Hendrich Group – Starting Sept 2025 Prof Brian Hendrich Dr Nicola Reynolds Dr Ramy Ragheb Genna Davies Opportunity for LSI PHD studentship – starting in September 2025 or January 2026 PhD Studentship applications will open on 1st April (link will be here from 1st April), and the deadline will be 9th June 2025. For any information about these two projects, please contact the lead supervisor, Prof Brian Hendrich: B.Hendrich@exeter.ac.uk Project 1: Title of Project: Control of chromatin remodeller activity to direct cell fate decisions Supervisory Team: Prof Brian Hendrich (Bio/LSI), Dr Jonathan Phillips (Bio/LSI) Location: LSI Exeter Project Details: During development stem cells need to respond to extracellular signals in order to differentiate at the right time and in a lineage-appropriate fashion. Whether and how stem cells undergo lineage commitment depends upon how they control gene expression. Gene expression control is largely determined by how the relevant regulatory sequences are packaged into chromatin. Changes in gene expression are enacted by remodelling of the chromatin at regulatory sequences. Here, we aim to understand critical molecular mechanisms of the chromatin remodelling process. The chromatin remodelling protein CHD4 plays a central role in control of gene expression by determining which genes are able to respond to signals during developmental decisions. It does this by controlling the activity of enhancers, which in turn control gene expression, as part of a multiprotein chromatin remodelling complex called NuRD. NuRD activity is essential for embryonic stem cells to undergo lineage commitment in vitro and in vivo. CHD4 is also very important during human development, where mutation of only one of the two CHD4 alleles causes pleiotropic developmental disorders. We have found that CHD4 activity differs depending upon the protein partners with which is associates. In this project the student will define whether and how binding to different protein partners changes the structure, dynamics and stability of the CHD4 protein, and how that influences its remodelling activity. We will aim to modulate that activity by using this information to make specific mutations and to design proteins that bind to precise regions of CHD4. We will then test the ability of these perturbations to influence CHD4 activity in mammalian cells, and how this modulation influences the ability of different cell types to respond to inductive signals. This will provide training and experience with: protein expression, HDX-MS, NMR, in vitro remodelling assays, cloning/mutagenesis, ES cell culture and manipulation, RT-qPCR, ChIP, Cut&Run, bioinformatic sequence analyses, generative AI protein design (e.g. RFdiffusion) and deep learning models (e.g. BioEmu; DeepPath). Project 2: Title of Project: Molecular dissection of the acute signalling response in human pluripotent cells. Supervisory Team: Prof Brian Hendrich (Bio/LSI), Dr Ge Guo (CBS/LSI) Location: LSI Exeter Project Details: The student will determine how and when enhancers are activated in human pluripotent stem cells to drive lineage-specific gene expression as naïve cells undergo lineage specification. We will characterise protein binding patterns, chromatin accessibility and transcriptional output which occurs as cells are responding to a change in signalling levels at high temporal resolution. Using gene editing in human naïve pluripotent stem cells, the student will create inducible depletion alleles for key chromatin regulators and/or modifiers, and then determine the role played by each of these proteins during the signal response. Armed with knowledge of the molecular changes enabling cell fate specification, the student will then define how cell fate specification is enabled at the chromatin level in embryo-like structures created in cell culture which mimic the very first cell fate specification events in human embryogenesis. Here we will define in precise molecular detail how enhancers are configured to drive the second cell fate decision in human development. We will use the information gained to devise strategies for controlling the signal responsiveness of human pluripotent cells as they undergo developmentally relevant cell fate decisions. Basu, S. et al. Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD. (2023) https://doi.org/10.1038/s41594-023-01095-4 Bornelöv, S. et al. The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression. (2018) https://doi.org/10.1016/j.molcel.2018.06.003 Dattani, A. et al. Naive pluripotent stem cell-based models capture FGF-dependent human hypoblast lineage specification. (2024) https://doi/org/10.1016/j.stem.2024.05.003.