Cas12a-based combinatorial knockout screens define the genetic architecture of the DNA Damage response [END-seq]

To elucidate the architecture of the DNA damage response (DDR), we conducted genetic interaction screens using Cas12a to disrupt 233 DDR genes frequently mutated in cancer and other genetic diseases, either individually or in pairwise combinations, assessing the phenotypic effects of >27,000 gene pair disruptions under unperturbed cell growth conditions. We identified >750 high-confidence positive (buffering) and negative (synthetic lethal/sick) gene-gene interactions, along with connections between previously unlinked DDR pathways.

Among these interactions, we uncovered synthetic lethal relationships between genes encoding 1) the translesion polymerase REV1-Pol ζ complex and the MCM8-MCM9-HROB DNA helicase complex; 2) Fanconi Anemia proteins and the mitotic DNA repair factors GEN1, CIP2A, and RHINO; and 3) the DNA translocase SMARCAL1 and components of the FANCM complex. We also identified suppressor interactions between genes encoding the APOLLO nuclease and non-homologous end joining factors.