About the Project
Vertebrate development depends on precise regulation of genes that specify cell identity. Many developmental transcription factor (TF) genes are controlled by highly conserved non-coding elements (HCNEs), regulatory DNA sequences preserved across hundreds of millions of years of vertebrate evolution. Using comparative functional genomics, the Nelson lab identified HCNEs associated with TF genes involved in pancreas development by analysing developing zebrafish endoderm and differentiated human embryonic stem cells (hESCs). These TFs also have essential roles in nervous system development. Functional studies in zebrafish showed HCNEs identified in endoderm can drive expression in the nervous system, suggesting shared HCNE-mediated networks may control pancreatic and neural development across vertebrates (Riley et al. 2026 PMID:41781333).
This project will investigate selected HCNEs in zebrafish and human developmental systems. CRISPR genome editing will be used to delete HCNEs in hESCs, followed by differentiation into pancreatic and neural lineages. Expression of predicted target genes will be analysed and compared with phenotypes resulting from target gene deletion.
HCNE activity will be examined using fluorescence reporter assays and imaging to determine when and where these elements drive expression during zebrafish development. Mutagenesis of specific TF binding sites will identify sequences required for enhancer function.
Quantitative imaging and analysis, supported by the Saunders lab, will link regulatory activity to developmental outcomes. Neuroscience expertise will be provided by the Huckstepp lab.
The project will reveal how gene expression is regulated during pancreas and nervous system development, determine whether the same HCNEs and TF binding sites function in both contexts, and provide new insights into vertebrate evolution. The findings may also improve understanding of how regulatory mutations contribute to developmental disorders.
