Novel functions of alternative pre-mRNA splicing coupled with nonsense-mediated decay
Lead Research Organisation:
King's College London
Department Name: Developmental Neurobiology
Abstract
Precise regulation of cell- and tissue-specific genes is indispensable for proper development and function of our organism. Importantly, abnormal gene expression has been linked to devastating neurological and neuropsychiatric diseases such as myotonic dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, Alzheimer's disease and dementias. Yet another example of potentially dire consequences caused by defective genes is provided by a range of hereditary disorders affecting multiple tissues and organs. Many of these conditions are associated with considerable patient suffering and mortality and constitute a serious burden for the national health system.
Expression of our genes proceeds as a succession of distinct molecular steps that include transcription, processing of primary transcripts into messengers, and ultimately translation of the messengers into proteins. Several control mechanisms operating at each of these steps ensure that protein products of our genes appear in the right place and at the right time. One such control called nonsense-mediated decay, or NMD, eliminates messengers with defective protein-coding capacity thus allowing the cell to cope with deleterious mutations and occasional errors in primary transcript processing. Surprisingly, recent studies suggest that this mechanism is also used to regulate gene expression under normal circumstances. In this case, corresponding primary transcripts can be processed to generate two or more alternative messenger variants, with some variants encoding proteins and the others degraded by NMD. Several genes indispensible for our nerve cells appear to be regulated in this manner and additional research in this field promises further exciting discoveries.
Here we propose to uncover novel genes that are controlled by alternative processing/NMD during brain development and to begin understanding their functional significance. We will advance our research by combining molecular, cellular and developmental biology techniques with advanced bioinformatics approaches. Our work will have important biomedical implications. Indeed, at least one novel gene, Hps1, identified in our preliminary experiments has been directly linked to a hereditary disease called Hermansky-Pudlak Syndrome and understanding regulation of this gene will likely provide important insights into this and a large group of other metabolic disorders associated with similar molecular defects. Wider medical relevance of our study will be guaranteed by its general relevance to neurological and neuropsychiatric diseases associated with aberrant regulation of genes.
Expression of our genes proceeds as a succession of distinct molecular steps that include transcription, processing of primary transcripts into messengers, and ultimately translation of the messengers into proteins. Several control mechanisms operating at each of these steps ensure that protein products of our genes appear in the right place and at the right time. One such control called nonsense-mediated decay, or NMD, eliminates messengers with defective protein-coding capacity thus allowing the cell to cope with deleterious mutations and occasional errors in primary transcript processing. Surprisingly, recent studies suggest that this mechanism is also used to regulate gene expression under normal circumstances. In this case, corresponding primary transcripts can be processed to generate two or more alternative messenger variants, with some variants encoding proteins and the others degraded by NMD. Several genes indispensible for our nerve cells appear to be regulated in this manner and additional research in this field promises further exciting discoveries.
Here we propose to uncover novel genes that are controlled by alternative processing/NMD during brain development and to begin understanding their functional significance. We will advance our research by combining molecular, cellular and developmental biology techniques with advanced bioinformatics approaches. Our work will have important biomedical implications. Indeed, at least one novel gene, Hps1, identified in our preliminary experiments has been directly linked to a hereditary disease called Hermansky-Pudlak Syndrome and understanding regulation of this gene will likely provide important insights into this and a large group of other metabolic disorders associated with similar molecular defects. Wider medical relevance of our study will be guaranteed by its general relevance to neurological and neuropsychiatric diseases associated with aberrant regulation of genes.
Technical Summary
An important transcriptome-wide event in differentiating neurons involves coordinated down-regulation of multiple genes expressed at high levels in neural precursors (NPs). Here we will investigate a novel mechanism mediating this transition by switching alternative splicing (AS) patterns of NP-specific transcripts and triggering their nonsense-mediated decay (NMD). We hypothesise that RNA-binding protein Ptbp1 that is expressed at high levels in NPs but down-regulated in neurons, may coordinate a large part of this AS-NMD program. Indeed, our preliminary studies have begun uncovering genes expressed at optimal level in the presence of Ptbp1 but undergoing NMD in its absence.
