Background

SFPQ (Splicing Factor Proline- and Glutamine-rich) is a multifunctional RNA-binding protein that coordinates transcription, RNA processing, and nuclear organisation. It plays central roles in splicing, RNA biogenesis, and the assembly of paraspeckles, nuclear bodies that help maintain gene expression homeostasis under stress. Despite its broad importance, the essential function of SFPQ remains poorly understood.

Our recent data show that depletion of SFPQ in triple-negative breast cancer (TNBC) cells leads to a catastrophic breakdown in transcriptional control. Transcription initiates normally, but elongation and termination fail, causing widespread readthrough, R-loop accumulation, and replication stress. This collapse, which we term transcriptional exhaustion, represents a fundamental failure of the transcription cycle and provides a new lens through which to understand how loss of nuclear organisation leads to cell death.

This project will investigate how SFPQ prevents transcriptional exhaustion and define the molecular events that occur when this safeguard fails.

Project aims

The overarching goal is to understand how cells maintain transcriptional stability and what happens when this control is lost. Specifically, the project will:

1. Characterise the cell death response that follows SFPQ loss, examining apoptosis, checkpoint activation, and replication stress signatures.

2. Map the landscape of transcriptional exhaustion, using nascent RNA-seq, RNAPII ChIP-seq, and R-loop profiling to define how gene expression collapses in real time.

3. Dissect the roles of SFPQ domains and paraspeckles, employing mutant add-back systems, NEAT1_2 manipulation, and live-cell imaging of nuclear body dynamics.

4. Integrate computational and systems-level approaches to model the transcriptional collapse network and identify pathways that could restore stability.

Significance and training

This project tackles a fundamental biological question: how do cells keep transcription running smoothly, and what causes this process to fail? The findings will transform our understanding of SFPQ’s essential role in maintaining genome integrity and provide new insights into how its dysregulation contributes to cancer.

You will receive comprehensive training in advanced molecular and cell biology techniques, next-generation sequencing, and computational analysis. The project offers the opportunity to work across complementary research environments at Leeds Beckett University and the University of Leeds, combining expertise in RNA biology, nuclear organisation, and transcriptional regulation within a highly collaborative and supportive supervisory team.

Lab websites and links:

https://www.leedsbeckett.ac.uk/staff/professor-jim-boyne/

https://biologicalsciences.leeds.ac.uk/molecular-and-cellular-biology/staff/156/professor-ade-whitehouse

https://www.leedsbeckett.ac.uk/staff/dr-chinedu-anene/

For informal enquiries about the project, please contact Prof Jim Boyne [j.boyne@leedsbeckett.ac.uk].

About the BBSRC Yorkshire Bioscience Doctoral Training Partnership (YBDTP):

The YBDTP brings together world-class bioscience research and innovation, as well as excellence in doctoral supervision, across the Yorkshire and Teesside region. The YBDTP will fund postgraduate researchers at the Universities of Leeds, Sheffield, York, Bradford, Huddersfield, Hull, Leeds Beckett, Sheffield Hallam and Teesside forming a strong regional training partnership. In YBDTP you'll benefit from a regional doctoral training programme that has interdisciplinary collaboration at its core. The aim is to enable you to develop a range of research skills in biological, biotechnology and biochemical areas as well as equip you with core data analysis and professional skills that are necessary for bioscience research and related non-academic careers.

https://www.yorkshirebiosciencedtp.ac.uk

Eligibility:

Open to International (including EU) and UK (home) students.

You can apply if you have, or are expecting to gain, at least an upper second-class honours degree or equivalent. Due to the interdisciplinary nature of this programme, we welcome applications if your background is in any biological, chemical or physical science or mathematics and are interested in using your skills in addressing biological questions. International students should check if they meet the entry requirements for the host university.

We aim to support the most outstanding applicants from outside the UK and are able to offer a very limited number of bursaries that will enable full studentships to be awarded to international (EU and non-EU) applicants. These full studentships will only be awarded to exceptional quality candidates, due to the highly competitive nature of this scheme.

The YBDTP is committed to recruiting extraordinary future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Not all projects will be funded; a limited number of candidates will be appointed via a competitive process.

English language: If English isn't your first language, you may need to provide evidence of your English language ability. Please see the English language requirements for the host university.

https://www.leedsbeckett.ac.uk/the-graduate-school/research-degrees/faqs/

How to apply:

Application deadline: 5pm (UK time), Wednesday 7th January 2026

To submit your application, complete anExpression of Interest form. You can apply for up to two YBDTP projects (which can be at different universities).

If you have any questions about the application process, please email YBDTP@leeds.ac.uk

If you have any questions about the project you are interested in, please email the project supervisor.

How we allocate:

Shortlisting will take place as soon as possible after the closing date and successful applicants will be notified promptly. If you're shortlisted, you'll be invited for an interview on a date to be confirmed in February 2026. You'll be notified as soon as possible after the interview dates whether your application has been successful, placed on a reserve list or unsuccessful. If you are successful, you'll be required to confirm your intention to accept the studentship within 10 days.

Terms and conditions:

The studentships are fully funded for four years, and you must complete your PhD in four years.

You'll receive the UKRI minimum doctoral stipend per year for your living costs, which is paid to you in regular instalments. The UK Research and Innovation (UKRI) stipend is tax free and does not need to be paid back.

International students will need to have sufficient funds to cover the costs of their student visa, NHS health surcharge, travel insurance and travel to the UK as these are excluded from UKRI funding.

Leeds Beckett University

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Uncovering how SFPQ prevents transcriptional collapse