skip to content

Department of Physiology, Development and Neuroscience


Supervisor:  Srinjan Basu

Co-Supervisor: Jenny Nichols


Project 1:  Role of Mll complexes

Project 2:  Fgf signalling in regulating the dynamics of mouse pluripotent cell differentiation


The generation of diverse cell types in the early embryo from pluripotent cells is a hallmark of metazoan biology, yet the mechanisms that initiate and subsequently stabilise cell type-specific gene expression programmes remain ill-defined. These early cell fate decisions are thought to be governed by chromatin regulators (such as the mixed lineage leukemia MLL complex) but also the presence of positional cues from signalling molecules (such as Fgf).

While it is understood which cells produce certain signalling molecules and the specific signalling cascades which induce different genes to be expressed, little is known about how signalling molecules are delivered between cells or how the binding dynamics of these chromatin regulators change in response to these signals. Even less is known about how these dynamics differ inside the embryo versus in vitro where specific positional cues may be difficult to reconstruct.

To probe these dynamics at the sensitivity of single proteins, we have established imaging approaches that allow 3D tracking of signalling receptor molecules on cell membranes and the binding of proteins to chromatin in mouse embryonic stem cells in vitro (1-3). We have also established single-cell high-throughput sequencing approaches for determining the folding of the mouse genome at the level of single cells to determine how genome architecture is re-organised in response to specific signals(2). In on-going work, we are currently establishing similar approaches within mouse embryos. Ultimately, we aim to bridge the gap between signalling and the binding of chromatin regulators in vivo as well as in vitro.

The PhD project will therefore involve taking advantage of some of these novel interdisciplinary approaches to investigate either (Project 1) how specific chromatin regulators such as the MLL complexes or (Project 2) how specific signalling molecules such as Fgf4 impact early cell fate transitions during mouse embryo development. The project can entail single-molecule imaging of mouse embryonic stem cells or chimeric mouse embryos, or bulk and single-cell high-throughput sequencing approaches such as chromosome conformation capture, ChIP-seq or RNA-seq.

Relevant references:

1.  Carr et al. Three-Dimensional Super-Resolution in Eukaryotic Cells Using the Double-Helix Point Spread Function. Biophys J 112(7): 1444-1454 (2017).

2.  Stevens, Lando & Basu et al. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature 544: 59–64 (2017).

3.  Basu et al. Studying the dynamics of chromatin-binding proteins in mammalian cells using single-molecule localisation microscopy. Methods Mol Biol 1431: 235-263 (2016).

Social media