Fig. 1. Insertions of extranuclear DNA species in stationary phase cells.

a Schematic of the Break-Ins method. b Schematic of PCR amplification of the repaired MAT locus with two sets of indexes. Two sets of indexes were used to limit incorrect sample assignment by index hopping. c PCR amplification of uncut and repaired MAT locus in WT, dna2Δ pif1-m2 mutant, and WT stationary phase cells. The experiments were repeated 3 times with similar results. d Frequency and types of DNA inserted at DSBs in wild-type stationary phase cells among cells that repaired DSB by NHEJ. “All insertions” includes single and complex events. There was no single mtDNA insertion in growing cells. n–number of NHEJ products tested is shown in Supplementary Data 1. e Insertion size analysis of NUMTs. The insertions originating from mtDNA were from 16 days stationary phase cells (n = 21,348 independent NUMTs). Red dashed line indicates minimal size of DNA for efficient Ku70/80 heterodimer binding²⁸. f Survival and respiration proficiency of cells plated on rich media after 1–16 days in stationary phase, (mean ± SD; n = 3. n represents biological repeats). Source data are provided as a Source Data file.