Unlocking the regulatory code at single cell resolution in vivo

Department: Institute of Genetics and Cancer

Number of current Students: 0

Completed Supervisor training: Completed

Co Supervisors: Prof. Ferenc Mueller, Department of Cancer and Genomic Sciences / University of Birmingham, Email: f.mueller@bham.ac.uk

The vertebrate body contains hundreds of specialised cell types, produced by tightly controlled activation of genes in specific places and times during development. This control depends on enhancers—noncoding DNA elements that recruit transcription factors to switch genes on in the right cellular contexts. Scattered across long stretches of the “dark genome,” to form large regulatory landscapes, their conserved arrangement in position, order and orientation across vertebrate evolution suggests underlying organisational principles that remain largely unknown. Until these rules are defined, we cannot fully explain how gene expression variation drives evolutionary change or predict how disease associated mutations disrupt regulatory architecture. 

A key step toward this understanding is mapping the precise cell‑ and tissue‑specific activities of enhancers in vivo. Dr. Shipra Bhatia’s research at the Institute of Genetics and Cancer addresses this challenge by developing zebrafish models that enable real‑time visualisation and functional testing of enhancer activity. Using the PAX6 locus—an exemplar of enhancer‑mediated regulation and a master controller of eye development (Bhatia et al., 2021; Uttley et al., 2023)—the team has established methods to synthesise large genomic regions de novo, deliver them into zebrafish, and assay synthetic regulatory landscapes during embryogenesis. Combining single‑cell omics with high‑resolution live imaging, they have uncovered previously unrecognised layers of regulatory logic within the PAX6 domain.

Functional delineation of cell type specific enhancer activities within the PAX6 regulatory domain

Phase 1: Hypothesis Development (Months 0–6)

Single cell datasets (RNA seq and ATAC seq) generated by the host laboratory across multiple stages of zebrafish development, will be analysed to identify enhancers or enhancer clusters active in PAX6 expressing eye and brain cell types. This analysis will lead to developing a hypothesis describing spatial and temporal enhancer dynamics at both synthetic and endogenous PAX6 loci.

Phase 2: Resource Generation (Months 3–18)

CRISPR–Cas9 engineering will be used to modify synthetic regulatory landscapes in existing transgenic zebrafish lines, generating targeted deletions of individual enhancers or enhancer groups.

Phase 3: Data Generation and Analysis (Months 18–36)

Embryos carrying engineered deletions will be analysed using confocal and lattice light sheet microscopy, alongside single cell technologies (CAGE and ATAC seq), to determine how perturbations alter enhancer activity and gene expression outputs.

Training environment 

This PhD project will provide interdisciplinary training in synthetic biology, single cell omics, advanced imaging, and computational analysis. It aligns closely with ongoing work in the host laboratory on BBSRC funded consortium Decoding the Genome’s Hidden Grammar, ensuring extensive mentoring, training, and networking opportunities.

BBSRC Remit Area: Understanding the Rules of Life (within Advancing the Frontiers of Bioscience Discovery)