To further test our hypothesis, we will first identify corresponding target genes in mouse neuroblastoma cells by transcriptome-wide RNA sequencing followed by advanced bioinformatics interpretation of condition-dependent changes in the numbers of exonic, intronic and splice junction RNA-seq reads. We will validate neuroblastoma data and refine our understanding of the Ptbp1/AS-NMD network using an in vitro neurogenesis model, primary cultures of neural stem cells and neurons and ex vivo neural tube explants. Finally, we will elucidate biological significance of the most promising Ptbp1/AS-NMD targets in cell lines and primary cultures through a combination of molecular, cellular and developmental biology approaches.
By focusing on a novel class of Ptbp1/AS-NMD targets and performing differentiation stage-resolved analyses the proposed program will be poised to generate valuable insights into fundamental mechanisms underlying brain development and function. Importantly, at least one Ptbp1-activated AS-NMD target, Hps1, has been linked to a hereditary condition called Hermansky-Pudlak Syndrome. Wider medical implications of our study will be guaranteed by its general relevance to neurological and neuropsychiatric diseases associated with aberrant regulation of genes.
To further test our hypothesis, we will first identify corresponding target genes in mouse neuroblastoma cells by transcriptome-wide RNA sequencing followed by advanced bioinformatics interpretation of condition-dependent changes in the numbers of exonic, intronic and splice junction RNA-seq reads. We will validate neuroblastoma data and refine our understanding of the Ptbp1/AS-NMD network using an in vitro neurogenesis model, primary cultures of neural stem cells and neurons and ex vivo neural tube explants. Finally, we will elucidate biological significance of the most promising Ptbp1/AS-NMD targets in cell lines and primary cultures through a combination of molecular, cellular and developmental biology approaches.
By focusing on a novel class of Ptbp1/AS-NMD targets and performing differentiation stage-resolved analyses the proposed program will be poised to generate valuable insights into fundamental mechanisms underlying brain development and function. Importantly, at least one Ptbp1-activated AS-NMD target, Hps1, has been linked to a hereditary condition called Hermansky-Pudlak Syndrome. Wider medical implications of our study will be guaranteed by its general relevance to neurological and neuropsychiatric diseases associated with aberrant regulation of genes.
Planned Impact
We anticipate that the proposed programme will generate considerable economic and societal impacts by contributing to medicine, education and staff training.
Medicine
Underscoring medical significance of our work, many human diseases are associated with defects in posttranscriptional control of gene expression. Importantly, RNA-based processes are deregulated in several devastating neurological and neuropsychiatric disorders including myotonic dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, frontotemporal dementia, and possibly Alzheimer's and Huntington's diseases. These conditions accompanied by considerable patient morbidity and mortality also account for an extremely large fraction of the annual £112 billion cost of brain disorders in the UK (J. Psychopharmacol. 2013, 27:761-770). By shedding light on important aspects of RNA metabolism in the nervous system context the proposed programme should improve our understanding of molecular aetiology of these and other diseases and ultimately lead to developing advanced therapies and diagnostic tools. Our work will also have another important biomedical dimension. At least one gene identified in our preliminary experiments, Hps1, has been directly linked to Hermansky-Pudlak Syndrome, a hereditary disease related to a larger cohort of lysosomal storage diseases occurring with collective incidence of ~1 in 7000-8000 live births (Biochem. Soc Trans. 2000, 28:150-154). New insights into Hps1 regulation generated by our program may eventually improve the way these diseases are detected and treated in clinical settings. Although materialisation of these important benefits may require years and possibly decades, we are convinced that contribution of our work to this process will be substantial.
