Fig. 3: SSA deficiency in C. elegans lacking HELQ-1.

a Schematic representation of the single-strand annealing (SSA) reporter¹⁴. A DSB can be introduced at the I-SceI recognition site by the I-SceI endonuclease. DSB repair by annealing of ~250 bp region of sequence identity placed up and downstream of the I-SceI recognition site leads to a functioning LacZ open reading frame. Small arrows depict primers used in the PCR analysis. b Representative pictures of lig-4 mutant animals carrying the reporter transgenes that were heat-shocked or mock-treated to induce I-SceI expression, followed by staining for B-galactosidase expression. c Histogram depicting the percentage of LacZ positive worms for the indicated genotype. Experiments were performed in triplicate (***P < 0.01; Chi-square test). Each dot represents the average percentage of each replicate. Error bars represent SEM. Staining quantifications are provided as a Source Data file. d Representative images of PCR-based analysis of the reporter locus at the I-SceI site for the indicated genotypes. Each well contains the DNA of one animal. Wild-type bands are expected because many cells in the animal are insensitive to heat shock-driven I-SceI expression. 2-Log DNA ladders are used as markers for size reference. e Histogram depicting the percentage of PCR samples containing a deletion. Each dot represents the percentage of deletions found in 96 samples. Experiments were performed in triplicate (***P < 0.01; Chi-square test). Error bars represent SEM. Deletion counts are provided as a Source Data file. f Spectra of deletions occurring at the I-SceI site of the SSA reporter for the indicated genotype. Single deletion events are piled and sorted from top to bottom by deletion end-point relative to the I-SceI cut site set at 0. Deletion events are colour-coded according to the following mutational classification: grey for simple deletions without apparent MH at the junction, blue for simple deletions with MH at the junction, wherein the saturation level of the blue colour increases with an increasing amount of homology identified. Deletions containing insertions are in red: bright red for insertions that can be reliably mapped to the flank of the deletion, dark red for insertions of which the origin could not be determined with certainty. Deletion sequences are provided as a Source Data file.