Project Objectives

• Identify shared genetic ‘switches’ that control skeletal cell fate specification across species using comparative genomics.
• Develop a computational pipeline to analyse cross species transcriptomic datasets and prioritise candidate regulators.
• Functionally test these candidates in vivo using multiplexed CRISPR/Cas9 perturbations in chicken embryos.
• Combine CRISPR editing with single cell RNA sequencing (scRNA seq) to map regulatory network changes at cellular resolution.
• Establish the chicken embryo as a scalable, ethically favourable model for reverse genetics screening.

3Rs Impact

• This project replaces mammalian in vivo screening with chicken embryos, avoiding the need to sacrifice pregnant female animals.
• Comparative genomics narrows down candidate genes, reducing the number of embryos required for functional testing.
• Multiplexed CRISPR/Cas9 screening maximises information gained per embryo, improving efficiency and reducing overall animal use.
• The workflow provides a scalable alternative to mouse‑based genetic screens, with potential to reduce large numbers of animals used in developmental biology and skeletal research.

Background

Understanding how different cell types form during embryonic development is essential for regenerative medicine, where scientists aim to recreate specific cell types for tissue repair. However, many of the processes that guide cell fate decisions only occur correctly within a developing embryo, making it difficult to study them using cell cultures alone. Traditional in vivo studies often rely on mammalian models such as mice, which require large numbers of animals and involve procedures that raise ethical concerns.

This project aims to overcome these challenges by combining comparative genomics with innovative CRISPR/Cas9 screening directly in chicken embryos. By analysing gene expression patterns across species, the team identifies core regulatory ‘switches’ that consistently drive the formation of specific skeletal cell types. These candidate regulators are then tested in chicken embryos using multiplexed CRISPR-based gene perturbations, allowing researchers to observe how changes in these genes influence cell fate at single‑cell resolution.

Using the chicken embryo provides a more accessible and ethically favourable model, avoiding the need to sacrifice pregnant mammals and reducing overall animal use. The resulting platform will help researchers uncover fundamental developmental mechanisms while supporting more humane and efficient approaches to studying cell fate specification.