Education
Our work will rely on a multidisciplinary strategy combining bioinformatics and systems biology with more traditional approaches. This trend is becoming increasingly prevalent in life sciences thus necessitating corresponding updates to secondary and tertiary science education. By reaching out to school and undergraduate students we hope to generate valuable experience that may impact future long-term changes in the education sector. Of note, a number of undergraduate students successfully completed short, typically 2-12 month research projects in PI's lab in the past. In 2015-2017, the lab is expected to host students from the Judd School (Tonbridge, Kent) and KCL undergraduates. We plan to engage these students in experimental and computational biology projects outlined in this proposal, which will provide them with first-hand experience in multidisciplinary research. We will additionally use our methodology and data as a teaching device in lectures and tutorials for KCL undergraduate and graduate students.
Staff training
The proposed project will provide a natural framework for training of a postdoctoral fellow who will master a wide range of molecular biology, cell engineering, developmental neurobiology and bioinformatics techniques and will additionally acquire advanced communication and managerial skills. This comprehensive training will maximise his or her value as a skilled employee capable of making important contributions to the UK academia and industry within 3-6 years since the start of the programme. Moreover, by interacting with other lab members the postdoctoral fellow will undoubtedly facilitate their professional growth.
Medicine
Underscoring medical significance of our work, many human diseases are associated with defects in posttranscriptional control of gene expression. Importantly, RNA-based processes are deregulated in several devastating neurological and neuropsychiatric disorders including myotonic dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, frontotemporal dementia, and possibly Alzheimer's and Huntington's diseases. These conditions accompanied by considerable patient morbidity and mortality also account for an extremely large fraction of the annual £112 billion cost of brain disorders in the UK (J. Psychopharmacol. 2013, 27:761-770). By shedding light on important aspects of RNA metabolism in the nervous system context the proposed programme should improve our understanding of molecular aetiology of these and other diseases and ultimately lead to developing advanced therapies and diagnostic tools. Our work will also have another important biomedical dimension. At least one gene identified in our preliminary experiments, Hps1, has been directly linked to Hermansky-Pudlak Syndrome, a hereditary disease related to a larger cohort of lysosomal storage diseases occurring with collective incidence of ~1 in 7000-8000 live births (Biochem. Soc Trans. 2000, 28:150-154). New insights into Hps1 regulation generated by our program may eventually improve the way these diseases are detected and treated in clinical settings. Although materialisation of these important benefits may require years and possibly decades, we are convinced that contribution of our work to this process will be substantial.
Education
Our work will rely on a multidisciplinary strategy combining bioinformatics and systems biology with more traditional approaches. This trend is becoming increasingly prevalent in life sciences thus necessitating corresponding updates to secondary and tertiary science education. By reaching out to school and undergraduate students we hope to generate valuable experience that may impact future long-term changes in the education sector. Of note, a number of undergraduate students successfully completed short, typically 2-12 month research projects in PI's lab in the past. In 2015-2017, the lab is expected to host students from the Judd School (Tonbridge, Kent) and KCL undergraduates. We plan to engage these students in experimental and computational biology projects outlined in this proposal, which will provide them with first-hand experience in multidisciplinary research. We will additionally use our methodology and data as a teaching device in lectures and tutorials for KCL undergraduate and graduate students.
Staff training
The proposed project will provide a natural framework for training of a postdoctoral fellow who will master a wide range of molecular biology, cell engineering, developmental neurobiology and bioinformatics techniques and will additionally acquire advanced communication and managerial skills. This comprehensive training will maximise his or her value as a skilled employee capable of making important contributions to the UK academia and industry within 3-6 years since the start of the programme. Moreover, by interacting with other lab members the postdoctoral fellow will undoubtedly facilitate their professional growth.
