Research
We develop highly multiplexed CRISPR/Cas-based technologies for precision genome engineering in microbes.
Research in the lab combines development of innovative high-throughput genome editing tools with large-scale genetic screens to study fundamental principles in molecular and complex trait genetics.
High-throughput CRISPR-based genome perturbation
Individuals within a species exhibit substantial differences in their genome sequence, and consequently the gene variants they express, or their regulation. These differences have important implications as they can account for the extensive phenotypic variation we see in nature, for example the variable disease severity or treatment response in humans, or differences in drug resistance and stress tolerance in microbes. However, while identifying these DNA sequence variants has become simple, deciphering exactly how they impact specific traits remains a significant challenge. To address this challenge, we use a unique combination of high-throughput genome editing, genomics, massively parallel reporter assays and computational methods. Genome editing tools that can engineer specific mutations with high efficiency, precision, and at scale, and that can be coupled to large-scale functional assays are especially crucial, as they overcome a long-standing bottleneck for directly probing genome variants for function.
Our core technology is MAGESTIC (Multiplexed Accurate Genome Editing with Short, Trackable, Integrated Cellular barcodes), a CRISPR/Cas9-based method that can engineer thousands of defined mutations in parallel in a single test tube in yeast. MAGESTIC uses pools of array-synthesized oligos encoding a gRNA and a donor DNA to introduce a designed mutation. Importantly, strains are tagged by DNA barcodes, allowing to efficiently track mutations in cell populations during functional screens and read out mutation identities via barcode sequencing. Inspired by MAGESTIC, we develop other CRISPR-based technologies for massively parallel precision genome perturbation and direct functional screening in microbes.
Applying precision editing to study how genotype impacts phenotype
By providing a direct link between sequence and function, at unprecedented scale, MAGESTIC allows us to gain principally new insights into how subtle genome variation impacts phenotype and enables massively scaled screens to accelerate construction of designer strains in biotechnology and synthetic biology. We are particularly interested in studying the impact of synonymous mutations - mutations that do not alter a protein's amino acid sequence - on protein expression and function, and eventually phenotype, and understanding how the impact of a mutation changes depending on its context. Our main models are the yeast S. cerevisiae, a biotechnologically important organism with a long history as a model for fundamental processes in higher eukaryotes, and the bacterium E. coli. However, many industrially or medically relevant phenotypes cannot easily be studied in these classical model species, and the scarcity of genome-scale tools for most other microbes leaves us with an incomplete understanding of their genetic basis. To bridge this gap, we aim to improve CRISPR tools and screens for microbes, for which we collaborate with diverse partners. Using our tools we can also efficiently design, engineer and screen large libraries of mutants for advantageous properties for industrial and medical applications, as well as for directed evolution campaigns.