Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism.

The Holliday junction recombination intermediate, an X-shaped DNA molecule (xDNA), was analyzed at rDNA in mitotically growing yeast. In wild-type cells, xDNA is only detected at S phase, suggesting that recombination is stimulated to repair replication-related lesions. A search for mutations that increase the level of xDNA uncovered a gene encoding a subunit of DNA polymerase alpha. Systematic examination of replication mutants revealed that defects in polymerase alpha and delta but not the epsilon complex stimulate the level of xDNA. These xDNAs are Holliday junctions and not replication intermediates. The level of Holliday junctions is greatly reduced in rad52 mutants, but surprisingly, not in mutants defective in the three known mitotically expressed yeast RecA homologs.