Organisations
- King's College London (Lead Research Organisation)
- University of Tartu (Collaboration)
- Francis Crick Institute (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- University College London (Collaboration)
- NANYANG TECHNOLOGICAL UNIVERSITY (Collaboration)
- Tallinn University of Technology (Collaboration)
- University of Helsinki (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
Publications
Hamid FM
(2016)
Exaptive origins of regulated mRNA decay in eukaryotes.
in BioEssays : news and reviews in molecular, cellular and developmental biology
Yap K
(2016)
Polarizing the Neuron through Sustained Co-expression of Alternatively Spliced Isoforms.
in Cell reports
Yap K
(2016)
Functional impact of splice isoform diversity in individual cells.
in Biochemical Society transactions
Rehwinkel J
(2016)
Is anti-viral defence the evolutionary origin of mRNA turnover? (Comment on DOI 10.1002/bies.201600100)
in BioEssays
Qian X
(2016)
Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases.
in The Journal of biological chemistry
Hamid FM
(2017)
A mechanism underlying position-specific regulation of alternative splicing.
in Nucleic acids research
Collins KM
(2017)
An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion.
in Nucleic acids research
Verbeeren J
(2017)
Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA.
in PLoS genetics
Yap K
(2018)
A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival
in Molecular Cell
Ehsan M
(2018)
Mutant Muscle LIM Protein C58G causes cardiomyopathy through protein depletion.
in Journal of molecular and cellular cardiology
Description | As a part of our research program we systematically analyzed splice isoforms expressed at an optimal level only in the presence of an RNA-binding protein called PTBP1. We carried out extensive molecular characterization of several targets of the alternative splicing - nonsense mediated decay (AS-NMD) pathway and are currently preparing a manuscript describing these analyses. Briefly, our work suggests that regulation of gene expression by PTBP1/AS-NMD in developing brain is substantially more widespread than currently thought. We also identified an interesting category of PTBP1 targets that show a tendency for increased co-expression of their alternatively spliced variants during neuronal development. We showed that this results in stable co-expression of two distinct splice isoforms of the cell polarity factor Cdc42 and that both of these isoforms are essential for correct neuronal development. Our work describing this finding was published in Cell Reports (2016) and highlighted in our review in Biochemical Society Transactions (2016) as well as several science news websites. We also identified a new repeat-containing long-noncoding RNA, PNCTR, that controls PTBP1 activity in cancer cells. Importantly, we showed that this RNA promotes cancer cell survival at least in part by regulating expression levels of a specific AS-NMD target of PTBP1 encoding a checkpoint kinase, CHEK2. Results of this study have been published in a reputable scientific journal (Molecular Cell 2018) and highlighted in a press-release article published in the same issue. Relevant to our RNA biology interests in general and this project in particular, we additionally participated in collaborative work aiming to delineate mechanisms underlying evolution of new properties in protein families involved in eukaryotic RNA metabolism. One important conclusion emerging from this study so far is that functional innovation in evolutionarily related RNA metabolic enzymes may occur through relatively minor alterations in their protein folds and quaternary structures (JBC 2016). This grant also helped us generate important insights into regulation of RNA splicing and cleavage/polyadenylation in human and mouse cells (two publications in Nucleic Acids Research 2017; PLoS Genetics in 2017; Nature Communications 2020). We used bioinformatics tools developed as a part of our BBSRC-supported work to help our colleagues to illuminate molecular mechanisms contributing to a heart disorder called hypertrophic cardiomyopathy (collaborative paper in Journal of Molecular and Cellular Cardiology 2018) and normal differentiation of neural progenitors (collaborative paper in Developmental Cell 2020). Finally, this grant helped us develop a robust protocol for differentiation of embryonic stem cells into neurons in vitro. This new resource has been instrumental for our collaborative project on understanding nuclear mechanisms regulating expression of distinct isoforms of an important neurotrophic factor (Elife 2021). . |
