Supervisors and Projects

Project Code M1

Transposable elements as key players in gene regulation

Transcriptional regulation is the process by which a cell regulates the conversion of DNA to RNA to control gene expression. A plethora of factors - i.e.: promoter strengths, enhancers - are known to control gene expression.  However, so far, we have largely ignored the role of transposable elements (TEs) in gene regulation. TEs make up 50% of the mammalian genome and harbour regulatory elements that can affect gene expression. Consequently, TEs are kept transcriptionally silent in most somatic cells by epigenetic modifications. But these modifications are lifted during early mammalian development, hence TEs are expressed. Furthermore, the expression of TEs is necessary for early mammalian development, as knockdown of TE RNA leads to arrest in development at the 2-cell stage embryo. Despite progress in our understanding of TE expression in the early embryo, the role of TEs as regulators of developmental gene expression is missing. This project aims to uncover the rules of how TEs primarily control developmental gene expression.

Conventional technologies, have inherent limitations that prevent precise characterisation of locus-specific TE expression and robust functional studies during development. The Berrens lab developed an innovative single-cell long-read RNA-seq method, CELLO-seq to study TE expression. CELLO-seq enables us to enrich for full-length cDNAs and map TE transcripts in single cells and thus enables unique mapping of TE transcripts in single cells.

To knockdown individual TEs we have developed a clonal mouse embryonic stem cell line with an inducible CRISPRi system. Upon doxycycline addition, we can target dead Cas9 and a KRAB domain with guide RNAs to specific genomic loci for transcriptional silencing. We have previously knocked down a specific TE locus that is highly expressed in mouse embryonic stem cells and confirmed the knockdown with ONT direct DNA-seq as well as CELLO-seq.

As a DPhil project we will expand on the comprehensive investigation of how TEs control gene expression. Specifically, we will knockdown several old and young TEs next to developmental genes (Aim-1). We will knock-in the same TEs from aim-1 into a synthetic platform upstream of a reporter gene in mouse embryonic stem cells (Aim-2). In this synthetic system, individual landing pads will enable us to assess TE insertions at different distances from the same reporter. In aim-3 we will knock-out specific TEs that have effects on gene expression in vivo during preimplantation development to functionally study the role of TE loci in gene expression important for development.

Project Details

The primary aim of this project is to understand the rules of how TEs control gene expression important for development.

Specifically, we aim to answer the following questions:

• How do old versus young TEs control gene expression primarily?
• Is chromatin spreading to silence TEs a major mechanism by which TEs control gene expression?
• At what distances from the gene can we see and effect of TEs controlling gene expression?
• What is the functional role of TEs in early mammalian development?

The project will provide experience in a wide range of techniques, including:

• Gene editing
• Molecular and cell biology
• Single cell transcriptomics
• Long read sequencing
• Tissue culture: Embryonic stem cells
• Bioinformatics

References:

• Berrens, R. V.#, et al., 2022. Locus-specific expression of transposable elements in single cells with CELLO-seq. Nature Biotechnology, 40(4), Article 4. https://doi.org/10.1038/s41587-021-01093-z 
• Deaville, L.A., Berrens, R.V., 2024. Technology to the rescue: how to uncover the role of transposable elements in preimplantation development. Biochemical Society Transactions, BST20231262. https://doi.org/10.1042/BST20231262
• Vasiliauskaite, L., Berrens, R.V., et al., 2018. Defective germline reprogramming rewires the spermatogonial transcriptome. Nat Struct Mol Biol 25, 394-404. https://doi.org/10.1038/s41594-018-0058-0        

Dr Rebecca Berrens | Biochemistry (ox.ac.uk)

For informal enquiries: rebecca.berrens@bioch.ox.ac.uk

Project Code M2

Imaging chromatin accessibility during X inactivation and X reactivation

X chromosome inactivation (XCI) in mammals is a developmentally regulated process required to equalise expression levels of X-linked genes in XX females relative to XY males. Chromosome silencing is orchestrated by the non-coding RNA Xist. Briefly, Xist RNA accumulates in cis on the inactive X chromosome (Xi) elect, where it recruits protein complexes that mediate formation of repressive chromatin with resultant gene silencing. Once established Xi silencing is highly stable and is inherited through subsequent cell divisions throughout the lifetime of the animal.

Recent work has revealed that the key pathways for establishing Xi silencing are histone deacetylation mediated by the NCoR-HDAC3 co-repressor complex and histone H2AK119ub1 and H3K27me3 mediated by the Polycomb repressor complexes PRC1 and PRC2.  We aim to explore how these chromatin modifications impact on interactions of general and sequence specific transcription factors on X-linked genes/enhancers on the Xi chromosome, and moreover, to define the relative contributions of the different chromatin modifications. To achieve these goals we propose to use single molecule tracking (SMT) and allied advanced microscopy approaches.

In related work we will investigate X chromosome reactivation which occurs in maturing female germ cells and also during experimentally induced reprogramming (eg in iPS cell genesis).  This sub-project will apply similar imaging based methods to investigate reopening of Xi chromatin. 

Prof Neil Brockdorff | Biochemistry

For informal enquiries: neil.brockdorff@bioch.ox.ac.uk

Project Code M3

Single-molecule studies of DNA and chromatin replication

The copying of DNA, or DNA replication, is essential to cellular function. In eukaryotes it is carried out with high fidelity by a multi-protein complex called the replisome. Failure to do so can lead to defects in the copied genome, slow down or stall the replisome, and result in genomic instability or cell death. Mechanistic insight into normal replisome functioning is a prerequisite for understanding such failure and its downstream consequences.

This is an exciting time in eukaryotic DNA replication, as advances in genetics, biochemistry, and structural biology have identified the essential replisome components together with their stable arrangements. However, in operation the replisome is an active molecular machine with transient parts. Thus, a full mechanistic insight into this molecular machine requires a description of its dynamics. Because the replisome is active on DNA that is compacted into chromatin, this description must include the duplication and reassembly of all DNA-associated proteins. Understanding the coupling between these processes has fundamental implications for epigenetic inheritance and cancer.

Here, using an integrated approach at the interface of single-molecule biophysics and biochemistry, we will gain a biophysical understanding of the operation of an individual eukaryotic replisome by examining its functioning on DNA and chromatin:

• We will reveal how the intricate interplay between replisome components differs on DNA and defined chromatin landscapes.

• We will dissect the contributions of physical forces and histone chaperoning in establishing proper reassembly of DNA-associated proteins on daughter DNAs.

Integrating our findings with biochemical and structural data will yield new models of eukaryotic DNA replication.

This places us in a unique position to make major contributions to the field of eukaryotic DNA replication and provide it with powerful biophysical tools to investigate both fundamental and biomedically targeted questions.

Prof Nynke Dekker | Biochemistry (ox.ac.uk) 

For informal enquiries: nynke.dekker@physics.ox.ac.uk or belen.solanohermosilla@physics.ox.ac.uk

Project Code M4

Mechanistic understanding of the ubiquitin code during cell survival and programmed cell death

Our lab uses structural biology techniques such as cryo-EM, NMR, and X-ray crystallography, along with biochemical assays and biophysical methods including SEC-MALS, ITC, and MST to understand how the ubiquitin code maintains the balance between cell survival and cell death at a molecular level. Recently, our lab determined the cryo-EM structure of a large ubiquitin ligase that regulates apoptosis. Ongoing and future research will build upon this work and investigate other ubiquitin ligase complexes. Additionally, we study how deubiquitinating enzymes, which reverse the ubiquitin code, function alongside ubiquitin ligases.

Dr Paul Elliott | Biochemistry (ox.ac.uk)

For more information about the Elliott lab see: https://elliottlab.web.ox.ac.uk

For informal enquiries: paul.elliott@bioch.ox.ac.uk

Project Code M5

mitotic chromosomes in epigenetic inheritance

To understand how cellular identity is propagated when cells divide, we use advanced flow cytometry combined with mass spectrometry to systematically profile the proteins and RNAs that are retained on chromosomes throughout division. To assess the importance of these factors in chromosome structure, condensation and epigenetic inheritance, we deplete, degrade or cleave factors specifically at metaphase, and compare ‘untreated’ and ‘treated’ chromosomes by CryoET and optical tweezer approaches. The impact of the removal of specific factors on identity is measured by looking at nascent RNA expression in post mitotic daughter cells. This project will generated and use tools (particularly, BirA-TRF1 expressing cells and advanced flow cytometry) to isolate individual chromosomes and study how epigenetic inheritance is achieved during mitosis

Prof Dame Amanda Fisher | Biochemistry (ox.ac.uk)

For informal enquiries: amanda.fisher@bioch.ox.ac.uk

Project Code M6

How phosphorylation shapes centrosome function

Background

Centrosomes are small, membrane-free organelles that play a vital role in many cellular processes including cell division. They are best known for their contribution to mitotic spindle assembly and cilia formation but are also important for internal organisation of cells as well as for trafficking and signalling. When centrosomes go awry, the consequences can be serious: mutations in centrosomal proteins cause severe developmental disorders, and centrosome abnormalities are a common feature of many cancers.

Centrosomes are built of nearly 200 different proteins, and although our understanding of centrosome biogenesis has greatly improved, there is still much to discover about how their assembly and function are regulated. One key focus of our group is post-translational modification, particularly phosphorylation. Several essential kinases (e.g., members of the Aurora, Cdk and Polo-like kinase families) are known to modify centrosomal proteins, however, the full range of their targets withing the centrosome and, more importantly, the functional significance of these phosphorylation events remain largely unknown.

This study will investigate how phosphorylation regulates key centrosome protein modules, and more broadly, centrosome function. This is a discovery-driven project at the intersection of cell biology, molecular biology, and biochemistry. You will gain hands-on experience in a wide range of techniques, from cloning and mass spectrometry to advanced imaging and genome editing.

Ideal project for students who are curious, creative and motivated by the challenge of understanding complex cellular systems.

Project details

i. Discovery

We will map phosphorylation sites on centrosomal proteins using our recently developed mass-spectrometry-based CAPture method (Carden, Vitiello et al., 2023), combined with specific kinase inhibitors. The most compelling hits well be selected for validation and further analysis, focusing on proteins already linked to centrosome and cilia biogenesis, or microtubule organisation and dynamics.

ii. Building tools  

You will develop tools such as CRIPSR/Cas9-edited knockout and degron knock-in cells, fluorescently tagged cell lines and phospho-specific antibodies. These will enable you to dissect the roles of specific phosphorylation events in cells.

iii. Functional analyses

You will combine the toolkit you developed with cutting-edge technologies (i.e., super-resolution microscopy and proteomics) to investigate how regulatory sites on centrosomal proteins influence downstream cellular processes such as microtubule organisation, vesicle trafficking, and mitotic spindle formation in fixed and live cells.

iv Explore cellular diversity

We are particularly interested in whether centrosome regulation is consistent across different cell types. For instance, our lab has shown that erythroid progenitors remodel their centrosomes differently during mitosis (Tatrai and Gergely, 2022). You will investigate whether certain phosphorylation sites and their effects are cell-type specific.

Why this project?

Centrosome dysfunction can affect many physiological processes in an organism.  Indeed, as well as contributing to developmental disease, centrosome dysfunction is a hallmark of cancer. By understanding how phosphorylation regulates centrosome behaviour, we may uncover new insights into how cells maintain internal order, and what happens when that order is lost.

