Emerging technologies in genotoxicity testing: measuring DNA damage in entire genomes at high resolution

Knowing where DNA damage occurs within a genome is crucial to the understanding of the potential genetic consequences of such damage. We here reported a new development based on microarray technology which uses ultraviolet light induced DNA damage as a paradigm to determine the position and frequency of DNA damage and its subsequent repair throughout the entire yeast genome (1). Analyses of genome-wide DNA repair can be undertaken, alongside examination of the DNA damage-induced changes in chromatin that facilitate repair. The approach should be applicable to examining a spectrum of DNA damages provided either the antibodies or the tagged DNA damage recognition enzymes are available to immunoprecipitate those specific DNA damages, and provided that any of those damages that block PCR can be repaired to enable PCR. The method is applicable to studies with human cells via the available higher resolution human microarrays and experiments are underway to optimize this approach with such cells. DNA samples prepared for this microarray-based approach can be readily processed for high throughput sequencing analysis if this detail is required, or if microarrays are unavailable for the organism of interest. The technique has substantial implications for monitoring the DNA targets during genotoxicity testing. It will enable an estimation of the target sequences for DNA damage and whether these interactions persist in cells; an important facet if one considers threshold levels for DNA damage along the lines employed in estimating the risk associated with radiation exposure. A patent application covering the approach has entered the international PCT phase.