Exploitation Route | Our findings so far illuminate important aspects of post-transcriptional gene regulation in mammalian nervous system and will be useful to other scientists who study related problems in other biological systems. This work may also be used as teaching material for undergraduate and PhD students attending lectures, tutorials and seminars on gene regulation mechanisms and neurobiology. |
Sectors | Education Healthcare |
URL | https://www.sciencedaily.com/releases/2016/04/160428131939.htm |
Description | The PDRA involved in this project obtained valuable transferable skills that allowed them to secure a job in the Wellcome Trust charity. |
First Year Of Impact | 2022 |
Sector | Education,Healthcare |
Impact Types | Cultural Societal |
Description | Linking the mechanisms generating protein and cortical cell diversity |
Amount | £215,742 (GBP) |
Organisation | The Leverhulme Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2022 |
End | 09/2025 |
Description | Marie Sklodowska-Curie Postdoctoral Fellowship |
Amount | £128,418 (GBP) |
Funding ID | 751739 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 04/2017 |
End | 10/2019 |
Description | Novel Function of Splicing factors in Establishment and Maintenance of Neuronal Connectivity |
Amount | £642,144 (GBP) |
Funding ID | BB/P001599/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2017 |
End | 09/2020 |
Description | Research and Innovation Staff Exchange (RISE) |
Amount | £1,117,464 (GBP) |
Funding ID | 734791 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 01/2017 |
End | 12/2020 |
Title | A new computational tool to annotate custom transcriptomes |
Description | Together with our collaborators from King's and the University of Tartu in Estonia, we developed an R/Bioconductor package, factR, for functional annotation of custom transcriptomes. |
Type Of Material | Physiological assessment or outcome measure |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | This tool is helping our group to perform BBSRC-funded studies. It is also used by other researchers interested in genomics, alternative splicing, and nonsense-mediated decay. |
URL | https://bioconductor.org/packages/release/bioc/html/factR.html |
Title | Hybridization-proximity labeleing |
Description | We developed a new technology termed Hybridization-Proximity (HyPro) labeling that allows discovery of protein and RNA neighbors of a transcript of interest in genetically unperturbed cells. The method is described in our recently published papers in Mol Cell (https://doi.org/10.1016/j.molcel.2021.10.009) and STAR Protocols (https://doi.org/10.1016/j.xpro.2022.101139). |
Type Of Material | Technology assay or reagent |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | We have received several requests from academia and industry to adapt HyPro labeling to a wide range of biomedical projects. |
URL | https://doi.org/10.1016/j.molcel.2021.10.009 |
Title | Inducible embryonic stem cells |
Description | We developed an embryonic stem cell line that can be induced to differentiate into glutamatergic neurons by simple doxycycline treatment. |
Type Of Material | Cell line |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | This cell line will be useful for many academic and industrial labs interested in brain development and function. |
URL | https://doi.org/10.7554/elife.65161 |
Title | New method to quantify co-expression of alternatively processed messenger RNA isoforms |
Description | As a part of our project, we introduced a novel statistic called isoform co-expression index. It allows one to quantify co-expression of alternatively processed messenger RNA isoforms in any biological sample, from an individual cell to entire organism. We published this new approach in Cell Reports in 2016. |
Type Of Material | Physiological assessment or outcome measure |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | The expected beneficiaries of this innovation will be researchers investigating alternative splicing in different biological contexts. |
URL | http://www.cell.com/cell-reports/comments/S2211-1247(16)30411-9 |
Title | HyPro-MS analysis of proteins proximal to nuclear noncoding RNAs in HeLa cells |
Description | HyPro-MS dataset |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | This dataset provides a valuable resource for researchers investigating noncoding RNAs, RNA-containing nuclear compartments and RNA-protein interactions. |
URL | http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD025264 |
Title | HyPro-seq analysis of HeLa and ARPE-19 cells |
Description | HyPro-seq dataset |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | This dataset provides a valuable resource for researchers investigating noncoding RNAs, RNA-containing nuclear compartments and RNA-protein interactions. |