References:

Primary papers:

• Holder J+, Miles JA+, Batchelor M, Popple H, Walko M, Yeung M, Kannan N, Wilson AJ, Bayliss R*, Gergely F. (2024) CEP192 localises mitotic Aurora-A activity by priming its interaction with TPX2. EMBO J. 43 (22), 5381-5420.
• Carden S+, Vitiello E+, Rosa e Silva I, Holder J, Quarantotti V, Kishore K, Roamio Franklin VN, D'Santos C, Ochi T ^*, van Breugel M and Gergely F (2023). Proteomic profiling of centrosomes across multiple cell and tissue types by a new affinity capture method. Dev. Cell. 58, 21, 2393-2410. ..
• Tatrai P and Gergely F (2022) Centrosome function is critical during terminal erythroid differentiation. EMBO J. Jul 18;41(14):e108739.
• Quarantotti V, Chen J-X+, Tischer J+, Gonzalez Tejedo C, Papachristou E, D’Santos CS, Kilmartin JV, Miller ML, Gergely F (2019) Centriolar satellites are acentriolar assemblies of centrosomal proteins. EMBO J 38:e101082.

Reviews:

• Tischer J, Carden S, Gergely F (2021) Accessorizing the centrosome: new insights into centriolar appendages and satellites. Curr Opin Struct Biol. Feb;66:148-155. doi: 10.1016/j.sbi.2020.10.021.
• Chavali PL, Pütz M and Gergely F.  (2014) Small organelle, big responsibility: the role of centrosomes in development and disease. Phil. Trans. R. Soc. B 2014 (Theme Issue on the Centrosome).

For more information about the Gergely lab see: https://gergelylab.com

Dr Fanni Gergely | Biochemistry (ox.ac.uk)

For informal enquiries: fanni.gergely@bioch.ox.ac.uk

Project Code M7

Structural biology of bacterial molecular machines

Research in Ghilarov lab aims to reveal fundamental principles of how bacterial molecular machines use energy to manipulate three-dimensional structure of peptides and nucleic acids. Understanding these principles allows to control the activities of molecular machines, and ultimately to design artificial nanoscale devices. We are using a combination of cryoEM, X-ray crystallography, biochemistry, genetics and chemical biology approaches and collaborate with experts in modelling, protein design and single-molecule methods. Specific DPhil & MSc projects will be tuned to candidates’ interests, but must be related to one of the three lab themes:

Theme I: Ribosomally synthesized post-translationally modified peptides (RiPPs)

RiPPs enable bacterial competition, virulence, and defense against bacteriophages. RiPPs are genetically encoded, and converted into bioactive molecules by multienzyme complexes. Harnessing these complexes’ ability to modify custom peptides will allow synthesis of engineered molecules with programmed sequence. We are working on  different RiPP systems, including LAPs, lasso-peptides and thiopeptides, to get insights about RiPP biosynthesis, their ecological role, and to engineer them to create new-to-nature natural products[1,2].

Theme II: Bacterial DNA topoisomerases & antibiotic resistance

Bacterial type II topoisomerases gyrase and topoisomerase IV are essential for removing positively supercoiled DNA in front of the progressing polymerases, introducing negative supercoiling required for chromosomal homeostasis, and segregating daughter chromosomes after replication. They work in close connection with the replisome and SMC proteins, directly and indirectly affecting all genomic transactions in the cell. The research in the lab aims to address a fundamental question of how topoisomerases use energy of ATP to introduce defined topology in DNA. We have developed cryoEM approaches to study gyrase and topoisomerase IV, resulting in a determination of the first gyrase structure in complex with chirally wrapped DNA[3]. We are also interested in protein and small molecule inhibitors of topoisomerases as inspiration for a new generation of antibacterial drugs[4,5], and in mechanisms of resistance to antibiotics related to topoisomerases.

Theme III: Bacterial antiviral defense systems

The field of bacterial phage immunity is rapidly expanding and is one of the most exciting topics of contemporary microbiology. We are studying a complex defense system called BREX (bacteriophage exclusion system). BREX components are dissimilar to any other proteins, and their functions cannot be easily predicted or deduced. Many of them bear similarity to eukaryotic proteins such as ORC/Cdc6. BREX complex assemble on DNA in a megadalton-size multiprotein complex, preventing phage replication by an unknown mechanism. We have recently determined structures of methytransferase BrxX[6] responsible for the self/non-self discrimination within the complex, and are actively investigating other components and homologous systems.

[1] Ghilarov et al. Mol Cell (2019) https://doi.org/10.1016/j.molcel.2018.11.032

[2] Travin et al. JACS (2018) https://doi.org/10.1021/jacs.8b02277

[3] Michalczyk et al. PNAS (2024) https://doi.org/10.1073/pnas.2407398121

[4] Bakker et al. Nat Chem (2024) https://doi.org/10.1038/s41557-024-01516-x

[5] Michalczyk et al. Nat Catal (2023) https://doi.org/10.1038/s41929-022-00904-1

[6] Drobiazko et al. Nat Comm (2025)  https://doi.org/10.1038/s41467-025-57006-2

Ghilarov lab website: ghilarovlab.com

Associate Prof Dmitry Ghilarov | Biochemistry

For informal enquiries: Dmitry.ghilarov@bioch.ox.ac.uk

Project Code M8

Harnessing the power of computer simulations and AI to design new antibiotics

It is very likely that the next pandemic will be due to pathogenic bacteria. While bacteria evolve at a rapid rate and are very quickly becoming resistant to currently available antibiotics, pharmaceutical companies are hesitant to invest in the development of novel antibiotics. Therefore, the burden of doing so, falls upon the non-profit sector, i.e. academics and charities. To this end we are using molecular dynamics simulations and artificial intelligence (AI) methods to understand how bacteria protect themselves against antibiotics, so this knowledge can be exploited to develop novel therapeutic agents. We collaborate with experimental and computational groups within the UK and the USA including national laboratories in the USA. We are using experimentally determined data about the organisation and vulnerabilities of bacterial membranes to initiate our modelling and simulations which in turn provide key mechanistic information. The student will be trained in state-of-the-art molecular modelling and simulation techniques and AI approaches and will have the opportunity to work alongside exciting collaborators and attend national and international meetings.

Prof Syma Khalid | Biochemistry

For informal enquiries: syma.khalid@bioch.ox.ac.uk

Project Code M9

Immune and homeostatic regulation of intestinal stem cells in Drosophila

The intestinal interphase is where epithelial renewal and tissue maintenance is balanced alongside immunological regulation. How these functions integrate with cellular signalling is still under investigation. In the Drosophila gut, asymmetric mitosis of Intestinal Stem Cells (ISCs) produces Enteroblasts (EBs) that differentiate into Enterocytes (ECs). We study the role of the evolutionarily conserved innate immune Toll/NF-κB pathway in intestinal regeneration. We have found that the core components of the canonical Toll pathway are needed for ISC mitosis in homeostasis and infection. Conversely, Toll gain of function (with its ligand Spaetzle acting as a mitogen) pushes ISCs into mitosis and the EB fate but blocks EB to EC differentiation resulting in intestinal dysplasia. Moreover, gut bacteria density is increased. Toll activity is mediated by JNK and Akt/mTOR signalling. When JNKK, JNK, Akt or mTOR activity is reduced in gut progenitors, ISC mitosis is suppressed both during infection as well as in a Toll gain of function context. These results identify Toll as a regulator of the intestinal landscape integrating JNK and Akt signals to achieve gut tissue renewal and control of commensal bacteria.

The next step in this investigation is to identify if ISCs “sense” the gut lumen (both commensals and pathogens) and so able to activate responses pertaining to ISC proliferation and differentiation. We can isolate ISCs through FACS sorting. We will take advantage of the fact that Toll activation leads to perpetual ISC division to culture FACS-isolated ISCs to a) identify whether they are “cancer-like” and b) conduct cell-microbe interaction studies as well as transcriptomics and proteomics analysis to characterise the ISC response to Toll activity. Genetic manipulation of ISCs both in cell culture and in vivo will identify both upstream regulators of Toll activity as well as important effectors downstream of NF-κB function

Prof Petros Ligoxygakis | Biochemistry

For informal enquiries: petros.ligoxygakis@bioch.ox.ac.uk

Project Code M10

The role of epigenetics in evolution

The classic theory of Darwinian evolution puts genetic changes at the heart of the evolutionary process- changes in the DNA sequence are thought to be the source of variation upon which natural selection and drift can act.  However, it is becoming clear that some epigenetic changes, that affect gene expression but don’t change the underlying sequence of DNA, can be inherited between generations.  The contribution of this process to evolution is still largely unknown, and represents a fundamental question at the heart of contemporary study of evolution.   We have previously shown that spontaneous epigenetic changes, known as epimutations, occur in C. elegans as a result of small non-coding RNAs.  We showed that they arise in populations of the nematode C. elegans, and lead to changes in gene expression that can be inherited over a short number of generations in a laboratory setting (Wilson et al., PLoS Genetics 2023). These studies were performed in the absence of natural selection.  In this project, we now aim to investigate what happens to epimutations during conditions of selection.  We will use the development of resistance to nematocidal drugs as a model to test whether epimutations contribute to the evolution of resistance to drugs in C. elegans grown in the lab.  We will compare our results with studies on epigenetics in parasitic nematodes to understand whether epimutations might contribute to acquisition of resistance to drugs in nematodes that infect animals and plants.  Together, this work will address an important question in evolutionary biology: do epimutations contribute to the heritable variation that natural selection acts on in evolution? It will also give new insights into how epigenetic differences might be important in driving resistance to drugs in parasitic nematodes.  The work will involve both laboratory studies using C. elegans and computational analyses using a wide range of different types of data, including small non-coding RNAs, chromatin structure and comparative genomic analyses

Associate Prof Peter Sarkies | Biochemistry

For informal enquiries: peter.sarkies@bioch.ox.ac.uk

Project Code M11

Interrogating nuclear structure-function relationships in mammalian cells by advanced super-resolution imaging

Three-dimensional (3D) chromatin organisation plays a crucial role in regulating mammalian genome functions such as RNA transcription, replication and DNA repair. Population-based sequencing approaches (e.g. Hi-C) have highlighted the compartmentalisation of chromatin into 0.5-1 MB sized topologically associating domains (TADs). However, many of the physical features at the single-cell level are still underexplored. Our primary research objective is to identify principles and underlying mechanisms of functional chromatin organisation in mammalian cells. Specifically, we aim to understand the interplay between biophysical forces, epigenetic memory, and cohesin complex activity to modulate cell-type-specific transcriptional programs by directly visualising dynamic nuclear organisation and gene activity in living or 3D-preserved cells. To this end, we employ a combination of genetic editing with innovative in vivo/in situ fluorescence labelling and super-resolution imaging approaches. Our activities are closely linked to the Micron Oxford Advanced Bioimaging Unit and supported by our well-established ties to leading chromatin and epigenetic research groups within the Department and across the University of Oxford.

For a MSc/PhD project, we seek (an) enthusiastic, proactive, and adventurous student(s) eager to immerse themselves in the latest imaging technologies to study topographical and biophysical aspects of gene regulation in an interdisciplinary environment. The topic of the project can be along the lines of either (1) studying transcription factor dynamics within the context of mesoscale chromatin domains using correlative single-molecule tracking and super-resolution SIM imaging, (2) analysing loop-extruding and sister chromatid cohesive and loop-extruding cohesin complexes by super-resolution expansion microscopy (ExM) and/or super-resolution 3D correlative light and electron microscopy (CLEM), (3) studying the effect of directed phase separation on mesoscale domain organisation and transcriptional modulation, (4) examining mechanisms of gene reactivation during de-differentiation and/or epigenetic memory (e.g. after IFγ response), or (5) examining enhancer-promoter interactions e.g. in the alpha-globin locus, using multiplexed RNA-DNA-Immuno-FISH and correlative 3D super-resolution light end electron microscopy. The details of any project will be subject to personal preferences and will be worked out closer to the start date.

