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Understanding the role that the RNA helicase UPF1 plays in sorting ribonucleoprotein (RNP) complexes and the mechanism by which this role of UPF1 might reduce cellular stress and cell degeneration.

   School of Biosciences

   Sunday, January 09, 2022  Competition Funded PhD Project (Students Worldwide)

Birmingham United Kingdom Bioinformatics Cell Biology Molecular Biology Neuroscience

About the Project

Project outline:

UPF1 is a universally conserved RNA helicase in eukaryotes. We recently reported that UPF1 is a mobile protein in all cell compartments and that constantly shuttles between nucleus and cytoplasm, with its intracellular distribution reflecting that of the mRNA, which is characteristically more abundant in the cytoplasm than in the nucleus. Crucially, our observations show that UPF1 associates with nascent pre-mRNA transcripts and that it plays genome-wide roles in nuclear RNA-based processes – including Pol II pausing, mRNA export and most strikingly transcription site retention. These observations radically change our understanding of the roles of UPF1 protein in gene expression and convert UPF1 from a specialised mRNA decay factor to being a global player in mRNA based processes both in the nucleus and in the cytoplasm. The proposed research aims to unveil the specific molecular function(s) that UPF1 performs on ribonucleoprotein (RNP) complexes, and how might these function help to explain why mutations that affect its expression cause disease; and in particular, why even a modest over-expression of UPF1 can restore motoneurons functionality in a rat model of ALS, a deadly neurodegenerative disease for which there is no satisfactory treatment.

Techniques that will be undertaken during the project:

In addition to training in bioinformatics detailed above, thee project will provide advanced training in molecular biology, yeast (or Drosophila) molecular genetics, genomics. The project will involve one or more of the following leading-edge techniques: CRISPR-Cas9 gene editing, NET-seq, ChIP-seq and advanced cell imaging.

Contact: Dr Saverio Brogna, University of Birmingham


Funding Notes

Projects are open to both home and International students (EU students are now classed as international). BBSRC have indicated that up to 30% of the cohort are allowed to be international students.
UoB are waiving International Fees, however international students will still have to pay for their own visas and a healthcare surcharge which is approximately £2500.


Singh et al. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. Elife. 2019 Mar 25;8.
BBSRC Strategic Research Priority: Understanding the Rules of Life: Neuroscience and behaviour & Systems Biology & Integrated Understanding of Health: Ageing,
For others see

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