URL | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10365 |
Title | RNA-seq analysis of HeLa cells treated with GapmeR antisense oligonucleotides |
Description | RNA-seq dataset |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | This dataset provides a resource for researchers interested in biological functions of nuclear RNA-containing compartments. |
URL | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6529 |
Title | RNA-seq and ChIP-seq analyses of PTBP1-controlled co-transcriptional splicing |
Description | We used high-throughput sequencing of RNAs and chromatin immunoprecipitation products (RNA-seq and ChIP-seq) to identify co-transcriptional and post-transcriptional splicing events regulated by the RNA-binding protein PTBP1 in embryonic stem cells. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | These data helped us publish a paper in Mol. Cell. (https://pubmed.ncbi.nlm.nih.gov/36626906/). We currently use this resource for our ongoing PTBP1-related analyses. |
URL | https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11544?accession=E-MTAB-11544 |
Description | Bioinformatics pipeline to analyze gene evolution |
Organisation | Francis Crick Institute |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We developed bioinformatics pipeline to analyze gene evolution. |
Collaborator Contribution | Our collaborators carried out experiments to dissect the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome. |
Impact | A paper is published in Current Biology. The collaboration is multidisciplinary since it combines cell biology, evolutionary biology, lipidomics, and bioinformatics. |
Start Year | 2019 |
Description | Developing an AS-NMD analysis pipeline |
Organisation | University of Tartu |
Country | Estonia |
Sector | Academic/University |
PI Contribution | Participated in development of an R/BioConductor package for discovery of new genes regulated by alternative splicing coupled with nonsense-mediated decay (AS-NMD) |
Collaborator Contribution | Participated in development of an R/BioConductor package for discovery of new genes regulated by alternative splicing coupled with nonsense-mediated decay (AS-NMD) |
Impact | A prototype package developed. This multi-disciplinary activity combines our expertise in molecular biology with extensive bioinformatics expertise of the BIIT group, Tartu University (https://biit.cs.ut.ee/). |
Start Year | 2018 |
Description | Evolution of eukaryotic RNA-interacting proteins |
Organisation | Nanyang Technological University |
Country | Singapore |
Sector | Academic/University |
PI Contribution | This collaboration aims to understand mechanisms underlying evolution of new properties in eukaryotic enzyme families involved in RNA metabolism. My lab has contributed to this effort by analyzing phylogeny and biochemical properties of a representative group of these proteins. |
Collaborator Contribution | Our collaborators determined crystal and electron microscopy structures of orthologously related RNA metabolic enzymes and predicted how structural differences may lead to functional innovation. They are currently working on structural characterization of complexes between these proteins and their RNA ligands. |
Impact | Results of this multidisciplinary collaboration were published in the following article: Qian X, Hamid FM, El Sahili A, Darwis DA, Wong YH, Bhushan S, Makeyev EV*, Lescar J* .J Biol Chem. 2016 Apr 22;291(17):9295-309. doi: 10.1074/jbc.M115.685933. Epub 2016 Feb 23. (*= co-corresponding authors). Relevant research disciplines include biochemistry, molecular biology, structural biology and evolutionary biology. |
Start Year | 2015 |
Description | Gene regulation in neuronal progenitor cells |
Organisation | King's College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We helped our colleague at the Centre for Developmental Neurobiology to analyze gene expression in neuronal progenitor cells |
Collaborator Contribution | Experimental work on neuronal progenitor cells |
Impact | A paper published in Developmental Cell in 2020 |
Start Year | 2018 |
Description | In vitro neuronal differentiation protocol |
Organisation | Tallinn University of Technology |
Country | Estonia |
Sector | Academic/University |
PI Contribution | We developed a robust protocol for differentiation of embryonic stem cells into neurons in vitro. |
Collaborator Contribution | Our collaborators carried out a series of experiments to understand nuclear mechanisms regulating expression of distinct isoforms of an important neurotrophic factor, BDNF |
Impact | Collaborative papers published in Elife (https://elifesciences.org/articles/65161) and Glia (https://onlinelibrary.wiley.com/doi/10.1002/glia.24463) |
Start Year | 2018 |
