New functions of Ctf18-RFC in preserving genome stability outside its role in sister chromatid cohesion

Abstract

Expansion of DNA trinucleotide repeats causes at least 15 hereditary neurological diseases, and these repeats also undergo contraction and fragility. Current models to explain this genetic instability invoke erroneous DNA repair or aberrant replication. Here we show that CAG/CTG tracts are stabilized in Saccharomyces cerevisiae by the alternative clamp loader/unloader Ctf18-Dcc1-Ctf8-RFC complex (Ctf18-RFC). Mutants in Ctf18-RFC increased all three forms of triplet repeat instability--expansions, contractions, and fragility--with effect over a wide range of allele lengths from 20-155 repeats. Ctf18-RFC predominated among the three alternative clamp loaders, with mutants in Elg1-RFC or Rad24-RFC having less effect on trinucleotide repeats. Surprisingly, chl1, scc1-73, or scc2-4 mutants defective in sister chromatid cohesion (SCC) did not increase instability, suggesting that Ctf18-RFC protects triplet repeats independently of SCC. Instead, three results suggest novel roles for Ctf18-RFC in facilitating genomic stability. First, genetic instability in mutants of Ctf18-RFC was exacerbated by simultaneous deletion of the fork stabilizer Mrc1, but suppressed by deletion of the repair protein Rad52. Second, single-cell analysis showed that mutants in Ctf18-RFC had a slowed S phase and a striking G2/M accumulation, often with an abnormal multi-budded morphology. Third, ctf18 cells exhibit increased Rad52 foci in S phase, often persisting into G2, indicative of high levels of DNA damage. The presence of a repeat tract greatly magnified the ctf18 phenotypes. Together these results indicate that Ctf18-RFC has additional important functions in preserving genome stability, besides its role in SCC, which we propose include lesion bypass by replication forks and post-replication repair.

Figure 1. Contraction, expansion, and fragility phenotypes of SCC mutants.

For all panels, * denotes p<0.05 and ** designates p<0.01 compared to the respective wild type strain. All assays are described in Table S1. (A) Contraction rates of (CAG)₂₀ and contraction frequencies of (CAG)₇₀, normalized to wild type. (B) Percentage of colonies showing contractions of medium (CAG)₇₀ or long (CAG)₁₅₅ tracts. (C) Expansions of (CAG)₇₀ tracts, normalized to wild type. (D) Fragility rates with no repeat tract, or with medium (CAG)₇₀ or long (CAG)₁₅₅ tracts. Error bars denote ± one standard error of the mean (SEM).

Figure 2. Triplet repeat phenotypes for mutants in three different alternative RFC complexes.

Assays, display, and symbols are as in legend to Figure 1. (A) Contractions and expansions normalized to wild type. (B) Rates of fragility for strains with no repeat tract, medium (CAG)₇₀, or long (CAG)₁₅₅ tracts. Error bars, ±1 SEM.

Figure 3. Analysis of rad52 effects on triplet repeat instability phenotype of dcc1.

Contractions, expansions, and fragility were measured as described in Table S1. (A) Contraction and expansion phenotypes normalized to wild type. *, p<0.05, **, p<0.01 compared to wild type; ^Δ, p<0.05 compared to dcc1. (B) Fragility measurements as in Figure 1; the dcc1 rad52 mutant had a (CAG)₆₅ repeat. Error bars, ±1 SEM.

Figure 4. Cell cycle distribution and morphological abnormalities of dcc1 and ctf18 mutants.

(A) Quantification of cell morphology in log phase cultures. Several hundred cells (range 227–723) were scored for each genotype. Note that the dcc1Δ long tract was a mixture of cells with 155 repeats and contracted tracts by the end of the experiment; we were not able to complete a ctf18 long tract experiment without substantial contractions. Differences in the percentage of multi-budded cells were analyzed by a pooled variance t test using the Systat program; *, p<0.05, **, p<0.01 compared to wild type of the same tract length; ^∧, p<0.05 compared to the no tract control of the same strain (e.g. p = 0.054 for dcc1-70 compared to dcc1 no tract, and p = 0.013 for ctf18-70 compared to ctf18 no tract). (B) Microscopic images of cells; all images are at the same scale, dcc1 and ctf18 mutants are characterized by an increase in cell size and the formation of protruded and multiple buds. Dotted lines indicate an overlay of another image to provide additional examples of cells of that genotype.

Figure 5. Single cell analysis of cell cycle dynamics.

Aliquots from mid-logarithmic phase liquid cultures were plated onto solid media. Single unbudded cells were isolated by micromanipulation, and their progression was monitored by microscopy every 30 min for 6.0–8.5 h (1–4 cell divisions). (A) Examples of how cells were followed and scored. (B) Time spent in each phase of the cell cycle, as scored by budding index (see Materials and Methods). Red bars, S phase; green bars, G2 phase; blue bars, G2+G1 phases.

Figure 6. Cell cycle dependency of Rad52 focus formation in ctf18 cells.

(A) Cultures of wild type and ctf18 cells were grown to mid-log phase before mounting on a microscope slide. The panel shows differential interference contrast (DIC), DAPI-stained DNA, and Rad52-yellow fluorescent protein (Rad52-YFP) images of selected cells among WT and ctf18 cells with no tract (−) or with a medium (CAG)₇₀ tract (M). Scale bar is 10 µm. (B) Quantification of Rad52 foci formation in WT or ctf18 cells with no tract (−), medium (CAG)₇₀ tract (M) or long (CAG)₁₅₅ tract (L). *, p<0.05, **, p<0.01 compared to wild type of same tract length; ^∧, p<0.05, ^∧∧, p<0.01 compared to no tract of the same strain. (C) Cell cycle distribution of Rad52 foci. The occurrence of Rad52 foci in G1, S or G2 cells was determined after incubation with α-factor, 40 min after release from G1 or nocodazole, respectively (see Methods for details). Representative examples of ctf18 cells with medium (CAG)₇₀ tract in S or G2 are shown as DIC images (top) or Rad52-YFP foci (bottom). (D) Quantification of Rad52 foci in G1, S, or G2 cell cycle stage. Labels and statistical analysis are as in (B). Percentages obtained for WT cells treated with α-factor are indicated. See Table S2 for complete set of data.