Limits...
Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast.

Lang GI, Parsons L, Gammie AE - G3 (Bethesda) (2013)

Bottom Line: The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%).Additionally, repeat regions with proximal repeats are more likely to be mutated.A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites.

View Article: PubMed Central - PubMed

Affiliation: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544-1014.

ABSTRACT
DNA mismatch repair is a highly conserved DNA repair pathway. In humans, germline mutations in hMSH2 or hMLH1, key components of mismatch repair, have been associated with Lynch syndrome, a leading cause of inherited cancer mortality. Current estimates of the mutation rate and the mutational spectra in mismatch repair defective cells are primarily limited to a small number of individual reporter loci. Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. We performed mutation accumulation assays and next generation sequencing on 19 strains, including 16 msh2 missense variants implicated in Lynch cancer syndrome. The mutation rate for DNA mismatch repair strains was approximately 1 mutation per genome per generation, 225-fold greater than the wild-type rate. The mutations were distributed randomly throughout the genome, independent of replication timing. The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%). Additionally, repeat regions with proximal repeats are more likely to be mutated. A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites. Interestingly, 5% of the single base pair substitutions might represent double-slippage events that occurred at the junction of immediately adjacent repeats, resulting in a shift in the repeat boundary. These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells.

Show MeSH

Related in: MedlinePlus

Mutations in mismatch repair defective cells occur randomly across the genome. (A) Chromosomal distribution of mutations including the single base pair substitutions (open circles) and the insertions/deletion at mono-, di-, and trinucleotide microsatellites (filled circles) are shown at their chromosomal position for each of the 16 yeast chromosomes. Mutation number was plotted against chromosome size for single-base pair substitutions (B) and for insertions/deletions at microsatellites (C). Single-base substitutions in (B) represent data pooled from two independent mutation accumulation experiments. R2 values were generated in Microsoft Excel (Redmond, WA) and are indicated on the graphs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3755907&req=5

fig1: Mutations in mismatch repair defective cells occur randomly across the genome. (A) Chromosomal distribution of mutations including the single base pair substitutions (open circles) and the insertions/deletion at mono-, di-, and trinucleotide microsatellites (filled circles) are shown at their chromosomal position for each of the 16 yeast chromosomes. Mutation number was plotted against chromosome size for single-base pair substitutions (B) and for insertions/deletions at microsatellites (C). Single-base substitutions in (B) represent data pooled from two independent mutation accumulation experiments. R2 values were generated in Microsoft Excel (Redmond, WA) and are indicated on the graphs.

Mentions: Previous experimental and comparative genomic analyses in yeast showed that there are mutational differences with respect to the chromosomal context (Hawk et al. 2005; Ito-Harashima et al. 2002) and replication timing (Agier and Fischer 2012; Lang and Murray 2011). Examining the mutations across the entire genome allowed us to determine if there were any position effects that might relate to chromosomal structure or replication timing. We determined that both single base pair substitutions and insertions or deletions at repeats occurred randomly across the genome (Figure 1A). In keeping with this, the number of single base pair substitutions (Figure 1B) and insertions/deletions (Figure 1C) per chromosome correlated with chromosome size (R2 = 0.91 and 0.87, respectively).


Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast.

Lang GI, Parsons L, Gammie AE - G3 (Bethesda) (2013)

Mutations in mismatch repair defective cells occur randomly across the genome. (A) Chromosomal distribution of mutations including the single base pair substitutions (open circles) and the insertions/deletion at mono-, di-, and trinucleotide microsatellites (filled circles) are shown at their chromosomal position for each of the 16 yeast chromosomes. Mutation number was plotted against chromosome size for single-base pair substitutions (B) and for insertions/deletions at microsatellites (C). Single-base substitutions in (B) represent data pooled from two independent mutation accumulation experiments. R2 values were generated in Microsoft Excel (Redmond, WA) and are indicated on the graphs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3755907&req=5

fig1: Mutations in mismatch repair defective cells occur randomly across the genome. (A) Chromosomal distribution of mutations including the single base pair substitutions (open circles) and the insertions/deletion at mono-, di-, and trinucleotide microsatellites (filled circles) are shown at their chromosomal position for each of the 16 yeast chromosomes. Mutation number was plotted against chromosome size for single-base pair substitutions (B) and for insertions/deletions at microsatellites (C). Single-base substitutions in (B) represent data pooled from two independent mutation accumulation experiments. R2 values were generated in Microsoft Excel (Redmond, WA) and are indicated on the graphs.
Mentions: Previous experimental and comparative genomic analyses in yeast showed that there are mutational differences with respect to the chromosomal context (Hawk et al. 2005; Ito-Harashima et al. 2002) and replication timing (Agier and Fischer 2012; Lang and Murray 2011). Examining the mutations across the entire genome allowed us to determine if there were any position effects that might relate to chromosomal structure or replication timing. We determined that both single base pair substitutions and insertions or deletions at repeats occurred randomly across the genome (Figure 1A). In keeping with this, the number of single base pair substitutions (Figure 1B) and insertions/deletions (Figure 1C) per chromosome correlated with chromosome size (R2 = 0.91 and 0.87, respectively).

Bottom Line: The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%).Additionally, repeat regions with proximal repeats are more likely to be mutated.A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites.

View Article: PubMed Central - PubMed

Affiliation: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544-1014.

ABSTRACT
DNA mismatch repair is a highly conserved DNA repair pathway. In humans, germline mutations in hMSH2 or hMLH1, key components of mismatch repair, have been associated with Lynch syndrome, a leading cause of inherited cancer mortality. Current estimates of the mutation rate and the mutational spectra in mismatch repair defective cells are primarily limited to a small number of individual reporter loci. Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. We performed mutation accumulation assays and next generation sequencing on 19 strains, including 16 msh2 missense variants implicated in Lynch cancer syndrome. The mutation rate for DNA mismatch repair strains was approximately 1 mutation per genome per generation, 225-fold greater than the wild-type rate. The mutations were distributed randomly throughout the genome, independent of replication timing. The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%). Additionally, repeat regions with proximal repeats are more likely to be mutated. A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites. Interestingly, 5% of the single base pair substitutions might represent double-slippage events that occurred at the junction of immediately adjacent repeats, resulting in a shift in the repeat boundary. These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells.

Show MeSH
Related in: MedlinePlus