Professor Cyril Dominguez

Supervisor Details

Contact Details

Department of Molecular Cell Biology, University of Leicester

Scientific Background

Research Interests

Alternative splicing of pre-mRNA is a centrally important and extraordinary cellular process that allows the generation of proteomic diversity from only 20000 human genes. The process of alternative splicing is very complex and still poorly understood. It is regulated by many proteins called splicing factors that may either enhance or prevent the recognition of a particular splice site in a time cell-type and cell-cycle dependent manner. Cell signalling also plays a major role in the regulation of alternative splicing through post-translational modifications of splicing factors demonstrating a tight link between cell signalling and alternative splicing regulation.

Our research interest is to understand at the molecular level the role of splicing factors on alternative splicing. Additionally we are interested in the role of pre-mRNA secondary and tertiary structures on alternative splicing regulation.

To this aim we are studying RNA protein-protein and protein-RNA complexes using structural biology techniques (NMR and X-ray) biophysical methods (ITC Fluorescence polarization) and biochemical methods (RNA footprinting EMSA).

Research Groups

Structure and function of RNA processing complexes

Supervision Style

In a few words or phrases: Student-centred.

Provision of Training

I believe that PhD students should demonstrate a certain level of independence and creativity. Initially I will provide training and guidance on the project. I will then expect you to lead the project and suggest your own experiments.

Progression Monitoring and Management

I will expect you to take full ownership of your progression but will discuss your data on a weekly basis and provide guidance when necessary.

Communication

The team has a WhatsApp group chat to discuss general laboratory issues. We have a weekly group meeting where 2-3 people present their work to the team. My door is always open for informal chats.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per week

In year 1 of PhD study

At least once per fortnight

In year 2 of PhD study

At least once per fortnight

In year 3 of PhD study

At least once per fortnight

These meetings will be a mixture of face to face and via video chat or telephone, and I am usually contactable for an instant response on every working day.

Work 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 2 weeks' notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Structure and dynamics of the intrinsically disordered regions of the RNA binding protein Sam68: implication for RNA binding and phosphorylation

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).

Structure and dynamics of the intrinsically disordered regions of the RNA binding protein Sam68: implication for RNA binding and phosphorylation

Secondary Supervisor(s): Professor Andrew Hudson

University of Registration: University of Leicester

BBSRC Research Themes:

Understanding the Rules of Life (Structural Biology)
Integrated Understanding of Health (Ageing)

Project Outline

A large proportion of the human proteome is composed of unstructured regions, termed intrinsically disordered regions (IDRs). Over recent years, it has been demonstrated that these regions are crucial for almost all cellular functions but structural studies of these IDRs to unravel the molecular mechanisms of their function remain largely unknown.

A typical example is the oncogenic RNA-binding protein Sam68, a multifunctional protein contributing to regulation of RNA metabolism, and signal transduction that is often overexpressed in many types of cancers (1-3). While the role of Sam68 central RNA binding domain in RNA recognition is well characterized (4), it is currently unknown how Sam68 N-terminal (Nter) and C-terminal (Cter) IDRs contributes to RNA binding and function of the protein, although these regions are targeted by multiple post-translational modifications (PTMs) that modulate Sam68 functions. By investigating the role of PTMs in regulating the cellular functions of Sam68, we have demonstrated that Sam68 Nter and Cter IDRs bind RNA specifically and that phosphorylation of these regions by Cdk1 modulates their RNA binding and the cellular functions of the protein (5). How do these regions bind specifically RNA and how phosphorylation of a single amino acid affect the interaction are still unknown.

Our hypothesis is that Sam68’s IDRs adopt transient structural features that are crucial for specific RNA recognition and that phosphorylation of these regions modulate these features, preventing RNA binding. Our hypothesis is supported by our preliminary NMR data.

Experimental Methods

We will combine biochemical techniques, NMR, Fluorescence correlation spectroscopy (FCS), single-molecule fluorescence resonance energy transfer (sm-FRET), small angle X-ray scattering (SAXS) and molecular dynamics (MD) to decipher the structural properties of Sam68 IDRs either free, in complex with RNA or following phosphorylation by CDK1.

Research Proposal

i. We will define the minimum regions of Sam68 Nter and Cter IDRs capable of RNA binding and the minimum RNA region sufficient for specific binding to Sam68 IDRs: We will test the interaction (NMR and biochemical assays) of truncated version of Sam68 IDRs with truncated version of the RNAs. This will allow us to define the minimum regions of the protein and the RNA sufficient for specific binding.

ii. We will determine the structural properties of Sam68 Nter and Cter in complex with RNA and upon phosphorylation: We will combine NMR, FCS, sm-FRET, SAXS and MD to decipher the structural properties of Sam68 IDRs either free, in complex with RNA or following phosphorylation by CDK1. This will provide crucial structural and mechanistic insight into the specific RNA-binding by these IDRs and the role of phosphorylation.

Expected outcome and Impact

Over recent years, it has become evident that IDRs play a key role in cellular processes. However, the structural and the molecular mechanisms regulating such processes are clearly lacking. This multi-disciplinary project will provide unique structural and mechanistic insights into RNA binding properties of IDPs/IDRs. Furthermore, Sam68 is overexpressed in many types of cancer. The structural study on this project will provide structural ensembles of Sam68 IDRs that are crucial for its function. It might therefore be possible, in the future, to design molecules that trap these IDRs in a non-functional conformation, therefore inhibiting their function.

Techniques

Techniques that will be undertaken during the project:

Protein expression (E. coli) and purification
Nuclear Magnetic Resonance (NMR)
Fluorescence Correlation Spectroscopy (FCS)
Single-molecule Foerster Resonance Energy Transfer (sm-FRET)
Small-Angle X-ray scattering (SAXS)
Molecular dynamics simulations

References

1. Bielli, P., et al. (2011) Endocr Relat Cancer, 18, R91-R102.

2. Busa, et al. (2007) Oncogene, 26, 4372-4382.

3. Fu, et al. (2016) Elife, 5.e21957

4. Feracci, et al. (2016) Nat Commun, 7, 10355.

5. Malki, et al. (2022) Nucleic Acids Res, 50, 13045-13062.

Previous Projects (2024-25)

Primary supervisor for:

Molecular characterization of Sam68-driven cytoskeletal reorganization

Previous Projects (2023-24)

Primary supervisor for:

Molecular characterization of Sam68-driven cytoskeletal reorganization