Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
Keywords: DNA breaks; DNA repair centers; DNA resection; DSBs; Holliday junctions; R-loops; chromatin dynamics; chromosome rearrangements; crossovers; fluorescent proteins; gene amplification; gene conversion; genome instability; gross chromosome rearrangements; homologous recombination; mitotic recombination; mutagenesis; pulsed field gel electrophoresis; replication fork stalling; single-particle tracking; sister chromatid recombination; sister repetitive sequences; site-specific chromosome breaks; toxic recombination intermediates; yeast artificial chromosome.