The relative roles of three DNA repair pathways in preventing Caenorhabditis elegans mutation accumulation

Abstract

Mutation is a central biological process whose rates and spectra are influenced by a variety of complex and interacting forces. Although DNA repair pathways are generally known to play key roles in maintaining genetic stability, much remains to be understood about the relative roles of different pathways in preventing the accumulation of mutations and the extent of heterogeneity in pathway-specific repair efficiencies across different genomic regions. In this study we examine mutation processes in base excision repair-deficient (nth-1) and nucleotide excision repair-deficient (xpa-1) Caenorhabditis elegans mutation-accumulation (MA) lines across 24 regions of the genome and compare our observations to previous data from mismatch repair-deficient (msh-2 and msh-6) and wild-type (N2) MA lines. Drastic variation in both average and locus-specific mutation rates, ranging two orders of magnitude for the latter, was detected among the four sets of repair-deficient MA lines. Our work provides critical insights into the relative roles of three DNA repair pathways in preventing C. elegans mutation accumulation and provides evidence for the presence of pathway-specific DNA repair territories in the C. elegans genome.

Figure 1.—

Mutation rates observed in DNA repair-deficient MA lines. (A) Genotype-specific total mutation rates (mutations per base pair per generation) for repair-deficient MA lines. (B) Mutation rates specific for base substitutions (shaded bars) and indels (open bars). Indels at mononucleotide runs ≥8 bp in length were excluded for all rate calculations. Error bars indicate SEM as described in materials and methods. Rates for msh-2 and msh-6 are from Denver et al. (2005) and rates for N2 (WT) are from Denver et al. (2004).

Figure 2.—

Distributions of mutations across loci. The observed distributions (solid bars) of mutations across the 24 surveyed loci were compared to expectations based on Poisson distributions (hatched bars). Mutational distributions in the (A) nth-1 MA lines, (B) xpa-1 MA lines, (C) msh-2 MA lines, and (D) msh-6 MA lines are shown (data for the latter two are from Denver et al. 2005). Significant deviations from Poisson expectations were observed for the nth-1, xpa-1, and msh-6 MA lines, but not for the msh-2 MA lines (see text). Arrows indicate loci defined here as mutational hotspots.

Figure 3.—

Three mutation hotspots. Schematics of the three loci characterized as repair pathway-specific mutational hotspots are shown. Dashed lines represent the PCR product locus surveyed; below dashed lines, boxes indicate exon (EX) sequence and solid lines indicate noncoding sequence—intron (IN) or intergenic (IG). Four-pointed stars indicate nth-1 mutations, triangles indicate msh-6 mutations, arrows indicate xpa-1 mutations, and the diamond indicates an msh-2 mutation. (A) The ZK337 locus—exon and intron sequence is from the ZK337.1 gene that encodes a protein in the α-2-macroglobulin family. (B) The F59F5 locus—exon and intron sequence is from the F59F5.6 gene that encodes a liprin-α protein. (C) The intergenic M106 locus.