Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

Abstract

Maintaining genome integrity is particularly important in germ cells to ensure faithful transmission of genetic information across generations. Here we systematically describe germ cell mutagenesis in wild-type and 61 DNA repair mutants cultivated over multiple generations. ~44% of the DNA repair mutants analysed showed a >2-fold increased mutagenesis with a broad spectrum of mutational outcomes. Nucleotide excision repair deficiency led to higher base substitution rates, whereaspolh-1(Polη) andrev-3(Polζ) translesion synthesis polymerase mutants resulted in 50–400 bp deletions. Signatures associated with defective homologous recombination fall into two classes: 1)brc-1/BRCA1andrad-51/RAD51 paralog mutants showed increased mutations across all mutation classes, 2)mus-81/MUS81andslx-1/SLX1nuclease, andhim-6/BLM,helq-1/HELQorrtel-1/RTEL1helicase mutants primarily accumulated structural variants. Repetitive and G-quadruplex sequence-containing loci were more frequently mutated in specific DNA repair backgrounds. Tandem duplications embedded in inverted repeats were observed inhelq-1helicase mutants, and a unique pattern of ‘translocations’ involving homeologous sequences occurred inrip-1recombination mutants.atm-1/ATM checkpoint mutants harboured structural variants specifically enriched in subtelomeric regions. Interestingly, locally clustered mutagenesis was only observed for combinedbrc-1andcep-1/p53 deficiency. Our study provides a global view of how different DNA repair pathways contribute to prevent germ cell mutagenesis.

Helicase Q promotes homology-driven DNA double-strand break repair and prevents tandem duplications

“…tandem duplications (TDs) (Fig. 4f ), corroborating recent data describing mutational signatures in C. elegans DNA repair mutants 48 , 49 . These TDs, which are rarely found in wild-type nematodes 36 , 49 , range in size from ~100 bp to 10 kb, with a median of ~1 kb.…”

BRCA1/BRC-1 and SMC-5/6 regulate DNA repair pathway engagement during C. elegans meiosis

“…2008), brc-1 mutants are known to incur small mutations more frequently (Kamp et al . 2020; Meier et al . 2021).…”

“…Notably, DSB repair in the IH assay which produces in-frame insertions or deletions can also yield non-Unc progeny which are phenotypically indistinguishable from noncrossover recombinants (Robert et al 2008). While mutagenic repair in the IH assay is rare in a wild type context (Robert et al 2008), brc-1 mutants are known to incur small mutations more frequently (Kamp et al 2020;Meier et al 2021). We therefore sequenced the repaired unc-5 locus of putative noncrossover non-Unc progeny in the IH assay to confirm whether the repaired sequence matched the homolog repair template or indicated mutations at the site of Mos1 excision (see Methods).…”

C. elegans genome-wide analysis reveals DNA repair pathways that act cooperatively to preserve genome integrity upon ionizing radiation

“…Overall, 6% of all mutations occurred in clusters ( P < 1.7x10 -7 ) with ~ 1.2 clusters induced per 80 Gy per genome ( P < 1x10 -7 ) (Figs 5A and 5B and S7 and S2 Table ) Clustering was not observed in unchallenged C . elegans strains propagated over generations [ 38 ]. Clusters typically spanned 10–20 bp and on average consisted of 2–3 mutations ( Fig 5C ).…”