Main techniques: Mammalian tissue culture, molecular cloning, transfection, immunofluorescence labelling, fluorescence in situ hybridisation (DNA/RNA FISH), super-resolution structured illumination microscopy, single-molecule imaging, focussed ion beam scanning electron microscopy (FIB-SEM), computational image analysis.

Relevant papers:
 

Miron E, ..., Schermelleh L. 2020. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. Science Advances 6, eaba8811.

Brown JM, … Schermelleh L, Buckle VJ. 2022. RASER-FISH, a non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure. Nat Protoc 17, 1306-1331.

Ochs F, ..., Schermelleh L, Nasmyth KA. 2024. Sister chromatid cohesion is mediated by individual cohesin complexes. Science, 383: 1122-1130.
 

Schermelleh L et al. 2019. Super-resolution microscopy demystified. Nat Cell Biol 21: 72-84.

Associate Prof Lothar Schermelleh | Biochemistry (ox.ac.uk)

For informal enquiries: lothar.schermelleh@bioch.ox.ac.uk

Project Code M12

Protein structure and interactions in health and disease.

Our laboratory seeks to understand how protein functions arise from their molecular structure and interactions, and how these processes are involved in human health and disease. Projects in at least two areas are possible. (1) We have a long-standing interest in the molecular mechanisms by which Influenza virus proteins function. We are studying the protein-protein and lipid interactions of ‘flu’ proteins to better understand their role in the virus life cycle and to identify potential therapeutic targets. (2) More recently, we have begun to study the structure and function of chaperone proteins, especially J-domain proteins, to understand how they interact with misfolded/unfolded clients and with the HSP70 machinery.

A central technique of our laboratory is solution nuclear magnetic resonance (NMR) spectroscopy, which allows atomic-level studies of protein structures and their interactions. NMR can be uniquely informative in situations where the molecular conformations or interactions are dynamic or heterogeneous. However, we also use a wide variety of other biochemical and biophysical tools as needed for these investigations. We have collaborations with various research groups including virologists, cell biologists, and computational biologists.

Associate Prof Jason Schnell | Biochemistry (ox.ac.uk)

For informal enquiries: Jason.Schnell@bioch.ox.ac.uk

Project Code M13

Molecular mechanisms underlying viral evolution and host changes

We seek to understand how enveloped viruses evolve and use this knowledge to come up with ways to deal with future pandemics.

Many deadly human pathogens, such as influenza and SARS viruses, are made up of just a few components but can infect a number of different hosts. How is it possible that these components suffice to fulfil all the functions necessary for a virus to infect the cell and then to assemble into a new viral particle? How do viral proteins perform multiple functions and how does the virus manage to retain all these functions as it evolves? How does a virus infect different hosts using the same set of its own proteins to engage a range of machineries of different hosts? And, finally, how does a virus evolve and ‘learn’ to optimise its interactions with a new host?

The recent COVID-19 pandemic has demonstrated that these questions are key to understand where new viruses come from and how they evolve upon transmitting to a new host. We have used biochemical, biophysical, and structural methodologies, mainly cryoEM, to reveal the mechanisms by which SARS-CoV-2 became able to infect humans and then further evolved to optimise viral infectivity in the variants of concern. [1-7]

The lab continues to work on coronaviruses and studies influenza viruses to understand how their proteins achieve the versatility needed to infect diverse hosts and fulfil multiple functions during infection. In particular, we want to explain how related viral strains use similar glycoproteins to engage receptors as different as glycans and proteins. We are also interested in understanding how viral proteins come together during virus assembly: how do they find other viral components, how do they ‘coerce’ the host to transport them, and how do they exclude hosts proteins from growing viral particles.

Tackling these questions can directly impact public health. The more we understand the rules governing the evolution of viral proteins, the better we can predict the impact of emerging viruses and thus increase our pandemic preparedness. Our long-term aim is to use structural and mechanistic insights to guide design of much-needed new antivirals and vaccines against zoonotic viruses.

Several projects encompassing areas above are available in the lab. If you are interested, please apply and do not hesitate to get in touch earlier to discuss more details. I am committed to working with you to scope projects that combine your interests in specific research questions as well as methodologies, your long-term career aspirations, and available expertise and pilot data in the lab. In this way we will devise the MSc or DPhil project that bests suit you.

REFERENCES (#co-first, •corresponding):

1. Antoni G. Wrobel# (2023) “Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike” Current Opinions in Structural Biology 102619.

2. Valeria Calvaresi#, Antoni G. Wrobel#, Joanna Toporowska, Dietmar Hammerschmid, Katie J. Doores, Richard T. Bradshaw, Ricardo B. Parsons, Donald J. Benton, Chloë Roustan, Eamonn Reading, Michael H. Malim, Steven J. Gamblin, Argyris Politis#. (2023) “Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein” Nature Communications, 14 (1), 427

3. Antoni G. Wrobel*#, Donald J. Benton*#, Chloë Roustan, Annabel Borg, Saira Hussain, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin# (2022). “Evolution of the SARS-CoV-2 spike in the human host” Nature Communications 13, 1178.

4. Antoni G. Wrobel*#, Donald J. Benton*#, Pengqi Xu, Annabel Borg, Chloë Roustan, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin# (2021). “Structure and binding properties of Pangolin-CoV Spike glycoprotein inform the evolution of SARS-CoV-2.” Nature Communications, 12 (1), 837.

5. Donald J. Benton*#, Antoni G. Wrobel*#, Chloë Roustan, Annabel Borg, Pengqi Xu, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin#. (2021) “The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2” Proceedings of the National Academy of Sciences, 118(9), e2022586118.

6. Donald J. Benton*#, Antoni G. Wrobel*#, Pengqi Xu, Chloë Roustan, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin# (2020) “Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion” Nature 588(7837), 327–330.

7. Antoni G. Wrobel*#, Donald J. Benton*#, Pengqi Xu, Chloë Roustan, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin#  (2020) “SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.” Nature Structural and Molecular Biology 27, 763–767 (2020).

Dr Antoni Wrobel | Biochemistry

For informal enquiries: antoni.wrobel@bioch.ox.ac.uk

Project Code: M14

How cells make T-cell receptors

Accurate biogenesis of multi-subunit membrane protein complexes is vital for human health, with improper assembly of specific complexes associated with diverse diseases. Despite their critical roles in human physiology, our understanding of how these complexes assemble is still limited. Our group aims to address this knowledge gap, contributing fundamental insights into basic biology with important implications for translational science and human diseases.

To address this challenge, we will study the assembly of the human T-cell receptor as a foundational paradigm. T-cell receptors play essential roles in fighting pathogens, preventing autoimmunity, and developing personalised medicines, each of which relies on precisely controlled receptor assembly. Although downstream signalling pathways have been thoroughly characterised, how the T-cell receptor assembles from eight independently produced cognate subunits with accurate timing and stoichiometry remains elusive. Using a cell-free reconstitution approach, we have identified the first factor that is required for early steps of T-cell receptor assembly, which we will now thoroughly characterise using multi-disciplinary approaches such as in vitro reconstitution, flow cytometry, live-cell imaging, and structural studies. We will continue to systematically identify and characterise key factors required for each step of T-cell receptor assembly, providing comprehensive insights into the assembly pathway.

This project not only lays the foundation for understanding general principles of membrane protein complex assembly but also offers perspectives on exploring the therapeutic potential of targeting assembly pathways.

Some of my group's previous work, expertise, and techniques are highlighted here: https://tinyurl.com/haoxiwugooglescholar

Wu H, Smalinskaitė L, Hegde RS. EMC rectifies the topology of multipass membrane proteins. Nat Struct Mol Biol. 2024 Jan;31(1):32-41.

Wu H, Hegde RS. Mechanism of signal-anchor triage during early steps of membrane protein insertion. Mol Cell. 2023 Mar 16;83(6):961-973.e7.

Wu H, Voeltz GK. Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites. Dev Cell. 2021 Jan 11;56(1):52-66.e7.

Ho N*, Yap WS*, Xu J*, Wu H*, et al. Stress sensor Ire1 deploys a divergent transcriptional program in response to lipid bilayer stress. J Cell Biol. 2020 Jul 6;219(7):e201909165.

Wu H, Carvalho P, Voeltz GK. Here, there, and everywhere: The importance of ER membrane contact sites. Science. 2018 Aug 3;361(6401):eaan5835.

For informal enquiries: haoxiwu@mrc-lmb.cam.ac.uk 

Project code D1

Nanostructure labels for cryoET

Through electron cryotomography (cryoET) we can visualise cell environments at molecular resolution, revealing the structures and interactions that underpin cellular function (1). The full potential of cryoET remains untapped, in large part because specific molecules are challenging to identify. There is an unmet need for cryoET tags, analogous to fluorescent proteins in light microscopy (2). 

The Baker lab has pioneered DNA-based nanostructure tags known as SPOTs, which serve as markers for protein identification in cryoET (3). SPOTs are readily visualised within tomograms and can be engineered to selectively bind target proteins. The lab has successfully implemented this strategy for protein labelling on membranes in a number of different collaborative projects. 

This project will expand this tagging strategy for intracellular labelling in mammalian (and potentially bacterial) cells. The lab has demonstrated that SPOTs can be delivered to cells, and we now need to investigate how nanostructure designs, cell lines, surface coatings, and transfection strategies influence intracellular distribution, delivery efficiency, and binding behaviour to develop a robust pipeline for intracellular labelling. 

The Baker lab routinely uses cryoET, integrated with cryoFM and FIB-milling, to observe cell structure, and these techniques will be used to characterise intracellular labelling. There is also scope within the project to develop next-generation SPOT designs that incorporate conformational or fluorescent readouts upon binding their targets. Additionally, there are avenues to explore extending the capability of SPOTs through new targeting systems to expand their utility to broader classes of targets for both intracellular and extracellular labelling. 

References:  

Turk, Martin, and Wolfgang Baumeister. "The promise and the challenges of cryo‐electron tomography." FEBS letters 594.20 (2020): 3243-3261. 

Silvester E, Baker LA. Molecular tags for electron cryo-tomography. Emerging Topics in Life Sciences. 2024 Dec 5:ETLS20240006. 

Silvester, Emma, et al. "DNA origami signposts for identifying proteins on cell membranes by electron cryotomography." Cell 184.4 (2021): 1110-1121. 

Dr Lindsay Baker | Biochemistry (ox.ac.uk)

For informal enquiries: lindsay.baker@bioch.ox.ac.uk

Project Code D2

Bacterial nanomachines involved in cell envelope processes

Our group aims to understand how proteins and DNA are moved across and around the bacterial cell envelope and to characterize the nanomachines involved in these processes (https://benberksgroup.web.ox.ac.uk).

[i] Type 9 secretion system (T9SS). A newly-discovered outer membrane protein transport system important in pathogenic bacteria with many components and many open mechanistic questions.

[ii] Gliding motility. The most rapid known type of cellular motility across solid surfaces. A complex internal network of machines powers adhesins along the outer surface of the cell.

[iii] Horizontal gene transfer between bacteria by plasmid conjugation. The main route for the spread of antibiotic resistance (AMR) and other adaptive traits important for pathogens.

[iv] Outer membrane protein biogenesis in the Bacteroidota. In this major bacterial phylum that dominates the human gut microbiome, formation of the outer membrane is very different from the well-studied Escherichia coli model.

[v] Organisation and physical properties of the bacterial cell envelope. Analysis of protein behaviour in the cell envelope using advanced live cell fluorescence imaging techniques.

  We utilise a wide range of techniques to address these questions including protein characterisation (e.g pull-downs, purification, proteomics), bacterial genetics, cutting edge (single molecule) imaging of fluorescent proteins in live cells, and structural biology/structural bioinformatics.

