Dissecting complex regulatory landscapes in the non-coding genome

Genes with pleiotropic roles in development often reside in large, complex regulatory regions of the non-coding genome. Multiple enhancers in these regions can operate over huge genomic distances, ensuring precise spatial and temporal control of target gene expression. Disruption of enhancer-mediated gene regulation has been implicated in human disease, but our understanding of these disease mechanisms is hampered by the lack of information about the precise cell-type specific roles of each enhancer.

We address this knowledge gap by developing in vivo and ex vivo models to uncover the cell-type specific roles of developmental enhancers using PAX6 as a paradigm locus (Bhatia et al 2021, Uttley et al 2023). We combine high resolution live imaging, single cell omics and synthetic biology techniques in zebrafish and optic cup organoids models to define the cell-type specific functions of individual enhancers in the PAX6 locus. The proposed project will focus on specific components of this effort, particularly the consequences of loss/re-arrangement/replacement of PAX6 enhancers in large synthetic constructs bearing the complete PAX6 regulatory domain.

References:

• Bhatia et al 2021: https://elifesciences.org/articles/65601
• Uttley et al 2023: https://www.life-science-alliance.org/content/6/11/e202302126