Daisy-chain gene drives for the alteration of local populations

Significance CRISPR-based gene drive systems—genetic elements which could be engineered to rapidly spread traits through wild populations—could help solve some of humanity’s greatest ecological and public health problems. However, if released, current versions might spread through a nontarget population—possibly across political borders—greatly complicating decision-making. To address this issue, we describe a self-exhausting form of CRISPR-based gene drive called a “daisy-chain drive.” We develop mathematical models which suggest that daisy-chain-drive systems will not spread indefinitely through successive populations, and we report numerous CRISPR targeting sequences which could offer enhanced stability. Particularly if combined with threshold dependence, daisy-drive approaches may become a foundational technique for local ecological engineering. If they are able to spread in wild populations, CRISPR-based gene-drive elements would provide new ways to address ecological problems by altering the traits of wild organisms, but the potential for uncontrolled spread tremendously complicates ethical development and use. Here, we detail a self-exhausting form of CRISPR-based drive system comprising genetic elements arranged in a daisy chain such that each drives the next. “Daisy-drive” systems can locally duplicate any effect achievable by using an equivalent self-propagating drive system, but their capacity to spread is limited by the successive loss of nondriving elements from one end of the chain. Releasing daisy-drive organisms constituting a small fraction of the local wild population can drive a useful genetic element nearly to local fixation for a wide range of fitness parameters without self-propagating spread. We additionally report numerous highly active guide RNA sequences sharing minimal homology that may enable evolutionarily stable daisy drive as well as self-propagating CRISPR-based gene drive. Especially when combined with threshold dependence, daisy drives could simplify decision-making and promote ethical use by enabling local communities to decide whether, when, and how to alter local ecosystems.

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