     Papers that illustrate some of our experimental approaches:

Liu et al. (2025) A new paradigm for outer membrane protein biogenesis in the Bacteroidota.  https://doi.org/10.1101/2025.02.17.638638

Liu et al. (2025) A novel shared mechanism for Bacteroidota protein transport and gliding motility. https://doi.org/10.1101/2025.03.12.642685

Chen et al. (2025) Structure of the conjugation surface exclusion protein TraT. https://doi.org/10.1101/2025.05.27.656304

Lauber et al. (2024) Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. Nature Microbiology 9: 1089-1102.

Hennell James et al. (2021) Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility. Nature Microbiology 6: 221–233.

Lauber et al. (2018) Type 9 secretion system structures reveal a new protein transport mechanism. Nature 564: 77–82.

Alcock et al. (2016) Assembling the Tat protein translocase. eLife 5: e20718.

Alcock et al. (2013) Live cell imaging shows reversible assembly of the TatA component of the twin-arginine protein transport system. Proc Natl Acad Sci USA  110:  E3650–E3659.

Prof Ben Berks | Biochemistry (ox.ac.uk)

For more information about the Berks lab see: https://benberksgroup.web.ox.ac.uk

For informal enquiries: ben.berks@bioch.ox.ac.uk

Project Code D3

Transposable elements as key players in gene regulation

General Background

Transcriptional regulation is the process by which a cell regulates the conversion of DNA to RNA to control gene expression. A plethora of factors - i.e.: promoter strengths, enhancers - are known to control gene expression.  However, so far, we have largely ignored the role of transposable elements (TEs) in gene regulation. TEs make up 50% of the mammalian genome and harbour regulatory elements that can affect gene expression. Consequently, TEs are kept transcriptionally silent in most somatic cells by epigenetic modifications. But these modifications are lifted during early mammalian development, hence TEs are expressed. Furthermore, the expression of TEs is necessary for early mammalian development, as knockdown of TE RNA leads to arrest in development at the 2-cell stage embryo. Despite progress in our understanding of TE expression in the early embryo, the role of TEs as regulators of developmental gene expression is missing. This project aims to uncover the rules of how TEs primarily control developmental gene expression.

Conventional technologies, have inherent limitations that prevent precise characterisation of locus-specific TE expression and robust functional studies during development. The Berrens lab developed an innovative single-cell long-read RNA-seq method, CELLO-seq to study TE expression. CELLO-seq enables us to enrich for full-length cDNAs and map TE transcripts in single cells and thus enables unique mapping of TE transcripts in single cells.

To knockdown individual TEs we have developed a clonal mouse embryonic stem cell line with an inducible CRISPRi system. Upon doxycycline addition, we can target dead Cas9 and a KRAB domain with guide RNAs to specific genomic loci for transcriptional silencing. We have previously knocked down a specific TE locus that is highly expressed in mouse embryonic stem cells and confirmed the knockdown with ONT direct DNA-seq as well as CELLO-seq.

As a DPhil project we will expand on the comprehensive investigation of how TEs control gene expression. Specifically, we will knockdown several old and young TEs next to developmental genes (Aim-1). We will knock-in the same TEs from aim-1 into a synthetic platform upstream of a reporter gene in mouse embryonic stem cells (Aim-2). In this synthetic system, individual landing pads will enable us to assess TE insertions at different distances from the same reporter. In aim-3 we will knock-out specific TEs that have effects on gene expression in vivo during preimplantation development to functionally study the role of TE loci in gene expression important for development.

Project Details

The primary aim of this project is to understand the rules of how TEs control gene expression important for development.

Specifically, we aim to answer the following questions:

• How do old versus young TEs control gene expression primarily?
• Is chromatin spreading to silence TEs a major mechanism by which TEs control gene expression?
• At what distances from the gene can we see and effect of TEs controlling gene expression?
• What is the functional role of TEs in early mammalian development?

The project will provide experience in a wide range of techniques, including:

• Gene editing
• Molecular and cell biology
• Single cell transcriptomics
• Long read sequencing
• Tissue culture: Embryonic stem cells
• Bioinformatics

References:

• Berrens, R. V.#, et al., 2022. Locus-specific expression of transposable elements in single cells with CELLO-seq. Nature Biotechnology, 40(4), Article 4. https://doi.org/10.1038/s41587-021-01093-z 
• Deaville, L.A., Berrens, R.V., 2024. Technology to the rescue: how to uncover the role of transposable elements in preimplantation development. Biochemical Society Transactions, BST20231262. https://doi.org/10.1042/BST20231262
• Vasiliauskaite, L., Berrens, R.V., et al., 2018. Defective germline reprogramming rewires the spermatogonial transcriptome. Nat Struct Mol Biol 25, 394-404. https://doi.org/10.1038/s41594-018-0058-0        

Dr Rebecca Berrens | Biochemistry (ox.ac.uk)

For informal enquiries: Rebecca.berrens@bioch.ox.ac.uk

Project Code D4

1.  Antibiotic resistance 2. Transporters in cancer and antibiotic resistance 3.  Lysosomal ion channels.

We will have several potential projects in the lab that form part of our broader ambition to develop and/or use advanced computational methods to understand at the atomistic level key questions surrounding the transport of ions and molecules across different membranes.   Our main tool is molecular dynamics, but we also develop and use AI-based approaches (including deep-learning) and additionally, sometimes, quantum mechanics.  Understanding the details of proteins involved in transport also allows us to undertake aspects of early-stage drug design, which is another aspect we are particularly interested in.  Projects are highly flexible and can be tuned to build on student strengths or indeed focus on areas that students want to engage more with.  For that reason, the background of students that come to the lab is varied.  The only thing that is required is a desire to embed oneself in the project.

Prof Phil Biggin | Biochemistry (ox.ac.uk)

For informal enquiries: Philip.biggin@bioch.ox.ac.uk       

Project Code D5

Imaging chromatin accessibility during X inactivation and X reactivation

X chromosome inactivation (XCI) in mammals is a developmentally regulated process required to equalise expression levels of X-linked genes in XX females relative to XY males. Chromosome silencing is orchestrated by the non-coding RNA Xist. Briefly, Xist RNA accumulates in cis on the inactive X chromosome (Xi) elect, where it recruits protein complexes that mediate formation of repressive chromatin with resultant gene silencing. Once established Xi silencing is highly stable and is inherited through subsequent cell divisions throughout the lifetime of the animal.

Recent work has revealed that the key pathways for establishing Xi silencing are histone deacetylation mediated by the NCoR-HDAC3 co-repressor complex and histone H2AK119ub1 and H3K27me3 mediated by the Polycomb repressor complexes PRC1 and PRC2.  We aim to explore how these chromatin modifications impact on interactions of general and sequence specific transcription factors on X-linked genes/enhancers on the Xi chromosome, and moreover, to define the relative contributions of the different chromatin modifications. To achieve these goals we propose to use single molecule tracking (SMT) and allied advanced microscopy approaches.

In related work we will investigate X chromosome reactivation which occurs in maturing female germ cells and also during experimentally induced reprogramming (eg in iPS cell genesis).  This sub-project will apply similar imaging based methods to investigate reopening of Xi chromatin. 

Prof Neil Brockdorff | Biochemistry

For informal enquiries: neil.brockdorff@bioch.ox.ac.uk

Project Code D6

Structural biology of DNA topology remodelling machines

Genetic information is stored in spectacularly large and thread-like molecules, the chromosomal DNA. This poses the fundamental “spaghetti problem”: DNA entanglements must be prevented by creating structured entities called nucleoids or chromosomes. Structural maintenance of chromosomes (SMC) complexes and DNA topoisomerases solve this issue in most if not all organisms.

We are interested in:

1. How ring-like SMC complexes use the power of ATP hydrolysis to extrude large DNA loops
2. How SMC complexes cooperate with DNA topoisomerases to prevent DNA entanglements
3. How pathogens such as bacteriophages and infective plasmids manipulate host chromosomes, and interact with host defences that use the mechanisms above

We address these questions using biochemical reconstitution, cryo-EM, and advanced bacterial genetics. We capture bacterial and viral genome remodelling machines in action, aiming to directly visualize how they work. Our long-term goal is a full mechanistic understanding of the processes that control the three-dimensional structure of chromosomes across the tree of life.

Dr Frank Bürmann | Biochemistry (ox.ac.uk)

For informal enquiries: frank.burmann@bioch.ox.ac.uk

Project Code D7

Single-molecule studies of DNA and chromatin replication

The copying of DNA, or DNA replication, is essential to cellular function. In eukaryotes it is carried out with high fidelity by a multi-protein complex called the replisome. Failure to do so can lead to defects in the copied genome, slow down or stall the replisome, and result in genomic instability or cell death. Mechanistic insight into normal replisome functioning is a prerequisite for understanding such failure and its downstream consequences.

This is an exciting time in eukaryotic DNA replication, as advances in genetics, biochemistry, and structural biology have identified the essential replisome components together with their stable arrangements. However, in operation the replisome is an active molecular machine with transient parts. Thus, a full mechanistic insight into this molecular machine requires a description of its dynamics. Because the replisome is active on DNA that is compacted into chromatin, this description must include the duplication and reassembly of all DNA-associated proteins. Understanding the coupling between these processes has fundamental implications for epigenetic inheritance and cancer.

Here, using an integrated approach at the interface of single-molecule biophysics and biochemistry, we will gain a biophysical understanding of the operation of an individual eukaryotic replisome by examining its functioning on DNA and chromatin:

• We will reveal how the intricate interplay between replisome components differs on DNA and defined chromatin landscapes.

• We will dissect the contributions of physical forces and histone chaperoning in establishing proper reassembly of DNA-associated proteins on daughter DNAs.

Integrating our findings with biochemical and structural data will yield new models of eukaryotic DNA replication.

This places us in a unique position to make major contributions to the field of eukaryotic DNA replication and provide it with powerful biophysical tools to investigate both fundamental and biomedically targeted questions.

Prof Nynke Dekker | Biochemistry (ox.ac.uk) 

for informal enquiries: nynke.dekker@physics.ox.ac.uk or belen.solanohermosilla@physics.ox.ac.uk

Project Code D8

Mechanistic understanding of the ubiquitin code during cell survival and programmed cell death

Our lab uses structural biology techniques such as cryo-EM, NMR, and X-ray crystallography, along with biochemical assays and biophysical methods including SEC-MALS, ITC, and MST to understand how the ubiquitin code maintains the balance between cell survival and cell death at a molecular level. Recently, our lab determined the cryo-EM structure of a large ubiquitin ligase that regulates apoptosis. Ongoing and future research will build upon this work and investigate other ubiquitin ligase complexes. Additionally, we study how deubiquitinating enzymes, which reverse the ubiquitin code, function alongside ubiquitin ligases.

Dr Paul Elliott | Biochemistry (ox.ac.uk)

For more information about the Elliott lab see: https://elliottlab.web.ox.ac.uk

For informal enquiries: paul.elliott@bioch.ox.ac.uk

Project Code D9

mitotic chromosomes in epigenetic inheritance

To understand how cellular identity is propagated when cells divide, we use advanced flow cytometry combined with mass spectrometry to systematically profile the proteins and RNAs that are retained on chromosomes throughout division. To assess the importance of these factors in chromosome structure, condensation and epigenetic inheritance, we deplete, degrade or cleave factors specifically at metaphase, and compare ‘untreated’ and ‘treated’ chromosomes by CryoET and optical tweezer approaches. The impact of the removal of specific factors on identity is measured by looking at nascent RNA expression in post mitotic daughter cells. This project will generated and use tools (particularly, BirA-TRF1 expressing cells and advanced flow cytometry) to isolate individual chromosomes and study how epigenetic inheritance is achieved during mitosis.

