A CRISPR-Cas9-based system for the dose-dependent study of DNA double-strand break sensing and repair.

The integrity of DNA is put at risk by different lesions, among which double-strand breaks (DSBs) occur at a lower frequency but have the most life-threatening consequences. The study of DSB repair requires tools that can induce the accumulation of these breaks and includes the use of chemical genotoxins, ionizing radiation, or the expression of sequence-specific nucleases. While genotoxins and irradiation allow for dose-dependent studies, nuclease expression permits assessments at precise locations. In this work, we have leveraged the repetitive nature of the Ty transposon elements in the genome of Saccharomyces cerevisiae and the cutting activity of the RNA-guided Cas9 nuclease to create a tool that combines sequence specificity and dose-dependency. In particular, we can achieve the controlled induction of 0, 1, 15, or 59 DSBs in cells with an otherwise identical genetic background. We make the first application of this tool to better understand the behavior of the apical kinase of the DNA damage response Tel1 in the nuclear space. We found that Tel1 is capable of forming nuclear foci, which are clustered by condensin when DSBs occur in Ty elements. In striking contrast with other DSB-related protein foci, Tel1 foci are in tight contact with the nuclear periphery, therefore suggesting a role for the nuclear membrane in their congregation.