A 2026 Crick PhD project with James Briscoe & Ben Davies.

Project background and description

Recent developments in genome engineering technologies have created unprecedented opportunities to re-engineer and interrogate the mammalian genome. Recently developments include Bridge Recombinases, naturally occurring RNA-guided DNA recombinases that can insert, excise, and invert DNA sequences; and CRISPR-associated transposases (CAST), which exploit nuclease-deficient CRISPR machinery to integrate DNA at genomic locations specified by guide RNAs. These technologies provide a transformative opportunity to investigate the regulatory genome to understand how gene expression is controlled by distant cis-regulatory elements (CREs). Despite decades of genome sequencing and enhancer mapping, we still do not understand how the genome controls where, when, or how strongly a gene will be expressed. This fundamental limitation stems from our inability to quantitatively decode CREs. The ability to precisely insert, delete, and rearrange large genomic segments now enables systematic dissection of long-range regulatory interactions that have been difficult to study with conventional genome editing approaches.

The developing neural tube represents an ideal system in which to develop and implement these genome engineering strategies. The pattern of gene expression in the neural tube depends on well-characterized signals (notably the morphogen Sonic hedgehog, Shh), cell-type specific and ubiquitous transcription factors that act through CREs associated with key patterning genes. The system offers several advantages including robust in vitro differentiation protocols using mouse ES cells that recapitulate mouse spinal cord development. The combination of tractable in vitro models and established mouse genetics makes the neural tube particularly well-suited for CRE analysis, with principles established here being broadly applicable across developmental biology.

This project will focus on understanding the regulation of Olig2, a key transcription factor essential for motor neuron specification. Olig2 regulation is orchestrated by at least two prominent CREs located 33kb and 75kb from the coding region. Deletion studies in mouse embryos have revealed that the e33 CRE is critical for both the level and precision of Olig2 expression, while the e75 CRE, though having minimal effect alone, is essential when combined with e33 deletion, resulting in almost complete loss of Olig2 expression. These long-range interactions exemplify the complexity of regulatory control that new genome engineering technologies can now dissect systematically.

The project will adopt a two-stage strategy. Genome engineering will first be used in mouse stem cell models to systematically delete, rearrange, and introduce synthetic CREs within the Olig2 regulatory landscape, testing rules of long-range enhancer-promoter communication and quantitatively measuring effects on gene expression dynamics. Lead findings will then be validated in mouse embryos to determine how these engineered regulatory changes affect spatial patterning of Olig2 expression, temporal dynamics of motor neuron specification, and precision of cell fate decisions in the physiological context.

The project will combine state-of-the-art genome engineering, quantitative microscopy with computational modelling to build predictive understanding of CRE function. By using the unique capabilities of bridge recombinases and CAST to perform large-scale genomic rearrangements, this work will establish fundamental principles of long-range gene regulation and demonstrate how programmable genome engineering can unlock the regulatory code governing mammalian development.

Candidate background

This project would suit a candidate interested in receiving interdisciplinary training in molecular, developmental and computational biology and will involve both experimental work and data analysis. The candidate will gain expertise in genome engineering, embryology, tissue culture, including embryonic stem cell differentiation, molecular biology, flow cytometry, microscopy and biochemistry. This project would be suitable for anyone with an interest in cellular development and gene regulation, studying biological/biomedical sciences, or data science related subjects.

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