Prof Dame Amanda Fisher | Biochemistry (ox.ac.uk)

For informal enquiries: amanda.fisher@bioc.ox.ac.uk; 

Project Code D10

How phosphorylation shapes centrosome function

Background

Centrosomes are small, membrane-free organelles that play a vital role in many cellular processes including cell division. They are best known for their contribution to mitotic spindle assembly and cilia formation but are also important for internal organisation of cells as well as for trafficking and signalling. When centrosomes go awry, the consequences can be serious: mutations in centrosomal proteins cause severe developmental disorders, and centrosome abnormalities are a common feature of many cancers.

Centrosomes are built of nearly 200 different proteins, and although our understanding of centrosome biogenesis has greatly improved, there is still much to discover about how their assembly and function are regulated. One key focus of our group is post-translational modification, particularly phosphorylation. Several essential kinases (e.g., members of the Aurora, Cdk and Polo-like kinase families) are known to modify centrosomal proteins, however, the full range of their targets withing the centrosome and, more importantly, the functional significance of these phosphorylation events remain largely unknown.

This study will investigate how phosphorylation regulates key centrosome protein modules, and more broadly, centrosome function. This is a discovery-driven project at the intersection of cell biology, molecular biology, and biochemistry. You will gain hands-on experience in a wide range of techniques, from cloning and mass spectrometry to advanced imaging and genome editing.

Ideal project for students who are curious, creative and motivated by the challenge of understanding complex cellular systems.

Project details

i. Discovery

We will map phosphorylation sites on centrosomal proteins using our recently developed mass-spectrometry-based CAPture method (Carden, Vitiello et al., 2023), combined with specific kinase inhibitors. The most compelling hits well be selected for validation and further analysis, focusing on proteins already linked to centrosome and cilia biogenesis, or microtubule organisation and dynamics.

ii. Building tools  

You will develop tools such as CRIPSR/Cas9-edited knockout and degron knock-in cells, fluorescently tagged cell lines and phospho-specific antibodies. These will enable you to dissect the roles of specific phosphorylation events in cells.

iii. Functional analyses

You will combine the toolkit you developed with cutting-edge technologies (i.e., super-resolution microscopy and proteomics) to investigate how regulatory sites on centrosomal proteins influence downstream cellular processes such as microtubule organisation, vesicle trafficking, and mitotic spindle formation in fixed and live cells.

iv Explore cellular diversity

We are particularly interested in whether centrosome regulation is consistent across different cell types. For instance, our lab has shown that erythroid progenitors remodel their centrosomes differently during mitosis (Tatrai and Gergely, 2022). You will investigate whether certain phosphorylation sites and their effects are cell-type specific.

Why this project?

Centrosome dysfunction can affect many physiological processes in an organism.  Indeed, as well as contributing to developmental disease, centrosome dysfunction is a hallmark of cancer. By understanding how phosphorylation regulates centrosome behaviour, we may uncover new insights into how cells maintain internal order, and what happens when that order is lost.

References:

Primary papers:

• Holder J+, Miles JA+, Batchelor M, Popple H, Walko M, Yeung M, Kannan N, Wilson AJ, Bayliss R*, Gergely F. (2024) CEP192 localises mitotic Aurora-A activity by priming its interaction with TPX2. EMBO J. 43 (22), 5381-5420.
• Carden S+, Vitiello E+, Rosa e Silva I, Holder J, Quarantotti V, Kishore K, Roamio Franklin VN, D'Santos C, Ochi T ^*, van Breugel M and Gergely F (2023). Proteomic profiling of centrosomes across multiple cell and tissue types by a new affinity capture method. Dev. Cell. 58, 21, 2393-2410. ..
• Tatrai P and Gergely F (2022) Centrosome function is critical during terminal erythroid differentiation. EMBO J. Jul 18;41(14):e108739.
• Quarantotti V, Chen J-X+, Tischer J+, Gonzalez Tejedo C, Papachristou E, D’Santos CS, Kilmartin JV, Miller ML, Gergely F (2019) Centriolar satellites are acentriolar assemblies of centrosomal proteins. EMBO J 38:e101082.

Reviews:

• Tischer J, Carden S, Gergely F (2021) Accessorizing the centrosome: new insights into centriolar appendages and satellites. Curr Opin Struct Biol. Feb;66:148-155. doi: 10.1016/j.sbi.2020.10.021.
• Chavali PL, Pütz M and Gergely F.  (2014) Small organelle, big responsibility: the role of centrosomes in development and disease. Phil. Trans. R. Soc. B 2014 (Theme Issue on the Centrosome).

For more information about the Gergely lab see: https://gergelylab.com

Dr Fanni Gergely | Biochemistry (ox.ac.uk)

For informal enquiries: fanni.gergely@bioch.ox.ac.uk

Project Code D11

Structural biology of bacterial molecular machines

Research in Ghilarov lab aims to reveal fundamental principles of how bacterial molecular machines use energy to manipulate three-dimensional structure of peptides and nucleic acids. Understanding these principles allows to control the activities of molecular machines, and ultimately to design artificial nanoscale devices. We are using a combination of cryoEM, X-ray crystallography, biochemistry, genetics and chemical biology approaches and collaborate with experts in modelling, protein design and single-molecule methods. Specific DPhil & MSc projects will be tuned to candidates’ interests, but must be related to one of the three lab themes:

Theme I: Ribosomally synthesized post-translationally modified peptides (RiPPs)

RiPPs enable bacterial competition, virulence, and defense against bacteriophages. RiPPs are genetically encoded, and converted into bioactive molecules by multienzyme complexes. Harnessing these complexes’ ability to modify custom peptides will allow synthesis of engineered molecules with programmed sequence. We are working on  different RiPP systems, including LAPs, lasso-peptides and thiopeptides, to get insights about RiPP biosynthesis, their ecological role, and to engineer them to create new-to-nature natural products[1,2].

Theme II: Bacterial DNA topoisomerases & antibiotic resistance

Bacterial type II topoisomerases gyrase and topoisomerase IV are essential for removing positively supercoiled DNA in front of the progressing polymerases, introducing negative supercoiling required for chromosomal homeostasis, and segregating daughter chromosomes after replication. They work in close connection with the replisome and SMC proteins, directly and indirectly affecting all genomic transactions in the cell. The research in the lab aims to address a fundamental question of how topoisomerases use energy of ATP to introduce defined topology in DNA. We have developed cryoEM approaches to study gyrase and topoisomerase IV, resulting in a determination of the first gyrase structure in complex with chirally wrapped DNA[3]. We are also interested in protein and small molecule inhibitors of topoisomerases as inspiration for a new generation of antibacterial drugs[4,5], and in mechanisms of resistance to antibiotics related to topoisomerases.

Theme III: Bacterial antiviral defense systems

The field of bacterial phage immunity is rapidly expanding and is one of the most exciting topics of contemporary microbiology. We are studying a complex defense system called BREX (bacteriophage exclusion system). BREX components are dissimilar to any other proteins, and their functions cannot be easily predicted or deduced. Many of them bear similarity to eukaryotic proteins such as ORC/Cdc6. BREX complex assemble on DNA in a megadalton-size multiprotein complex, preventing phage replication by an unknown mechanism. We have recently determined structures of methytransferase BrxX[6] responsible for the self/non-self discrimination within the complex, and are actively investigating other components and homologous systems.

[1] Ghilarov et al. Mol Cell (2019) https://doi.org/10.1016/j.molcel.2018.11.032

[2] Travin et al. JACS (2018) https://doi.org/10.1021/jacs.8b02277

[3] Michalczyk et al. PNAS (2024) https://doi.org/10.1073/pnas.2407398121

[4] Bakker et al. Nat Chem (2024) https://doi.org/10.1038/s41557-024-01516-x

[5] Michalczyk et al. Nat Catal (2023) https://doi.org/10.1038/s41929-022-00904-1

[6] Drobiazko et al. Nat Comm (2025)  https://doi.org/10.1038/s41467-025-57006-2

Ghilarov lab website: ghilarovlab.com

Associate Prof Dmitry Ghilarov | Biochemistry

For informal enquiries: Dmitry.ghilarov@bioch.ox.ac.uk

Project Code D12

Structural biology of host-parasite interactions and structure-guided vaccine design.

Prospective applicants can learn about our research programs from our website (higginslab.web.ox.ac.uk) and we have a variety of possible projects related to host-parasite interactions and structure-guided vaccine design. Please contact Matt for more information.

For more information about the Higgins lab see: higginslab.web.ox.ac.uk    

Prof Matt Higgins | Biochemistry (ox.ac.uk)

For informal enquiries: matthew.higgins@bioch.ox.ac.uk

Project Code D13

Discovering mechanisms of chromatin-based inheritance of human centromeres

Our lab aims to discover how chromosome structure and patterns of gene expression are maintained through mitotic divisions. Specifically, histones and their modifications are implicated in heritable, self-templated feedback loops. Our goal is to discover the mechanistic basis of this chromatin-based cellular memory. We focus on the human centromere, which serves as a paradigm of heritable chromatin.

The Human Centromere

Centromeres are chromosomal loci that form the attachment site for spindle microtubules, driving chromosome segregation in mitosis. Centromeres are defined by a unique chromatin structure featuring the histone H3 variant CENP-A. Nucleosomes containing CENP-A are at the centre of an epigenetic feedback loop where chromatin-bound CENP-A is sufficient to initiate self-templated inheritance of centromeres, even on ectopic genomic loci, called neocentromeres. A DPhil project will be focused on questions related to 1) how CENP-A chromatin domains form de novo, driving centromere formation, 2) how CENP-A chromatin can be transmitted through cell division and 3) how its assembly is cell cycle controlled.

Key methodologies include mammalian cell culture, CRISPR-based genome editing to establish human cell models for human centromere assembly, microscopy-based fluorescent pulse labelling technologies to visualise both ancestral as well as nascent pools of CENP-A histones, live cell imaging, CUT&RUN-sequencing  as well as the latest nanopore long-read sequencing methods to understand chromatin structure at highly repetitive satellite repeats.

We run a dynamic team of postdocs and students that thrive on scientific enthusiasm and offer expertise and support. See www.jansenlab.org for more information. Do get in touch if you have any queries.

Prof Lars Jansen | Biochemistry (ox.ac.uk)

For informal enquiries: lars.jansen@bioch.ox.ac.uk

Project Code D14

Harnessing the power of computer simulations and AI to design new antibiotics

It is very likely that the next pandemic will be due to pathogenic bacteria. While bacteria evolve at a rapid rate and are very quickly becoming resistant to currently available antibiotics, pharmaceutical companies are hesitant to invest in the development of novel antibiotics. Therefore, the burden of doing so, falls upon the non-profit sector, i.e. academics and charities. To this end we are using molecular dynamics simulations and artificial intelligence (AI) methods to understand how bacteria protect themselves against antibiotics, so this knowledge can be exploited to develop novel therapeutic agents. We collaborate with experimental and computational groups within the UK and the USA including national laboratories in the USA. We are using experimentally determined data about the organisation and vulnerabilities of bacterial membranes to initiate our modelling and simulations which in turn provide key mechanistic information. The student will be trained in state-of-the-art molecular modelling and simulation techniques and AI approaches and will have the opportunity to work alongside exciting collaborators and attend national and international meetings.

