is available at http://www.genesdev.org.

Recombination at DNA replication fork barriers is not universal and is differentially regulated by Swi1

“…Previous studies have shown that DNA replicationassociated fragile sites can contain tRNA genes, implicating these elements in the generation of recombinogenic lesions (11,20). Also, tRNA genes use gene-conversion mechanisms to maintain their genome-wide sequence uniformity, suggesting they have recombination-initiating potential (38)(39)(40).…”

“…2E). This idea might provide an attractive explanation of why some S. cerevisae fragile sites contain multiple elements capable of blocking DNA replication, including tRNA genes (11). Some of these sites, however, become fragile only when the checkpoint pathways are perturbed (20), indicating that complex sites can be endured during normal S-phase and that the relationship between the level of the replicative blockage and fragility is not simple.…”

“…However, sites that aberrantly mediate gross chromosomal rearrangements are not programmed to initiate recombination; rather, they have some inherent instability or become unstable because of exogenous factors, generating an unscheduled recombinogenic potential (3,10). Studies in yeast aimed at identifying naturally occurring fragile chromosomal regions have found that such sites can be complex in nature and can consist of aggregates of distinct genetic elements, including transposons, LTRs of transposons, and tRNA genes (11,12). Interestingly, these sites exhibit higher levels of instability when DNA replication is compromised (11)(12)(13), suggesting that the inherent instability of these sites is related to DNA replication.…”

“…Studies in yeast aimed at identifying naturally occurring fragile chromosomal regions have found that such sites can be complex in nature and can consist of aggregates of distinct genetic elements, including transposons, LTRs of transposons, and tRNA genes (11,12). Interestingly, these sites exhibit higher levels of instability when DNA replication is compromised (11)(12)(13), suggesting that the inherent instability of these sites is related to DNA replication. This hypothesis is consistent with the proposal that perturbations in DNA replication may be among the primary oncogenic stresses in tumor formation (14).…”

Ccr4 contributes to tolerance of replication stress through control ofCRT1mRNA poly(A) tail length

“…To date, both Mec1 and Rad53 are implicated in stabilization of stalled replication forks (Lopes et al, 2001;Tercero and Diffley, 2001). Mec1-dependent signaling is also required for the fidelity of replication across regions of the genome that are prone to fork stalling and collapse, known as replication slow zones (RSZs) (Cha and Kleckner, 2002) or fragile sites (Lemoine et al, 2005;Admire et al, 2006). These fragile regions appear sensitive to deoxynucleotide levels, reduced DNA polymerase activity and compromised checkpoint function; for example, deletion of SML1 greatly reduces chromosome breakage at fragile sites in mec1 mutants (Cha and Kleckner, 2002).…”