Fulga Group: Genome Engineering and Synthetic Biology

1. Post-transcriptional regulation of gene expression

Every cell within our body carries the same genetic information, yet following iterative developmental transitions hundreds of morphologically and functionally distinct cell types are created and assembled into astonishingly complex biological structures. At the core of this fascinating cellular diversification lies a vast repertoire of finely orchestrated and sophisticated regulatory programs, which act to control the expression of thousands of genes with minute spatial and temporal precision. This property is essential for the ability of complex organisms to arise from a shared genome and is dependent on the combinatorial action of chromatin modifiers and readers, transcription factors and cofactors, and a vast repertoire of post-transcriptional regulatory layers. Gene expression perturbations caused by errors in these programs or mutations in the associated regulatory elements have devastating developmental consequences and lead to the onset and progression of many human genetic diseases.

We aim to decipher the logic of post-transcriptional gene regulation, harness this knowledge to create synthetic systems capable of rewiring or enhancing naturally evolved cellular behaviours, and use the emerging principles to advance the scope of somatic and stem cell engineering for basic research and therapeutic applications. Throughout the past few years our group has made several key contributions to miRNA research, such as developing in vivo technologies for conditional knockdown of miRNAs (Loya CM et al, Nature Methods, 2009;  Fulga TA et al, Nature Comm. 2015), establishing new experimental platforms for functional interrogation of miRNA response elements (Bassett AR et al, Nature Comm. 2014), and creating a CRISPR-based multiplex screening technology for analysis of RNA cis-regulatory functions in living cells (Wu Q et al, Nature Comm. 2017).

2. Genome and cell engineering

The recent adaptation of bacterial CRISPR-associated RNA-guided endonucleases for precise genome editing in eukaryotic cells has unlocked unprecedented dimensions in basic research, disease studies and therapeutic interventions. Consequently, within the span of only four years, CRISPR/Cas9 leaped from a basic experimental tool to a game-changing platform for biomedical research with far reaching implications in curative, regenerative and preventive medicine. Most notably, the astonishing wave of innovations in this field has radically expanded the scope of ex vivo somatic and stem cell engineering from simple viral transgene expression to site-specific knock-ins, controlled gene disruption, and direct correction of disease-causing mutations. By merging the core principles of cell/genome engineering and synthetic biology, we currently endeavour to develop programmable signalling pathways and gene networks responsive to exogenous cues and/or endogenous metabolites. To this end, we have created a technology platform for the assembly of parallel and orthogonal gene network modules (Ferry QR et al, Nature Comm. 2017), engineered the next-generation of programmable chimeric receptors for research and therapeutic applications (Baeumler TA et al, Cell Rep. 2017), and developed a powerful binary expression system for multiplexed activation of transgenes in distinct neighbouring cell types in vivo (Toegel M et al, Nature Comm. 2017). This research paves the way for the design of more sophisticated regulatory circuits enabling de novo implementation of custom cellular functions.