To find out more about the Khalid lab see: https://khalidlab.web.ox.ac.uk/

Prof Syma Khalid | Biochemistry (ox.ac.uk)

For informal enquiries: syma.khalid@bioch.ox.ac.uk

Project Code D15

Discovering how epigenetics regulate gene expression in stem cells

Controlling how our genes are expressed is fundamental to cell function and development. While the molecular biology revolution of the mid-twentieth century defined the central dogma which states that DNA instructs the production of RNA and then protein, the mechanisms that unpin how the earliest steps of this cascade are controlled, namely how DNA is read and transcribed into the RNA, remains very poorly understood. In eukaryotes, the ability to read DNA sequence is profoundly influenced by histones that package DNA into chromatin, and chromatin constitutes a central epigenetic regulator of RNA production and gene expression. However, our understanding of the mechanisms that enable epigenetic systems to control gene expression remain rudimentary at best. To address this fundamental problem, we use embryonic stems cells as a model to study how chromatin and epigenetic systems regulate gene expression to ensure stem cells remain pluripotent and can also support cellular differentiation and organismal development.

In the context of this overarching focus of the laboratory, a project is available to examine how proteins that function at CpG island elements (epigenetically defined elements associated with gene promoters in mammals) contribute to regulation of gene expression. The student will use and develop (via CRISPR-based genome engineering) embryonic stem cell lines containing degrons to rapidly deplete epigenetic regulators. They will then use genomic approaches coupled with next generation sequencing (ChIP-seq, RNA-seq, etc.) and/or live-cell imaging to determine how these systems affect chromatin modifications and gene expression. In particular, this will be applied to components of either the Polycomb repressive or Trithorax activator systems, which are paradigms of epigenetic gene regulation in mammals. As the project progresses there will also be an opportunity to dissect how these systems are used to regulate gene expression during cellular differentiation. The student will benefit from extensive support and training in the approaches necessary to tackle these fascinating problems, and will be at the forefront of uncovering how the epigenome shapes gene regulation and genome function.

(1) The PNUTS phosphatase complex controls transcription pause release. Kelley JR, Dimitrova E, Maciuszek M, Nguyen HT, Szczurek AT, Hughes AL, Blackledge NP, Kettenbach AN, Klose RJ. Molecular Cell, 2024.

(2) The Polycomb system sustains promoters in a deep OFF state by limiting pre-initiation complex formation to counteract transcription. Szczurek AT, Dimitrova E, Kelley JR, Blackledge NP, Klose RJ. Nature Cell Biology, 2024.

(3) A CpG island-encoded mechanism protects genes from premature transcription termination. Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. Nature Communications, 2023.

(4) Recycling of modified H2A-H2B provides short-term memory of chromatin states.

Flury V, Reverón-Gómez N, Alcaraz N, Stewart-Morgan KR, Wenger A, Klose RJ, Groth A. Cell, 2023.

(5) Distinct roles for CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction. Dimitrova E, Feldmann A, van der Weide RH, Flach KD, Lastuvkova A, de Wit E, Klose RJ. Nature Structural and Molecular Biology, 2022.

Prof Rob Klose | Biochemistry (ox.ac.uk)

For informal enquiries: rob.klose@bioch.ox.ac.uk

Project Code: D16

Cytoskeletal organisation of the malaria parasite

The malaria parasite, Plasmodium falciparum, infects various cell types within its insect and human hosts as part of a complex life cycle (1). In the human bloodstream, the parasite invades red blood cells to replicate inside, hidden away from the host immune system. To invade these cells, the parasite uses specialised invasive organelles, the rhoptries and micronemes (2).

The parasite cell needs to be precisely organised to successfully invade the host. The rhoptries and micronemes are held at the apical end of the cell, whereas its nucleus, mitochondria and other organelles are held toward the basal end (3). It is not known how the cell sets up and maintains this striking polarisation. One class of proteins proposed to contribute are the various cytoskeletal filaments that form fascinating structures throughout the parasite. This is exemplified by the microtubules, which form a beautiful array along the parasite membrane (4). However how these filaments link to other structures in the cell to carry out their function remains mysterious. Our lab is interested in how these filament systems position and shape organelles throughout the parasite cell. Our primary techniques are in vitro structural biology and biophysics, though we are expanding into in vivo techniques to examine these proteins within the malaria parasite itself.

The aim of this DPhil project is to further our understanding into how organelles are linked to the microtubule cytoskeleton in the malaria parasite. We will explore the following questions: We will identify and characterise novel microtubule-binding proteins to see how they link organelles to microtubules in vitro and in vivo. We will examine how they recruit organelles to the cytoskeleton using electron microscopy, then design assays to test their functional dynamics using biophysical techniques including TIRF microscopy. To dissect the protein function in cells we will use CRISPR/Cas9-based strategies to modify the protein inside the parasite. We will explore their localisation in cells and examine the consequences of knocking out the protein using light microscopy. Please contact clinton.lau@bioch.ox.ac.uk, and see https://laulab.web.ox.ac.uk/ for more details.

References

1. Venugopal, K. et al. Nat. Rev. Microbiol. 2020 183 18, 177–189 (2020). https://doi.org/10.1038/s41579-019-0306-2
2. Schrevel, J. et al. Parasitology 135, 1–12 (2008). https://doi.org/10.1017/S0031182007003629
3. Fowler, R. E. et al. Parasitology 117, 425–433 (1998). https://doi.org/10.1017/S003118209800328X
4. Ferreira, J. et al. bioRxiv (2022). https://doi.org/10.1101/2022.04.13.488170

Dr Clinton Lau | Biochemistry (ox.ac.uk)

For informal enquiries from prospective students: Clinton.lau@bioch.ox.ac.uk

Project Code D17

Immune and homeostatic regulation of intestinal stem cells in Drosophila.

The intestinal interphase is where epithelial renewal and tissue maintenance is balanced alongside immunological regulation. How these functions integrate with cellular signalling is still under investigation. In the Drosophila gut, asymmetric mitosis of Intestinal Stem Cells (ISCs) produces Enteroblasts (EBs) that differentiate into Enterocytes (ECs). We study the role of the evolutionarily conserved innate immune Toll/NF-κB pathway in intestinal regeneration. We have found that the core components of the canonical Toll pathway are needed for ISC mitosis in homeostasis and infection. Conversely, Toll gain of function (with its ligand Spaetzle acting as a mitogen) pushes ISCs into mitosis and the EB fate but blocks EB to EC differentiation resulting in intestinal dysplasia. Moreover, gut bacteria density is increased. Toll activity is mediated by JNK and Akt/mTOR signalling. When JNKK, JNK, Akt or mTOR activity is reduced in gut progenitors, ISC mitosis is suppressed both during infection as well as in a Toll gain of function context. These results identify Toll as a regulator of the intestinal landscape integrating JNK and Akt signals to achieve gut tissue renewal and control of commensal bacteria.

The next step in this investigation is to identify if ISCs “sense” the gut lumen (both commensals and pathogens) and so able to activate responses pertaining to ISC proliferation and differentiation. We can isolate ISCs through FACS sorting. We will take advantage of the fact that Toll activation leads to perpetual ISC division to culture FACS-isolated ISCs to a) identify whether they are “cancer-like” and b) conduct cell-microbe interaction studies as well as transcriptomics and proteomics analysis to characterise the ISC response to Toll activity. Genetic manipulation of ISCs both in cell culture and in vivo will identify both upstream regulators of Toll activity as well as important effectors downstream of NF-κB function.   

Prof Petros Ligoxygakis | Biochemistry

For informal enquiries: petros.ligoxygakis@bioch.ox.ac.uk

Project Code D18

Regulation of p53 by aberrant ribosome biogenesis

Introduction:

Ribosomes are essential molecular machines responsible for protein synthesis and their biogenesis is tightly regulated in normal human cells. In cancer cells, however, ribosome biogenesis often becomes grossly dysregulated, constituting a hallmark of malignancy ¹. A consequence of impaired ribosome biogenesis is the activation of the tumour suppressor p53, through a surveillance mechanism termed the Impaired Ribosome Biogenesis Checkpoint (IRBC). Despite its importance, many questions about the molecular mechanisms linking the IRBC and the p53 pathway remain unanswered².

Objectives:

This DPhil project will investigate how p53 is activated in response to disruption of ribosome biogenesis. Leveraging the complementary expertise of the Mardakheh (ribosome biology) and Barr (mitosis and p53 regulation) labs, the project will address three key questions:

1. What is the role of ribosomal components in IRBC?

It is postulated that disruption of ribosome large subunit biogenesis leads to accumulation of free 5S ribonucleoprotein complexes (5S ribosomal-RNA with RPL5 and RPL11), which bind to and inhibit MDM2, the E3 ligase that targets p53 for degradation². However, this model is insufficient to explain how ribosomal biogenesis defects that do not lead to free 5S complexes still trigger p53 activation. To resolve question, we will apply TREX, a novel proteomics-based method to map protein-RNA interactions within living cells³. By targeting ribosomal RNAs under normal and IRBC-activated conditions, we will generate region-specific RNA-protein interaction maps to systematically identify changes to the ribosome composition, detect aberrant complexes, and clarify which ribosomal disruptions engage with the MDM2-p53 machinery.

2. What are the changes to the MDM2–p53 axis upon IRBC?

We will also explore other known regulators of MDM2, such as the tumour suppressor ARF, may influence p53 stability under ribosomal stress⁴, as their roles in IRBC remain unexplored. Using mass spectrometry we will define the interactome of MDM2 following insults to ribosome biogenesis, identifying novel interactors and regulators. In addition we will define the post-translational modifications (PTMs) on p53 following ribosome disruption, using mass spectrometry. Follow up functional studies will explore the roles of the candidate proteins and PTMs in the IRBC.

3. Does translational control influence p53 activation during disrupted ribosome biogenesis?

Recent findings have shown that p53 can be activated in new G1 cells due to reduced MDM2 synthesis following delays in mitosis⁵. Whether similar translational constraints promote p53 stabilisation during impaired ribosome biogenesis is currently unknown. To test this, we will use single cell reporters for MDM2 and p53 mRNAs to monitor their synthesis rates following insults to ribosome synthesis⁶. Experiments with exogenously expressed MDM2 from altered mRNAs, or mutants with increased half-life, will be subsequently used to assess whether translational attenuation of MDM2 is an important trigger for p53 stabilisation during IRBC.

Outcomes and Impact:

This project will clarify the molecular mechanisms linking p53 activation to disrupted ribosome biogenesis. Given the prevalence of dysregulated ribosome biogenesis and protein synthesis in aneuploid cancers, insights from this study could inform new therapeutic strategies in the future.

References:

1     https://doi.org/10.1038/nrc.2017.104

2     https://doi.org/10.1016/j.trecan.2020.08.003

3     https://doi.org/10.1038/s41592-024-02181-1

4     https://doi.org/10.1038/8991

5     https://doi.org/10.1038/s41556-024-01592-8

6     https://doi.org/10.1038/s41596-019-0284-x

Associate Prof Faraz Mardakheh | Biochemistry

For informal enquiries: faraz.mardakheh@bioch.ox.ac.uk or francis.barr@bioch.ox.ac.uk

Project Code D19

Optimized sybody activators of lysosomal ion channels

TMEM175 and TRPML1 are promising lysosomal targets for Parkinson’s disease (PD). Genetic variants of TMEM175 and TRPML1 associated with Parkinson’s are known to be loss-of-function, suggesting that activating the channels is likely the necessary therapeutic approach. Antibodies are promising tool compounds for modulating the function of ion channels in disease models and as potential therapies. We have developed synthetic nanobodies (sybodies) that selectively activate either TMEM175 or TRPML1 using novel mechanisms of action. Our collaborative project will apply novel agonist sybody technology, developed by Newstead for targeting TMEM175 and TRPML1, to iPSC-dopamine neuronal models of PD characterised by Wade-Martins.. 

Prof Simon Newstead | Biochemistry (ox.ac.uk)

For informal enquiries: simon.newstead@bioch.ox.ac.uk  or joanne.parker@bioch.ox.ac.uk

Project Code D20

Dissecting Wnt//b-catenin pathway activation at the single-molecule level.

