Professor Ian Eperon

Supervisor Details

Contact Details

Department of Molecular Cell Biology, University of Leicester

Scientific Background

Research Interests

Research group activity

Gene expression in higher eukaryotes is dominated by two processes. Quantitative control of expression at any time is achieved by a range of processes, the dominant one of which is transcription. Qualitative control, the identity of what is expressed, is achieved by RNA splicing. Most genes produce multiple transcripts or isoforms as a result of splicing the initial transcript in different ways; some of these choices are tightly regulated and the encoded protein isoforms play essential roles in cell growth, development, circadian rhythms, memory etc.

The dramatic diversity of splicing patterns is achieved by weakening the standard signals for splicing and relying on the recognition of a very large number of short sequence motifs that are recognised by numerous activator or repressor proteins. This means that, for many genes, splicing involves an overwhelming number of choices and that the process of selection is very complex. Our work focuses on the mechanisms of selection and also on our ability to usurp these for therapeutic benefits.

We have made important contributions to identifying the roles of transcription, RNA folding and splice site sequences and the effects of regulatory proteins on the binding of core splicing components. Many of these were achieved using the one functional system available in vitro, a crude nuclear extract. However, we realised that the outcome of each event is the result of binding by numerous proteins, often in competition, and that the RNA-protein complexes being studied in extracts were likely to be very heterogeneous assemblages. To overcome this, we pioneered (in collaboration with Clive Bagshaw, Dmitry Cherny and Andrew Hudson) the use of single molecule methods in crude extracts, and we have used these to look at the numbers of molecules of particular proteins bound to each molecule of RNA and establish how this affects activation or repression.

Our aim now is to provide a complete description of the variety of assemblages forming on a pre-mRNA and to establish what defines an active complex. We are currently developing methods for monitoring the flexibility and dynamics of these complexes at the single molecule level, since we suspect that these overall properties of the complex integrate the inputs of the many individual bound proteins.

This work has connections to the development of therapies that exploit the vulnerability of splicing to nudges that push it to use alternative sites. We were involved in the first experiments to show that modified oligonucleotides could redirect splicing in the endogenous dystrophin gene. Our collaborators have pursued this, leading to the first approved drug for splice site switching, which targets certain cases of muscular dystrophy.

We have also developed a novel strategy for activating a specific splice, which is an important approach for therapy in spinal muscular atrophy. In the event, another splice-switching oligonucleotide was developed by others that proved to be more feasible; this has now been approved and is the first drug to halt the progression of the disease. In collaboration with Cyril Dominguez and Glenn Burley (Strathclyde), we are interested in the mechanisms by which four-stranded internal structures in the RNA (G4s) affect splicing and, in particular, switch splicing to produce pro-apoptotic isoforms of the genes Bcl-X and Mclk-1. By identifying molecules that bind to these structures and stabilise them, we hope to develop drugs that are of use in the treatment of some cancers.

Scientific Inspiration

My PhD supervisor, Fred Sanger. Despite being the only person until recently to win two Nobel prizes in chemistry, he was modest, quiet, kind and humorous, as well as insightful. He worked at the bench until the day he retired.

Research Groups

RNA Splicing: from single-molecules to therapy

Supervision Style

In three words or phrases: It depends on the student. Generally, guidance, advice, listening, support, encouraging.

Provision of Training

I provide advice, guidance, information about current research and an open door: anybody can walk in to discuss their ideas, problems and results. I do a lot of troubleshooting for problems with experiments! There are postdocs, students and technicians in the lab who help with demonstrating methods, but I know most of the methods extremely well and have protocols for them. I am very conscious that students need to achieve results for their thesis and publications for their future careers, but it is important to me that they achieve their goals at their own pace and find the lab a comfortable place in which to work. As students gain expertise and knowledge of the field, they are likely to pursue their own ideas, and if they wish to do so I encourage them.

Progression Monitoring and Management

The University of Leicester has a formal scheme for providing joint supervisors, a committee for supporting each student, requirements for regular reports and committee meetings, etc. In addition, the department runs a seminar programme to which PhD students contribute. In the laboratory, we hold meetings every week, at which every member of the lab presents their results and can discuss ideas or problems. My office is adjacent to the lab and the writing-up area; lab members drop in whenever they like for a chat, to present new results and discuss the next steps. I also talk to students to ask about their research on a more or less daily basis.

