Targeted manipulation of complex genomes often requires the introduction of a double-strand break at defined locations by site-specific DNA endonucleases. Here, we describe a monomeric nuclease domain derived from GIY-YIG homing endonucleases for genomeediting applications. Fusion of the GIY-YIG nuclease domain to threemember zinc-finger DNA binding domains generated chimeric GIYzinc finger endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions (Tev-ZFEs) function in vitro as monomers to introduce a double-strand break, and discriminate in vitro and in bacterial and yeast assays against substrates lacking a preferred 5′-CNNNG-3′ cleavage motif. The Tev-ZFEs function to induce recombination in a yeastbased assay with activity on par with a homodimeric Zif268 zincfinger nuclease. We also fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active in vivo and similarly discriminate against substrates lacking the 5′-CNNNG-3′ motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct from the FokI-derived zinc-finger nuclease and TAL effector nuclease platforms as the GIY-YIG domain alleviates the requirement to design two nuclease fusions to target a given sequence, highlighting the diversity of nuclease domains with distinctive biochemical properties suitable for genome-editing applications.

Precise genome editing in complex genomes is enabled by engineered nucleases that can be programmed to cleave in a site-specific manner. Here, we fused the small, sequence-tolerant monomeric nuclease domain from the homing endonuclease I-TevI to transcription-like activator effectors (TALEs) to create monomeric Tev-TALE nucleases (Tev-mTALENs). Using the PthXo1 TALE scaffold to optimize the Tev-mTALEN architecture, we found that choice of the N-terminal fusion point on the TALE greatly influenced activity in yeast-based assays, and that the length of the linker used affected the optimal spacing of the TALE binding site from the I-TevI cleavage site, specified by the motif 5′-CNNNG-3′. By assaying activity on all 64 possible sequence variants of this motif, we discovered that in the Tev-mTALEN context, I-TevI prefers A/T-rich triplets over G/C-rich ones at the cleavage site. Profiling of nucleotide requirements in the DNA spacer that separates the CNNNG motif from the TALE binding site revealed substantial, but not complete, tolerance to sequence variation. Tev-mTALENs showed robust mutagenic activity on an episomal target in HEK 293T cells consistent with specific cleavage followed by nonhomologous end-joining repair. Our data substantiate the applicability of Tev-mTALENs as genome-editing tools but highlight DNA spacer and cleavage site nucleotide preferences that, while enhancing specificity, do confer moderate targeting constraints.

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Genome duplication occurs once and only once in each cell cycle. During G1 phase, pre‐replicative complexes (pre‐RC), composed of ORC, Cdc6, Cdt1 and Mcm2–7, are assembled at replication origins. Mcm2–7 is the replicative helicase in eukaryotic cells; however, it does not unwind DNA in the pre‐RC. It is only in S‐phase, after activation of Mcm2–7, that DNA unwinding is detected. Cdt1 co‐purifies from yeast cells in a complex with Mcm2–7. Beyond being an escort for entry of Mcm2–7 into the nucleus and into the pre‐RC, the role of Cdt1 in DNA replication is not known. Using purified components from bacterial expression systems, we assembled Mcm2–7•Cdt1 complexes and compared its activity to that of Mcm2–7 alone. We show that Mcm2–7•Cdt1 has lower ATPase activity than Mcm2–7. In addition, DNA unwinding by Mcm2–7•Cdt1 is significantly lower than by Mcm2–7 alone. Furthermore and consistent with published reports, in vitro pre‐RC reconstitution experiments showed loading of Mcm2–7 to origins was dependent on ORC, Cdc6 and Cdt1. Together, the effects of Cdt1 on Mcm2–7 suggest mechanisms by which Cdt1 may carry out its essential role in the initiation of DNA replication.Research funded by CIHR