The Wnt/b-catenin signalling pathway is essential in embryonic development and has important functions in tissue regeneration and overall maintenance of tissue homeostasis throughout the lifespan of multicellular organisms (Rim et al 2022). The pathway is a highly orchestrated tug-of-war between two opposing multi-protein assemblies, the b-catenin destruction complex (DC) and the Wnt signalosome, that ultimately determines the fate of the transcriptional co-activator b-catenin. Furthermore, dysregulation of Wnt signalling is associated with many human diseases, most prominently cancer. Understanding how these pathways function at the molecular level is therefore of great importance.

Recent advances have significantly contributed to our understanding of the molecular mechanisms driving the destruction complex (Ranes et al 2021). However, much less is known about the mechanisms underlying the formation of the Wnt signalosome upon pathway activation. The aim of this Dphil project is to dissect the molecular mechanisms of Wnt pathway activation using cell- based single-molecule approaches, which will be aided by the development of (synthetic) nanobodies against specific pathway components. This project complements other projects within the lab and thus provides ample opportunities to collaborate within the lab.

This project provides an excellent training opportunity in cutting-edge research and to contribute to advancing our understanding of a highly disease-relevant cell signalling process.

References:

1. Ranes, M., Zaleska, M., Sakalas, S., Knight, R. & Guettler, S. Reconstitution of the destruction complex defines roles of AXIN polymers and APC in β-catenin capture, phosphorylation, and ubiquitylation. Mol Cell 81, 3246-3261.e11 (2021).

Dr Michael Ranes | Biochemistry (ox.ac.uk)

For informal enquiries: michael.ranes@bioch.ox.ac.uk

Project Code D21

The role of epigenetics in evolution

The classic theory of Darwinian evolution puts genetic changes at the heart of the evolutionary process- changes in the DNA sequence are thought to be the source of variation upon which natural selection and drift can act.  However, it is becoming clear that some epigenetic changes, that affect gene expression but don’t change the underlying sequence of DNA, can be inherited between generations.  The contribution of this process to evolution is still largely unknown, and represents a fundamental question at the heart of contemporary study of evolution.   We have previously shown that spontaneous epigenetic changes, known as epimutations, occur in C. elegans as a result of small non-coding RNAs.  We showed that they arise in populations of the nematode C. elegans, and lead to changes in gene expression that can be inherited over a short number of generations in a laboratory setting (Wilson et al., PLoS Genetics 2023). These studies were performed in the absence of natural selection.  In this project, we now aim to investigate what happens to epimutations during conditions of selection.  We will use the development of resistance to nematocidal drugs as a model to test whether epimutations contribute to the evolution of resistance to drugs in C. elegans grown in the lab.  We will compare our results with studies on epigenetics in parasitic nematodes to understand whether epimutations might contribute to acquisition of resistance to drugs in nematodes that infect animals and plants.  Together, this work will address an important question in evolutionary biology: do epimutations contribute to the heritable variation that natural selection acts on in evolution? It will also give new insights into how epigenetic differences might be important in driving resistance to drugs in parasitic nematodes.  The work will involve both laboratory studies using C. elegans and computational analyses using a wide range of different types of data, including small non-coding RNAs, chromatin structure and comparative genomic analyses.

To find out more about the Sarkies lab see: https://psarkies.wixsite.com/epievo

Associate Prof Peter Sarkies | Biochemistry (ox.ac.uk)

For informal enquiries: Peter.sarkies@bioch.ox.ac.uk

Project Code D22

Interrogating nuclear structure-function relationships in mammalian cells by advanced super-resolution imaging

Three-dimensional (3D) chromatin organisation plays a crucial role in regulating mammalian genome functions such as RNA transcription, replication and DNA repair. Population-based sequencing approaches (e.g. Hi-C) have highlighted the compartmentalisation of chromatin into 0.5-1 MB sized topologically associating domains (TADs). However, many of the physical features at the single-cell level are still underexplored. Our primary research objective is to identify principles and underlying mechanisms of functional chromatin organisation in mammalian cells. Specifically, we aim to understand the interplay between biophysical forces, epigenetic memory, and cohesin complex activity to modulate cell-type-specific transcriptional programs by directly visualising dynamic nuclear organisation and gene activity in living or 3D-preserved cells. To this end, we employ a combination of genetic editing with innovative in vivo/in situ fluorescence labelling and super-resolution imaging approaches. Our activities are closely linked to the Micron Oxford Advanced Bioimaging Unit and supported by our well-established ties to leading chromatin and epigenetic research groups within the Department and across the University of Oxford.

For a MSc/PhD project, we seek (an) enthusiastic, proactive, and adventurous student(s) eager to immerse themselves in the latest imaging technologies to study topographical and biophysical aspects of gene regulation in an interdisciplinary environment. The topic of the project can be along the lines of either (1) studying transcription factor dynamics within the context of mesoscale chromatin domains using correlative single-molecule tracking and super-resolution SIM imaging, (2) analysing loop-extruding and sister chromatid cohesive and loop-extruding cohesin complexes by super-resolution expansion microscopy (ExM) and/or super-resolution 3D correlative light and electron microscopy (CLEM), (3) studying the effect of directed phase separation on mesoscale domain organisation and transcriptional modulation, (4) examining mechanisms of gene reactivation during de-differentiation and/or epigenetic memory (e.g. after IFγ response), or (5) examining enhancer-promoter interactions e.g. in the alpha-globin locus, using multiplexed RNA-DNA-Immuno-FISH and correlative 3D super-resolution light end electron microscopy. The details of any project will be subject to personal preferences and will be worked out closer to the start date.

Main techniques: Mammalian tissue culture, molecular cloning, transfection, immunofluorescence labelling, fluorescence in situ hybridisation (DNA/RNA FISH), super-resolution structured illumination microscopy, single-molecule imaging, focussed ion beam scanning electron microscopy (FIB-SEM), computational image analysis.

Relevant papers:
 

Miron E, ..., Schermelleh L. 2020. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. Science Advances 6, eaba8811.

Brown JM, … Schermelleh L, Buckle VJ. 2022. RASER-FISH, a non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure. Nat Protoc 17, 1306-1331.

Ochs F, ..., Schermelleh L, Nasmyth KA. 2024. Sister chromatid cohesion is mediated by individual cohesin complexes. Science, 383: 1122-1130.

Schermelleh L et al. 2019. Super-resolution microscopy demystified. Nat Cell Biol 21: 72-84.

Associate Prof Lothar Schermelleh | Biochemistry (ox.ac.uk)

For informal enquiries: lothar.schermelleh@bioch.ox.ac.uk

Project Code D23

Protein structure and interactions in health and disease .

Our laboratory seeks to understand how protein functions arise from their molecular structure and interactions, and how these processes are involved in human health and disease. We have a long-standing interest in the molecular mechanisms by which Influenza virus proteins function. We are studying the protein-protein and lipid interactions of ‘flu’ proteins to better understand their role in the virus life cycle and to identify potential therapeutic targets. We also collaborate with several groups in the department. One of these projects include investigations into ligand-dependent conformational changes and dynamics in membrane transporters, and another project is investigating regulation of exoribonucleases in transcription termination.

A central technique of our laboratory is solution nuclear magnetic resonance (NMR) spectroscopy, which allows atomic-level studies of protein structures and their interactions. NMR can be uniquely informative in situations where the molecular conformations or interactions are dynamic or heterogeneous. However, we also use a wide variety of other biochemical and biophysical tools as needed for these investigations. We have collaborations with various research groups including virologists, cell biologists, and computational biologists.

Associate Prof Jason Schnell | Biochemistry (ox.ac.uk)

For informal enquiries: Jason.Schnell@bioch.ox.ac.uk

Project Code D24

Structural biology of brain development

How does a single cell give rise to the amazingly complex human brain?

Brain development hinges on the proliferation and self-assembly of cells to form highly organized brain tissues and circuits. This intricate process relies on specialized receptor proteins that orchestrate the movements of brain cells during development. These receptors, situated on the cell surface, function like a cellular navigation system: they detect various cues (ligands) in the cellular environment and initiate signaling cascades that guide cells in the right direction. Collectively, these receptor-ligand interactions ensure the correct positioning of cells and their axons/dendrites within brain tissue, thereby coordinating the formation of brain circuits.

Approach

Our lab is part of a network that adopts an interdisciplinary approach to understand molecular functions within complex tissues. We specialize in structural biology (especially cryo-electron microscopy and X-ray crystallography) and advanced cell biology techniques. We integrate our findings with cryo-electron tomography, in vivo models, and super-resolution fluorescence microscopy through close collaboration with world-leading experts in Oxford (Baker), Barcelona (del Toro), and Bordeaux (Naegerl).

Outcome

By leveraging our established experimental pipeline, you will lead an interdisciplinary project aimed at unraveling how specific receptor-ligand interactions direct brain development. This project will yield groundbreaking discoveries about the molecular mechanisms underlying brain formation and function, much of which remains unknown. The findings will be directly relevant to brain disorders associated with these receptors. The project offers training in multiple techniques, particularly in structural biology and cell biology. Additionally, you will benefit from regular meetings with collaborators, providing further training and networking opportunities. Our team frequently engages in hands-on collaborative work in other labs within MIGRATE: https://migrate.web.ox.ac.uk/

For more information about the Seiradake lab see: http://seiradake.web.ox.ac.uk

Prof Elena Seiradake | Biochemistry (ox.ac.uk)

For informal enquiries: elena.seiradake@bioch.ox.ac.uk

Project Code D25

Structural and Cellular Control of Virus Glycosylation

Our research centres on understanding how proteins are modified by complex carbohydrates, or glycans, and the roles of glycans in viral infection and immune detection. Although protein glycosylation is widespread in biology, the molecular mechanisms that determine their structural assembly are poorly understood. This is largely due to the fact that their biosynthesis is non-template driven and highly dynamical. However, there are two major factors that in principle dictate what glycan structures are present at a particular glycosylation site on a protein – 1) the structure of the underlying protein and steric restraints of the various glycosylation enzymes and 2) cellular pathways that feed into glycosylation, such as monosaccharide metabolism, enzyme turnover and localisation in the secretory pathway. Importantly, we have found that glycosylation of viral glycoproteins isolated from infectious virions differs to isolated glycoproteins made in the lab. This project will work to understand why.  

We focus on HIV, Ebola, Lassa and coronavirus glycoproteins and the development of two advanced structural and biophysical techniques – mass spectrometry and mass photometry. Here, the project will integrate mass spectrometry techniques in proteomics and glycomics with transcriptomics to assess how cellular responses shape glycosylation during infection. We will also explore how glycoprotein conformational dynamics of viral surface glycoproteins (e.g. HIV-1 Env, Ebola GP or SARS-CoV-2 S) influences site-specific glycosylation using hydrogen deuterium exchange mass spectrometry. Ultimately, this interdisciplinary project aims to learn how proteins are glycosylated and support the design of structure-based vaccines.

For more information about the Struwe lab see; https://struwe.web.ox.ac.uk

Associate Prof Weston Struwe | Biochemistry (ox.ac.uk)

For informal enquiries from prospective students: weston.struwe@bioch.ox.ac.uk

Project Code D26

Bacterial infection, stress response, DNA repair, antibiotic resistance

Bacteria are extremely adaptable, which allows them to infect new hosts, evade immune defences, and survive antibiotic treatments. Under harmful conditions, bacterial cells induce protective stress responses and can acquire mutations that make them more stress resistant. Research in the Uphoff lab aims at understanding the interplay between phenotypic responses and genetic adaptation to stress. We have pioneered single-molecule and single-cell microscopy techniques that allow us to trace bacterial adaptation across enormous spatial and temporal scales, from cell populations down to individual molecular events. Equipped with these tools, our research addresses three main themes. Specific DPhil projects will be designed together with interested candidates.

