Multiplexing CRISPR: thousands of mutations, endless possibilities for discovery

15 April 2017

​While basic CRISPR experiments are already transforming life sciences research, there are many
emerging CRISPR tools that open up previously unimaginable opportunities. An example is CRISPR’s potential for multiplex genome editing, which can be used for saturation mutagenesis of not only individual genes, but entire genomes. Below, we describe two technology platforms that have built on CRISPR’s multiplexing potential. Both technologies leverage oligonucleotide libraries to generate large CRISPR gRNA libraries for multiplexing.

Muse bio: accelerating CRISPR
CREATE, or CRISPR-enabled trackable genome engineering, is a high-throughput CRISPR technology that enables generation and parallel mapping of tens of thousands of amino acid and promoter mutations in a single experiment. CREATE can be used to identify mutations that are important in traits of interest. CREATE allows generation of gain-of-function mutations important for a phenotype of interest, which is a great advantage of this technique in comparison with other approaches.

This technology works in both bacteria and yeast and, with further tweaks, could also be adapted to work in higher eukaryotes. The CREATE technology is being commercialized by Muse Bio, which has created a product package called “ForgeCraft”. This package includes a powerful combination of design software, a set of reagents and algorithms, and an automated, easy-to-use instrument enabling high-throughput CRISPR editing of genomes.
Garst et al., Nature Biotechnology 2016

Engine biosciences:CombiGEM-CRISPR
Combinatorial genetics en masse (CombiGEM) is a technology for rapid, scalable assembly of high-order barcoded combinatorial genetic libraries. When applying CombiGEM with CRISPR gRNAs, researchers can create barcoded gRNA libraries that can be used to combinatorically modify the genome, screen for a particular phenotype and quickly profile the resulting hits. High-throughput screens are possible in bacteria and human cells.

The CombiGEM-CRISPR technology is being commercialized by the company Engine Biosciences. The company is interested in working with research institutions on exciting, collaborative projects that
can leverage the CombiGEM-CRISPR platform.

By linking the technology to single-cell sequencing technologies like Perturb-seq or CRISPR-seq, one could even envision complex combinatorial genetic perturbation screens in single cells.
Wong et al., Proc Natl Acad Sci U S A 2016