Investigation of nonsense mediated mRNA decay (NMD) mechanisms
Lead Research Organisation:
University of Birmingham
Department Name: Sch of Biosciences
Abstract
Gene expression typically refers to the process that leads from gene to functional protein and involves transcription of DNA into mRNA and translation of the transcript into protein. The process is particularly complex in eukaryotes (the group of organisms that, like yeast and humans but unlike bacteria, are made of cells which have the chromosomal DNA enclosed within a membrane-bounded nucleus); in these cells the primary mRNA transcript needs to undergo several modifications (pre-mRNA processing) in the nucleus and quality control steps before it is efficiently translated in the cytoplasm. Mutations or environmental conditions that reduce the accuracy of this process can lead to several human diseases. The research in the main applicant's laboratory focuses on understanding nonsense mediated mRNA decay (NMD), one of the more important cellular quality-control processes that removes abnormal mRNAs that could potentially encode for toxic truncated proteins. NMD also has a central role in modulating the expression of many normal genes and since NMD is interlinked with essentially all other processes in gene expression, a full understanding of this insufficiently understood mechanism will greatly advance our understanding of the fundamental question of how genes are correctly expressed in cells.
Although this research is aimed at understanding fundamental molecular biology so as to advance fundamental knowledge, long term it may also have an economic impact on society. It can for example advance our understanding of the molecular mechanisms that cause certain human diseases and possibly offer new treatments. Specifically, NMD is a promising drug target for a class of mutations that are linked to human diseases. A USA pharmaceutical company (PTC Therapeutics- www.ptcbio.com) reported that some forms of Duchenne muscular dystrophy (DMD) and possibly other human diseases caused by mutations that block mRNA translation prematurely, can be treated with a drug that emerged from NMD studies. This drug (Ataluren, trade name Translarna) has been recently approved by the European Medicine Agency for treating DMD and could shortly be available in the UK.
Although this research is aimed at understanding fundamental molecular biology so as to advance fundamental knowledge, long term it may also have an economic impact on society. It can for example advance our understanding of the molecular mechanisms that cause certain human diseases and possibly offer new treatments. Specifically, NMD is a promising drug target for a class of mutations that are linked to human diseases. A USA pharmaceutical company (PTC Therapeutics- www.ptcbio.com) reported that some forms of Duchenne muscular dystrophy (DMD) and possibly other human diseases caused by mutations that block mRNA translation prematurely, can be treated with a drug that emerged from NMD studies. This drug (Ataluren, trade name Translarna) has been recently approved by the European Medicine Agency for treating DMD and could shortly be available in the UK.
Technical Summary
Nonsense mediated mRNA decay (NMD) is an evolution conserved translation-dependent mechanism that degrades abnormal mRNAs which carry either a premature stop codon (PTC) or other NMD-inducing features such as an abnormal long 3' UTR. Although NMD was initially described as a specialized mRNA surveillance mechanism that prevents accumulation of abnormal mRNAs coding for potentially toxic truncated peptides, a number of later studies indicate that NMD affects the expression of a large fraction of the genome from yeast to human, for example by targeting aberrantly spliced transcripts which harbor an NMD-inducing PTC. It therefore appears that NMD has an important global function in fine-tuning eukaryotic gene expression. While it is well established that NMD is coupled to premature translation termination, the mechanism by which some but not other PTCs cause NMD is not sufficiently understood in any organism. Moreover, pre-mRNA splicing appears to be involved in this process across organisms, yet current models cannot account for many features of this still unsolved interconnection between pre-mRNA processing in the nucleus and translation in the cytoplasm. This research aims to understand the basic NMD mechanism in Schizosaccharomyces pombe, which as demonstrated by earlier studies and extensive preliminary observations in the main applicant's laboratory, is a promising experimental system to gain an alternative vantage point that could radically change our current understanding of NMD and unveil the mechanism of its links to translation, pre-mRNA processing and mRNA turnover.
Planned Impact
The research we have proposed is primarily driven by the quest to fully understand a specific cellular mechanism in an amenable experimental organism. While we cannot precisely predict what the benefit of this specific research will be to society, most of what is known about human health and diseases is built on fundamental knowledge of how genes and cells work. In the long term the knowledge that we will gain might help in our understanding of certain disease processes and suggest new treatments. The particular cellular mechanism we are studying, nonsense mediated mRNA decay (NMD) is a promising drug target for genetic diseases that are caused by nonsense mutations. The drug Ataluren (tradename Translarna) has been recently approved by the European Medicine Agency for treating Duchenne muscular dystrophy and could shortly be available in the UK. This drug is also in clinical trials for other diseases caused by this class of mutations (http://www.ptcbio.com/ataluren). PTC Therapeutics, the company that discovered Ataluren, was started by Dr Stuart Peltz and others following up on their pioneering work in characterising NMD in budding yeast. The mechanism of action of Ataluren remains controversial. It is likely that the knowledge that will emerge from our research into the basic NMD mechanism will provide insights into what might be its precise molecular target. This could therefore be of interest to pharmaceutical companies as they seek ways of addressing debilitating diseases such as Duchenne muscular dystrophy.
We believe that an effective way to convey the importance of basic science is to engage with the local public and, perhaps more importantly, with schools. The link between NMD and disease is a way of highlighting the importance of studying fundamental biological processes. We will communicate with the public through outreach activities, such as hosting pupils from local schools in our laboratories and organizing public exhibits at our yearly university Community Day. We will also publish the results of our research in prominent open-access journals, which as well as a means of communication is also the way we can contribute to the prestige of UK science and the educational sector, which are major assets and important economy-drivers in this country.