Theme 1: Unravelling the unexpected complexity of bacterial stress responses

Studying bacterial stress responses at the level of single molecules and single cells has challenged the conventional wisdom of how these processes are regulated and what their functions are. We found that diverse types of stresses (e.g. reactive oxygen species, alkylating agents, antibiotics, etc), induce phenotypic heterogeneity in bacterial populations. We want to understand what causes this diversification of behaviour, and how it affects the adaptability of individual cells and the population.

Theme 2: Tracing the route from phenotypic tolerance to genetic resistance

Mutation is one of the most fundamental features of life, and we are acutely aware that human pathogens constantly mutate and evolve. Although DNA sequencing can identify adaptive mutations, much less is known about the molecular events that lead to such mutations appearing. We are developing experimental methods to trace adaptive mutations back to their molecular origins, which will help to predict and curb pathogen evolution. This is a great challenge because many processes in cells act in the creation or prevention of mutations, and various regulatory mechanisms exist that control them. Our lab innovated the use of microscopy to detect mutation events in real-time, which allows linking phenotypic and genetic changes in individual cells. Furthermore, using microfluidic growth devices, we can image thousands of individual bacteria simultaneously and monitor their phenotypes and fates under precisely controlled treatments over days. Mutations are often viewed as a “molecular clock” with a constant and uniform rate in all individuals. Using our approaches, we instead found that mutation rates increase during stress and that intracellular noise causes cell-to-cell variation in mutation. We are now investigating if this means that evolutionary adaptation could be driven by subpopulations of cells with elevated mutation rates.

Theme 3: Understanding how bacteria adapt and survive within immune cells

Stress responses and tolerance mechanisms are particularly important for bacteria during infection. Phagocytes kill invading bacteria via a burst of reactive oxygen species that is thought to cause DNA damage. However, intracellular pathogens can withstand this damage and replicate within phagocytes. By adapting our single-molecule tracking approaches, we have succeeded in directly visualizing DNA repair functions in bacteria within live phagocytes. Using this approach, we can now investigate how intracellular bacteria survive the phagocyte immune defences.

Associate Prof Stephan Uphoff | Biochemistry (ox.ac.uk)

For informal enquiries: Stephan.uphoff@bioch.ox.ac.uk

Project Code D27

Evolution of chromatin across the tree of life

We are interested in how (and why!) chromatin evolved across the tree of life. What are the fundamental differences between chromatin in bacteria, archaea, and eukaryotes? Are there any? Why do eukaryotes only use histones as their principal chromatin protein? What’s so great about histones? Can we use proteins other than histones to build chromatin with similar properties? And can we imagine (and build!) a cell without chromatin whatsoever?

Our group combines computational (phylogenomics, structural modelling, functional genomics, machine learning) and experimental techniques (biochemistry, microbiology, genetics) to pursue these questions from multiple angles [1-5].

During this studentship, we want to tackle one of the following projects:

1. Ultimate compaction. Histones are the principal building blocks of chromatin in eukaryotes but were generally thought to be absent from bacteria. We have recently discovered that this is not 100% true – there are some bacteria that encode and use histones to make chromatin [4]. One of these is the predatory bacterium Bdellovibrio bacteriovorus, which hunts and invades other bacteria. B. bacteriovorus is remarkable because their swimming “attack phase” cells are very small and somehow manage to condense an E. coli-size genome into a fraction of the volume [6]. We want to find out how they do this. Are histones involved? If not, what do the histones in these bacteria actually do?

2. DNA glues. There are some proteins, like protamines in human sperm, that strongly compact DNA. They do so by virtue of being packed full of charged amino acids, notably arginine. Some bacteria also strongly compact their DNA (e.g. B. bacteriovorus, see above). Do they use similar proteins? For some species, like Chlamydia trachomatis, the answer appears to be yes [7]. For most others, we do not know. Do they encode their own unique toolkits? How do they manage the (often rapid) transition from a condensed to a decondensed state? This project will combine computational and high-throughput experimental approaches to characterize the repertoire and logic of these bacterial DNA glues.

What will you learn during your DPhil?

I am keen for students to master a broad range of tools, including both computational and experimental approaches. You can expect to learn how to culture and genetically manipulate a variety of microbes, to describe prokaryotic genome function using systems-level functional genomics approaches, and to analyze microbial evolution on a genome-wide scale.

1. Rojec et al. Chromatinization of E. coli with archaeal histones. (2019) eLife 8:e49038
2. Hocher et al. Growth temperature and chromatinization in archaea. (2022) Nature Microbiology 7:1932
3. Stevens et al. Histone variants in archaea and the evolution of combinatorial chromatin complexity. (2020) PNAS 117:33384
4. Hocher et al. Histone-organized chromatin in bacteria. (2023) Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus. Nature Microbiology 8(11):2006-2019.
5. Hocher & Warnecke (2024) Nucleosomes at the Dawn of Eukaryotes. Genom Biol Evol 16(3):evae029
6. Sockett. Predatory lifestyle of Bdellovibrio bacteriovorus. (2009). Annu Rev Microbiol 63:523
7. Barry et al. Nucleoid condensation in E. coli that express a chlamydial histone homolog. (1992) Science 256:377

Associate Prof Tobias Warnecke | Biochemistry

For informal enquiries: tobias.warnecke@bioch.ox.ac.uk

Project Code D28

Molecular mechanisms underlying viral evolution and host changes

We seek to understand how enveloped viruses evolve and use this knowledge to come up with ways to deal with future pandemics.

Many deadly human pathogens, such as influenza and SARS viruses, are made up of just a few components but can infect a number of different hosts. How is it possible that these components suffice to fulfil all the functions necessary for a virus to infect the cell and then to assemble into a new viral particle? How do viral proteins perform multiple functions and how does the virus manage to retain all these functions as it evolves? How does a virus infect different hosts using the same set of its own proteins to engage a range of machineries of different hosts? And, finally, how does a virus evolve and ‘learn’ to optimise its interactions with a new host?

The recent COVID-19 pandemic has demonstrated that these questions are key to understand where new viruses come from and how they evolve upon transmitting to a new host. We have used biochemical, biophysical, and structural methodologies, mainly cryoEM, to reveal the mechanisms by which SARS-CoV-2 became able to infect humans and then further evolved to optimise viral infectivity in the variants of concern. [1-7]

The lab continues to work on coronaviruses and studies influenza viruses to understand how their proteins achieve the versatility needed to infect diverse hosts and fulfil multiple functions during infection. In particular, we want to explain how related viral strains use similar glycoproteins to engage receptors as different as glycans and proteins. We are also interested in understanding how viral proteins come together during virus assembly: how do they find other viral components, how do they ‘coerce’ the host to transport them, and how do they exclude hosts proteins from growing viral particles.

Tackling these questions can directly impact public health. The more we understand the rules governing the evolution of viral proteins, the better we can predict the impact of emerging viruses and thus increase our pandemic preparedness. Our long-term aim is to use structural and mechanistic insights to guide design of much-needed new antivirals and vaccines against zoonotic viruses.

Several projects encompassing areas above are available in the lab. If you are interested, please apply and do not hesitate to get in touch earlier to discuss more details. I am committed to working with you to scope projects that combine your interests in specific research questions as well as methodologies, your long-term career aspirations, and available expertise and pilot data in the lab. In this way we will devise the MSc or DPhil project that bests suit you.

REFERENCES (#co-first, •corresponding):

1. Antoni G. Wrobel# (2023) “Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike” Current Opinions in Structural Biology 102619.

2. Valeria Calvaresi#, Antoni G. Wrobel#, Joanna Toporowska, Dietmar Hammerschmid, Katie J. Doores, Richard T. Bradshaw, Ricardo B. Parsons, Donald J. Benton, Chloë Roustan, Eamonn Reading, Michael H. Malim, Steven J. Gamblin, Argyris Politis#. (2023) “Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein” Nature Communications, 14 (1), 427

3. Antoni G. Wrobel*#, Donald J. Benton*#, Chloë Roustan, Annabel Borg, Saira Hussain, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin# (2022). “Evolution of the SARS-CoV-2 spike in the human host” Nature Communications 13, 1178.

4. Antoni G. Wrobel*#, Donald J. Benton*#, Pengqi Xu, Annabel Borg, Chloë Roustan, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin# (2021). “Structure and binding properties of Pangolin-CoV Spike glycoprotein inform the evolution of SARS-CoV-2.” Nature Communications, 12 (1), 837.

5. Donald J. Benton*#, Antoni G. Wrobel*#, Chloë Roustan, Annabel Borg, Pengqi Xu, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin#. (2021) “The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2” Proceedings of the National Academy of Sciences, 118(9), e2022586118.

6. Donald J. Benton*#, Antoni G. Wrobel*#, Pengqi Xu, Chloë Roustan, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin# (2020) “Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion” Nature 588(7837), 327–330.

7. Antoni G. Wrobel*#, Donald J. Benton*#, Pengqi Xu, Chloë Roustan, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin#  (2020) “SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.” Nature Structural and Molecular Biology 27, 763–767 (2020).

Dr Antoni Wrobel | Biochemistry

For informal enquiries: antoni.wrobel@bioch.ox.ac.uk

Project Code: D29

How cells make T-cell receptors

Accurate biogenesis of multi-subunit membrane protein complexes is vital for human health, with improper assembly of specific complexes associated with diverse diseases. Despite their critical roles in human physiology, our understanding of how these complexes assemble is still limited. Our group aims to address this knowledge gap, contributing fundamental insights into basic biology with important implications for translational science and human diseases.

To address this challenge, we will study the assembly of the human T-cell receptor as a foundational paradigm. T-cell receptors play essential roles in fighting pathogens, preventing autoimmunity, and developing personalised medicines, each of which relies on precisely controlled receptor assembly. Although downstream signalling pathways have been thoroughly characterised, how the T-cell receptor assembles from eight independently produced cognate subunits with accurate timing and stoichiometry remains elusive. Using a cell-free reconstitution approach, we have identified the first factor that is required for early steps of T-cell receptor assembly, which we will now thoroughly characterise using multi-disciplinary approaches such as in vitro reconstitution, flow cytometry, live-cell imaging, and structural studies. We will continue to systematically identify and characterise key factors required for each step of T-cell receptor assembly, providing comprehensive insights into the assembly pathway.

This project not only lays the foundation for understanding general principles of membrane protein complex assembly but also offers perspectives on exploring the therapeutic potential of targeting assembly pathways.

Some of my group's previous work, expertise, and techniques are highlighted here: https://tinyurl.com/haoxiwugooglescholar

Wu H, Smalinskaitė L, Hegde RS. EMC rectifies the topology of multipass membrane proteins. Nat Struct Mol Biol. 2024 Jan;31(1):32-41.

Wu H, Hegde RS. Mechanism of signal-anchor triage during early steps of membrane protein insertion. Mol Cell. 2023 Mar 16;83(6):961-973.e7.

Wu H, Voeltz GK. Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites. Dev Cell. 2021 Jan 11;56(1):52-66.e7.

Ho N*, Yap WS*, Xu J*, Wu H*, et al. Stress sensor Ire1 deploys a divergent transcriptional program in response to lipid bilayer stress. J Cell Biol. 2020 Jul 6;219(7):e201909165.

Wu H, Carvalho P, Voeltz GK. Here, there, and everywhere: The importance of ER membrane contact sites. Science. 2018 Aug 3;361(6401):eaan5835.

For informal enquiries: haoxiwu@mrc-lmb.cam.ac.uk