Understanding the role that the RNA helicase UPF1 plays in nuclear processes of gene expression.

Gene expression, the process that decodes the DNA sequences of genes into specific RNAs and proteins, is particularly complicated in organisms whose genes are enclosed in a nucleus: these, known as eukaryotes, include animals and plants. The primary RNA transcript (pre-mRNA) needs to undergo several modifications (pre-mRNA processing) and quality-control steps before it is ready to be translated into the correct protein; mutations that reduce the accuracy of this process can lead to several human diseases. The applicant's research focuses on understanding nonsense-mediated mRNA decay (NMD), which is an important process that removes abnormal mRNAs that cannot be efficiently translated and thereby modulates the expression of many genes in all organisms; moreover, changes in the efficiency of NMD have been linked to human diseases. This research primarily aims to improve our understanding of basic aspects of gene expression and hence will further the knowledge of fundamental biology - a quintessential requirement to any of the more applied biomedical research enterprises aimed at improving specific human conditions. However, in this specific instance, the results should provide useful insights into the mechanisms causing amyotrophic lateral sclerosis (ALS) and possible treatments for this condition. In particular, human UPF1 (the protein whose function we aim to clarify with the planned research) restores motor function in a rat model of ALS, so the results of this research might provide knowledge which could help in the development of a treatment for this devastating neurodegenerative disease.

This research aims to further our understanding of gene expression in eukaryotic cells. This project's specific objective is to study the molecular role(s) that the RNA helicase UPF1 plays in RNA processing and in nonsense-mediated mRNA decay (NMD). Mutations in UPF1 have been linked to human diseases; and, by an unknown mechanism, the expression of human UPF1 restores motor function in a rat model of amyotrophic lateral sclerosis (ALS). Unfortunately, neither the functional significance of NMD nor the role that UPF plays in NMD is sufficiently understood. It is widely believed that the primary reason for UPF1 conservation is that it is needed to target specific transcripts for NMD. Moreover, there is evidence that UPF1 may play a wider role in regulating gene expression than so far envisaged, including functions in nuclear RNA processing. The applicant's research team has recently reported observations 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 focuses on understanding its roles in the nucleus by unveiling: a) the specific molecular function(s) that UPF1 performs on nascent ribonucleoprotein (RNP) complexes; b) by which it is required for the release of mRNA from transcription sites and for correct RNA processing; and, how might these functions 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.

WHY WILL SOCIETY BENEFIT? The project aims to advance our understanding of the fundamental processes of eukaryotic gene expression in the amenable experimental organism Drosophila. How living organisms work and reproduce is a basic question that has interested humanity for millennia. Society and humankind are constantly benefitting from basic science. Much of what is known about human health and disease is built on prior basic knowledge of how genes and cells work. This knowledge primarily came from studying basic biology, and often not in humans or human cells, but in easy to study organisms like yeast and flies. Throughout history, fundamental advances in science were driven by the investigator's, seemingly of little significance, curiosity more than any specific foresight that she or he had about the usefulness of what may be discovered. In this specific instance though, we believe that the results of the research we have proposed will directly be relevant to patients affected by ALS and have plans to communicate this both to the public and to researchers studying ALS.

WHAT WILL WE DO TO COMMUNICATE TO SOCIETY THE IMPORTANCE OF BASIC SCIENCE SUCH AS THIS? To communicate this message of why basic science is quintessential to all of us we will engage with the public on social media, local schools, and particularly for this project, plan to engage with the local branch of the The Motor Neurone Disease Association (MNDA) and organise events in which we can talk about why the type of research we do could translate into medical benefits for patients affected by ALS. Moreover, as we have done for a number of years we will continue welcoming kids from local schools to visit our lab (we are in contact with local schoolteachers), and with colleagues here in the School we will give presentations and/or arrange displays of our research at the university Community Day, which is a very popular event when the University opens to local people to show the different research projects that are going on here. We believe such activities will encourage some good students to pursue a career in science or at least leave them and their families with the awareness that basic science is crucially important for society's progress and well-being.

WE ARE TRAINING HIGHLY SKILLED RESEARCHERS. The grant will directly support Dr Anand Singh (the named PDRA), a promising young scientist who has an excellent knowledge of Drosophila genetics, polytene chromosomes and advance microscopy imaging. By working on this project he will become proficient in molecular biology cutting-edge techniques such as CLIP and RNA-seq, and thanks to the collaboration we have in place, in advance bioinformatics. By the end of this project we predict he should publish 2-3 more quality papers, and with these and the additional training/experience acquired during this research he will be in a position to start as an independent scientist. Moreover, Anand is a mentor for others, an asset to the applicant's group and key for the training of the technician working on this project. The grant would also directly benefit the UG students who do their lab project in our group, and generally the quality of the students who graduate from UoB in biochemistry or similar programmes. Conversely, UoB provides several professional training courses for both PDRAs and technicians to develop other skills that can be applied in this and future jobs.
BENEFITS TO DRUG DEVELOPMENT. The proposed research should be directly relevant to those working on developing UPF1 as a treatment for ALS. This will include MeiraGTx, a USA and UK based gene therapy company, which aims to test UPF1 in ALS patients. To facilitate this, the results and insights that will emerge from this project will deposit all of our manuscripts in public servers before publication at the time of submission, in bioRxiv or similar.