We believe that an effective way to convey the importance of basic science is to engage with the local public and, perhaps more importantly, with schools. The link between NMD and disease is a way of highlighting the importance of studying fundamental biological processes. We will communicate with the public through outreach activities, such as hosting pupils from local schools in our laboratories and organizing public exhibits at our yearly university Community Day. We will also publish the results of our research in prominent open-access journals, which as well as a means of communication is also the way we can contribute to the prestige of UK science and the educational sector, which are major assets and important economy-drivers in this country.
Publications
Brogna S
(2016)
The Meaning of NMD: Translate or Perish.
in Trends in genetics : TIG
Singh AK
(2020)
Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells.
in microPublication biology
Singh AK
(2020)
Visualisation of ribosomes in Drosophila axons using Ribo-BiFC.
in Biology open
De S
(2022)
Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.
in Nucleic acids research
Description | The process of gene expression is fundamental to any living cell. We are conducting research in the experimental model organism fission yeast to better understad the mechanism that couple the of transcription of the gene to its translation in a functional protein. The work is still at its early stages. So far we have set up the key technique required for this work and published an article in which we discuss which hypotheses we will be testing. The Grant has had a big impact of a related project in which we aimed at understanding the association exon junction complex (EJC) with nascent RNA. The remarkable result is that at least in Drosophila it does appear to be any such complex. The discovery (see our eLife paper) has re-focused our yeast NMD project into finding out what is the role of EJC in fission yeast. We have also submitted to manuscript to bioXviv in which we reported that a protein termed Prp17 is required for splicing-dependent NMD. This is an exciting funding as it opens the possibility that Prp17 might be directly linking the ribosome with the spliceosome at transcription sites. |
Exploitation Route | Our papers are accessible to all and based on ResearchGate stat highly read |
Sectors | Education |
URL | http://www.sciencedirect.com/science/article/pii/S016895251630021X |
Description | MIBTP studentship |
Amount | £80,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start |
Description | Understanding the role that the RNA helicase UPF1 plays in nuclear processes of gene expression. |
Amount | £506,777 (GBP) |
Funding ID | BB/S017984/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2019 |
End | 04/2024 |
Title | Antibodies |
Description | Three monoclonal antibodies against UPF1 |
Type Of Material | Antibody |
Year Produced | 2018 |
Provided To Others? | No |
Impact | 1: Singh AK, Choudhury SR, De S, Zhang J, Kissane S, Dwivedi V, Ramanathan P, Petric M, Orsini L, Hebenstreit D, Brogna S. 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. pii: e41444. doi: 10.7554/eLife.41444. |
URL | https://doi.org/10.7554/eLife.41444 |
Title | Ribo-BiFC |
Description | Novel technique to visualise mRNA translation in Drosophila |
Type Of Material | Technology assay or reagent |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | None yet, just published |
URL | https://bio.biologists.org/content/8/12/bio047233.long |
Title | ChIP-chip and ChIP-seq datasets described in De et al 2022 |
Description | The ChIP-chip and ChIP-seq datasets as well as all associated metadata files are available from a Gene Expression Omnibus (GEO) SuperSeries record: GSE169425 -https://www.ncbi.nlm.nih.gov/geo/info/linking.html. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | These data should benefit researchers are working in the same field and will be part of the fission yeast database Pombase |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169425 |
Title | Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells |
Description | UPF1 is an RNA helicase that scans RNA to unwind secondary structures and to displace associated factors (Franks et al., 2010; Fiorini et al., 2015; Lee et al., 2015; Kanaan et al., 2018). UPF1 has been mostly studied for its role in nonsense mediated mRNA decay (NMD) and other translation-dependent RNA quality-control pathways in the cytoplasm (Isken and Maquat, 2008; Kim and Maquat, 2019). However, we have recently reported that UPF1 associates, genome wide, with nascent transcripts at most Pol II transcription sites in Drosophila (Singh et al., 2019). The association of UPF1 with nascent transcripts appears to be necessary for the release of processed polyadenylated mRNAs from their transcription sites and also for their export from nucleus to cytoplasm (Singh et al., 2019). |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | the paper described a set of ChIP-seq datasets that provide first evidence that Upf1 involved in transcription, data and analysis available from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157612 |
URL | https://www.micropublication.org/journals/biology/micropub-biology-000319 |
Title | GitHub repository of the bioinformatics methods used in De et al 2022 |
Description | The description of the bioinformatics pipelines used, custom-made scripts for correlation and metagene plots, raw data files and processed data tables are available at the GitHub repository: https://github.com/Brogna-Lab/PombeUpf1. |
Type Of Material | Data analysis technique |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | By publishing the bioinformatics detail of the analysis performed should be of benefit for both the critical analysis of the work we are published and should benefit researchers interested to apply similar methods with others datasets.. |
URL | https://github.com/Brogna-Lab/PombeUpf1 |
Title | Y14 ChIP-seq |
Description | We have conducted a set of ChIP experiments to assess the association of exon junction proteins with gene loci, one of this was published and al our Chip-seq data were deposited in the GEO repository (accession no. GSE84595). |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | r Chip-seq data were deposited in the GEO repository (accession no. GSE84595). |
Description | Understanding the role of EJC proteins in gene expression |
Organisation | University of Leicester |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have developped a biochemical procedure to purify ribonucleoprotein complexes in fission yeast |
Collaborator Contribution | Helped wit the initial setting up of the procedure, guidance and key helping with advance genetics manipulation. |
Impact | This technique and the initial results we obtained with it were used to apply for BBSRC grant |
Start Year | 2016 |
Description | School open week |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | We hosted for a week two local students pupils, one from Kings Norton Girls School and the other from Queen's Mary High School. Both of the girls and the teachers were very impressed and keen to send more students. Parents were also very happy. |
Year(s) Of Engagement Activity | 2016 |