Communication

Communication between myself and the lab members is more or less continuous. As noted above, there are always opportunities to talk. People may also discuss private matters with me, because these often can affect their work. Students are not left to suffer on their own.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per week

In year 1 of PhD study

Meetings are frequent (multiple times per week) but not scheduled

In year 2 of PhD study

Meetings are frequent (multiple times per week) but not scheduled

In year 3 of PhD study

Meetings are frequent (multiple times per week) but not scheduled

The meetings will be face to face and I am usually contactable for a response (if required) on every working day.

Working Pattern

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings), I expect students to manage their own time.

Notice Period for Feedback

I need at least 1 week’s notice to provide feedback on written work of up to 5000 words.

This is desirable; in practice I often read them straight away when a deadline for submission is imminent.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Mechanisms of cold-dependent neuroprotection

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Mechanisms of cold-dependent neuroprotection

Secondary Supervisor(s): Professor Andrew Hudson

University of Registration: University of Leicester

BBSRC Research Themes:

Understanding the Rules of Life (Neuroscience and Behaviour, Structural Biology)
Integrated Understanding of Health (Ageing)

Project Outline

Hypothermia is an important therapeutic tool for mitigating the neurological damage resulting from ischaemic brain injuries after cardiac arrest, stroke and other neurological insults. This benefit arises from increased expression of a cold-shock protein, RBM3, which is an RNA-binding protein that has effects on translation of selected mRNAs. Thus, there is considerable therapeutic interest in understanding how RBM3 is upregulated in the cold and whether it is possible to develop drugs to reproduce this effect.

How does cold increase expression of RBM3? Recent research has shown that the gene for RBM3 contains a poison exon. Inclusion of this exon in the spliced product, the mRNA, leads to its degradation. However, in cold conditions this exon is missed out, or 'skipped', leading to stabilisation of the mRNA and thus increasing the levels of protein expressed. This effect seems to depend on temperature-dependent binding of hnRNPH1 to the exon, which promotes skipping (Lin et al., 2023, EMBO J. 42: e113168).

The purposes of this project are to investigate the molecular mechanisms by which temperature affects the binding of hnRNPH1 and other proteins to the exon and to establish how hnRNPH1 mediates skipping when it binds. We have recently shown that we can recapitulate the temperature-dependent skipping in vitro, when synthetic pre-mRNA is added to a nuclear extract. This means that the process is amenable to molecular methods. We will use classical methods, such as cross-linking and affinity purification to identify RNA-bound proteins, SHAPE and other analyses to map the secondary structure of the RNA, and nuclease protection to monitor the binding of splicing factors. Mutagenesis of the proteins and RNA will be used to establish whether these biochemical properties are correlated with the exon skipping effect.

We have developed single molecule methods for establishing the numbers of proteins bound to the pre-mRNA (e.g., Cherny et al., 2010, EMBO J. 29, 2161-2172; Jobbins et al., 2022, EMBO J. 41: e107640). This is especially important for hnRNPH1, where there are multiple potential binding sites and the repression of the exon might be strongly dependent on the numbers bound. We can use the same methods to see whether hnRNPH1 binding excludes normal splicing factors or is correlated with the recruitment of co-repressors. Finally, single molecule FRET analyses will be done to understand whether repression of the exon at low temperatures affects the structure and dynamics of the exon and its flanking introns. These investigations may open the way to the development in future of new drugs that, for example, stabilise the interactions between specific proteins.

Techniques

Techniques that will be undertaken during the project:

We will use classical methods, such as cross-linking and affinity purification to identify RNA-bound proteins, SHAPE and other analyses to map the secondary structure of the RNA, and nuclease protection to monitor the binding of splicing factors. Mutagenesis of the proteins and RNA will be used to establish whether these biochemical properties are correlated with the exon skipping effect.

We will use the single molecule multicolour colocalization spectroscopy methods that we have developed for establishing the numbers of proteins bound to the pre-mRNA (e.g., Cherny et al., 2010, EMBO J. 29, 2161-2172; Jobbins et al., 2022, EMBO J. 41: e107640; Wills et al., 2024, Comp. Struct. Biotech. 23, 918-928). Single molecule FRET analyses will be done to probe the structure and dynamics of the exon and its flanking introns. NMR experiments may be done in collaboration with Professor Dominguez to look at the structures and dynamics of recombinant proteins and their interactions with RNA.