The effects of DNA repair factor-Cas9 fusions on homing gene drive performance

Abstract

CRISPR-based homing gene drives achieve super-Mendelian inheritance by converting wild-type alleles into drive alleles through homology-directed repair (HDR). However, competing end-joining repair can generate resistance alleles that limit drive spread. Although fusing Cas9 to DNA repair-associated proteins has improved HDR in conventional genome editing systems, its effectiveness in gene drives remains unclear. Here, we systematically evaluated in Drosophila melanogaster eight Cas9 fusion constructs previously reported to improve HDR in other systems. Although none of the fusion constructs significantly increased HDR-associated signals in S2 cells, several candidates retained relatively high activity comparable to standard Cas9. These candidates were then tested in vivo across multiple split drive systems, regulatory elements, target loci, and parental sexes. Cas9-POLD3 significantly increased female drive inheritance in contexts with low baseline efficiency or substantial nonfunctional resistance formation, likely by increasing effective cutting rate and potentially also by biasing repair outcomes toward drive conversion. Cas9-Geminin degron generally maintained germline drive performance while reducing embryo resistance. Together, these findings identify Cas9-POLD3 and Cas9-Geminin degron as complementary, context-specific tools for enhancing drive conversion and limiting embryo resistance, respectively. These results highlight the importance of matching fusion modules to the regulatory and genetic context of individual drive systems.