Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive.

Gene drive elements promote the spread of linked traits, providing methods for changing the composition or fate of wild populations. Drive mechanisms that are self-limiting are attractive because they allow control over the duration and extent of trait spread in time and space, and are reversible through natural selection as drive wanes. Self-sustaining Cleave and Rescue (ClvR) elements include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene, a tightly linked recoded version of the essential gene resistant to cleavage (the Rescue), and a Cargo. ClvR spreads by creating loss-of-function (LOF) conditions in which those without ClvR die because they lack functional copies of the essential gene. We use modeling to show that when the Rescue-Cargo and one or both components required for LOF allele creation (Cas9 and gRNA) reside at different locations (split ClvR), drive of Rescue-Cargo is self-limiting due to a progressive decrease in Cas9 frequency, and thus opportunities for creation of LOF alleles, as spread occurs. Importantly, drive strength and duration can be extended in a measured manner—which is still self-limiting—by moving the two components close enough to each other that they experience some degree of linkage. With linkage, Cas9 transiently experiences drive by hitchhiking with Rescue-Cargo until linkage disequilibrium between the two disappears, a function of recombination frequency and number of generations, creating a novel point of control. We implement split ClvR in Drosophila, with key elements on different chromosomes. Cargo/Rescue/gRNAs spreads to high frequency in a Cas9-dependent manner, while the frequency of Cas9 decreases. These observations show that measured, transient drive, coupled with a loss of future drive potential, can be achieved using the simple toolkit that make up ClvR elements—Cas9 and gRNAs and a Rescue/Cargo. Author summary: There is great interest in being able to spread beneficial traits throughout wild populations. However, many traits of interest do not provide a fitness benefit to those who carry them, and thus require some kind of a "push" to drive them to high frequency in the population. Selfish genetic elements are transmitted to viable, fertile progeny at rates greater than those of other genes, and can spread to high frequency even when they result in fitness costs to carriers—a phenomenon known as gene drive. If genes encoding traits of interest are incorporated into a selfish genetic element, they too can be forced to spread. Gene drive methods that provide a driving force that ultimately wanes to nothing over time (that are self-limiting) are attractive because they ensure that spread to high frequency will be limited in time and space, features that are likely to be important in many regulatory and social environments. Here we use modeling and experiments in Drosophila melanogaster to show how split versions of a gene drive method known as Cleave and Rescue (ClvR) can be used to bring about self-limiting drive whose strength and duration can be tailored to specific economic, ecological and/or regulatory needs. [ABSTRACT FROM AUTHOR]