Systems Virology Group

Genome-wide CRISPR/Cas9 screens in pigs and chicken

The Grey lab has developed CRIPSR/Cas9 knock-out (KO) libraries for the pig and chicken genomes in order to interrogate the role of specific genes in influenza virus infection as well as infection with other important pathogens.

Advances in genome sequencing of livestock have provided opportunities for increasingly sophisticated approaches to identifying links between gene sequence and desirable traits, such as resistance to infection. Improving genome editing technologies also provide an opportunity to translate the identification of desirable genetic traits to the generation of specifically engineered livestock. We have developed genome-wide CRIPSR/Cas9 KO libraries for pig and chicken, allowing genome-wide functional screens in these important livestock species.

The availability of large population sequence data sets and the ability to perform controlled challenge studies are significant advantages over equivalent genomics studies in human populations. Genomic studies in livestock animals are therefore likely to follow in the footsteps of human genomic advances and in some areas may eclipse human genomic studies. However, use of systematic functional screens at the cellular level have lagged far behind human and mouse studies.

To address this, we have developed genome-wide CRIPSR/Cas9 KO libraries for pig and chicken. CRISPR/Cas9 technology allows for specific manipulation of genomes based on the expression of modified Cas9 protein and simple small guide RNAs. Genome wide CRISPR/Cas9 KO libraries consist of pooled lentiviruses expressing multiple guide RNAs against every annotated transcript within a genome. With effective phenotypic screens these libraries provide the opportunity to interrogate the role of host genes in specific biological processes.

Initially we will be asking a relatively straightforward question using the technology. Influenza virus is an important pathogen both in humans and in livestock animals. Spread of the virus in livestock such as birds and pigs contributes to outbreaks of the virus in humans, including potentially dangers pandemics. In many cases genes expressed by the host (such as human, chickens and pigs) are required by the virus and can restrict the replication of the virus. Significant amounts of work have been dedicated to understanding which genes are important following infection of human cells. Relatively little research has been performed to answer the same question in other species. We will use this technology to answer these questions. Although this will be an important aspect of the research, it is only one of many ways in which this new technology will be of benefit to scientists working on livestock animals. This technology has the potential to greatly improve our ability to understand the link between the genes encoded in a genome the functional roles they play. Such advances will have major impacts on the potential for improved breeding of livestock and will also contribute to our basic understanding of biology.