Short-range, orientation-reversing template-switching events occur at a high frequency in the human and yeast genomes

The identification of structural variations in genomes using next-generation sequencing approaches greatly facilitates the study of genetic and genomic diseases. The data generated using these approaches also provide interesting new means to examine DNA repair, recombination, and replication to better understand sources of genomic instability. To better utilize this data, we developed SCARR (Systematic Combination of Alignments to Recreate Rearrangements) to identify DNA rearrangements, and used it to examine the occurrence of orientation-reversing events in human and budding yeast genomes. SCARR exceeds the sensitivity of previous genome sequencing approaches, and identifies rearrangements genome-wide with base-pair resolution, which helps provide insights into the mechanisms involved in their formation. We find that short-range orientation-reversing events occur at high rates in both human and yeast genomes. We quantified these rearrangements in yeast strains lacking various DNA repair factors, and propose that these short-range events often occur through template-switching events within a replication fork. We hypothesize that this mechanism may act as an error-prone alternative to fork reversal to restart stalled replication forks.