Daisy-chain gene drives for the alteration of local populations

Abstract

RNA-guided gene drive elements could address many ecological problems by altering the traits of wild organisms, but the likelihood of global spread tremendously complicates ethical development and use. Here we detail a localized form of CRISPR-based gene drive composed of genetic elements arranged in a daisy-chain such that each element drives the next. "Daisy drive" systems can duplicate any effect achievable using an equivalent global drive system, but their capacity to spread is limited by the successive loss of non-driving elements from the base of the chain. Releasing daisy drive organisms constituting a small fraction of the local wild population can drive a useful genetic element to local fixation for a wide range of fitness parameters without resulting in global spread. We additionally report numerous highly active guide RNA sequences sharing minimal homology that may enable evolutionary stable daisy drive as well as global CRISPR-based gene drive. Daisy drives could simplify decision-making and promote ethical use by enabling local communities to decide whether, when, and how to alter local ecosystems.

Evolution of Resistance Against CRISPR/Cas9 Gene Drive

“…Thus, even though a driver may initially spread to high frequency in the population, its ultimate fate will depend on whether resistance alleles have emerged during this process. While several strategies have been proposed for reducing resistance potential; including the use of multiple gRNAs, the targeting of essential genes, daisy chains, or poison-antidote systems Champer et al 2016;Noble et al 2016a); it remains to be seen how well these approaches can actually work in practice.It is clear that any informed decision about the potential consequences and risks of releasing a CGD construct into a wild population requires that we first understand the dynamics of this process on the population level, including potential resistance mechanisms. Here, we build on previous theoretical results to devise a comprehensive population genetic model of CGD, which allows us to quantitatively study the population dynamics of such systems, calculate the probability that resistance evolves, and predict how resistance alleles will interfere with the spread of a driver construct.…”

“…Thus, even though a driver may initially spread to high frequency in the population, its ultimate fate will depend on whether resistance alleles have emerged during this process. While several strategies have been proposed for reducing resistance potential; including the use of multiple gRNAs, the targeting of essential genes, daisy chains, or poison-antidote systems Champer et al 2016;Noble et al 2016a); it remains to be seen how well these approaches can actually work in practice.…”

Anomaly handling and the politics of gene drives

“…These strategies negate the two primary attributes of gene drives that the NASEM report used to justify its recommendations on regulatory changes (Noble et al 2016;Min et al 2017aMin et al , 2017b. Daisy drive work has also been undertaken with a belief that 'ethical gene drive research and development must be guided by the communities and nations that depend on the potentially affected ecosystems' (Noble et al 2016). Such guidance, however, 'becomes progressively more challenging as the size of the affected region increases'.…”

“…Two examples of this strategy are work on 'daisy drive' systems designed to allow gene drives to spread only at a local level, and on 'reversal' drive systems that overwrite previously released gene drives. These strategies negate the two primary attributes of gene drives that the NASEM report used to justify its recommendations on regulatory changes (Noble et al 2016;Min et al 2017aMin et al , 2017b. Daisy drive work has also been undertaken with a belief that 'ethical gene drive research and development must be guided by the communities and nations that depend on the potentially affected ecosystems' (Noble et al 2016).…”

Daisyfield gene drive systems harness repeated genomic elements as a generational clock to limit spread

“…We previously described 'daisy-chain drive' systems, which separate the CRISPR components into a series of linked genetic daisy elements such that each element promotes copying of the next 3 . Because the element at one end of the chain is not copied, it is only inherited by half of offspring, whose own offspring have only a 50% chance of inheriting the next element, and so on until all the daisy elements are lost and the 'payload' ceases to be copied (Fig.…”