Yeast EndoG regulates mitochondrial DNA transfer to nucleus

Mitochondrial DNA (mtDNA) can be captured at DNA double-strand breaks (DSB) resulting in nuclear mtDNA (NUMT). This inter-organelle gene transfer is ongoing and can cause disease. To identify enzymes regulating NUMTs, we used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. NUMTs show a significant increase in stationary phase or aging cells. EndoG (Nuc1) nuclease is needed for most NUMTs in stationary phase cells, while it plays less prominent role in aging. Unexpectedly, in Nuc1-deficient stationary phase cells or during meiosis, long mtDNA is transferred to the nucleus at a high rate (³1%) forming unstable circles that arise by annealing of short repeats or nonhomologous end joining. Nuc1 also eliminates retrotransposon replication intermediates, limiting their insertion at DSBs. Thus, Nuc1 preserves genome stability by degrading transposon cDNA and limiting transfer of long mtDNA into the nucleus, while rare NUMTs originate from incompletely degraded mtDNA