Description | Regulation of pre-mRNA splicing by RNA-binding protein RBM10 |
Organisation | University College London |
Department | Structural Molecular Biology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Expertise in bioinformatics and minigene splicing assays and general knowledge of splicing regulation pathways. |
Collaborator Contribution | Expertise in structural biology and knowledge of RNA-binding protein activities. |
Impact | Published the following paper: Collins KM, Kainov YA, Christodolou E, Ray D, Morris Q, Hughes T, Taylor IA, Makeyev EV*, Ramos A*. (2017) An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion. Nucleic Acids Res. 2017 Apr 4. doi: 10.1093/nar/gkx225. (*= Co-corresponding authors.) |
Start Year | 2016 |
Description | Role of alternative splicing and quality control mechanisms in regulation of minor spliceosome activity |
Organisation | University of Helsinki |
Department | Institute of Biotechnology |
Country | Finland |
Sector | Academic/University |
PI Contribution | Expertise in alternative splicing, RNA quality control pathways and culturing primary neural cells. |
Collaborator Contribution | Expertise in biology of the minor spliceosome. |
Impact | Published the following paper: Verbeeren J, Verma B, Niemelä EH, Yap K, Makeyev EV, Frilander MJ.(2017) Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA.PLoS Genet. 2017 May 26;13(5):e1006824. doi: 10.1371/journal.pgen.1006824. |
Start Year | 2016 |
Description | Role of mutant CSRP3 protein in cardiomyopathy |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We used bioinformatics pipelines developed as a part of our BBSRC-supported research to understand molecular mechanisms linking mutations in the cysteine and glycine rich protein 3 (CSRP3) with hypertrophic cardiomyopathy. |
Collaborator Contribution | Our collaborators developed a mouse model for hypertrophic cardiomyopathy (HCM) and carried out its extensive phenotypic characterization at the Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Oxford University. Data obtained as a result of these efforts suggest that reduced levels of functional CSPR3 may be a common mechanism underlying HCM. |
Impact | Results of this collaboration have been published in the following open-access paper: J Mol Cell Cardiol. 2018 Aug;121:287-296. doi: 10.1016/j.yjmcc.2018.07.248. Epub 2018 Jul 23. (https://www.jmmc-online.com/article/S0022-2828(18)30692-8/fulltext) |
Start Year | 2018 |
Description | Understanding RNA metabolism in Amyotrophic Lateral Sclerosis (ALS) |
Organisation | King's College London |
Department | MRC Centre for Developmental Neurobiology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We helped our colleague from King's to analyze the role of ALS-linked RNA binding proteins in regulation of mRNA splicing patterns and nucleoplasmic distribution. |
Collaborator Contribution | Zebrafish breeding and analysis, in vitro neuronal cultures, in situ hybridization and other molecular assays. |
Impact | We published the following 3 papers: 1. Taylor R, Hamid F, Fielding T, Gordon PM, Maloney M, Makeyev EV, Houart C. Prematurely terminated intron-retaining mRNAs invade axons in SFPQ null-driven neurodegeneration and are a hallmark of ALS. Nat Commun. 2022 Nov 22;13(1):6994. doi: 10.1038/s41467-022-34331-4. 2. Nikolaou N, Gordon PM, Hamid F, Taylor R, Lloyd-Jones J, Makeyev EV, Houart C. Cytoplasmic pool of U1 spliceosome protein SNRNP70 shapes the axonal transcriptome and regulates motor connectivity. Curr Biol. 2022 Dec 5;32(23):5099-5115.e8. doi: 10.1016/j.cub.2022.10.048. 3. Gordon PM, Hamid F, Makeyev EV, Houart C. Nat Commun. A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons. 2021 Mar 26;12(1):1918. doi: 10.1038/s41467-021-22098-z. |
Start Year | 2021 |
Description | Bioinformatics training for international students |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | We provided training in bioinformatics to 6 post-graduate students from Estonia and Germany who visited us for 1-2 month each as a part of SZ-TEST exchange program. Although the actual visits were funded by another grant (Marie Sklodowska-Curie Actions Research and Innovation Staff Exchange), we used bioinformatics tools developed as a part of our BBSRC-supported projects for training purposes. |
Year(s) Of Engagement Activity | 2018,2019,2020 |
URL | https://sztest.eu/ |
Description | CDN press release |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | We participated in a drafting a press release highlighting significance of our recently published paper in Nature Communications. The press release was published on the Centre for Developmental Neurobiology website: https://devneuro.org/cdn/news-detail.php?NewsID=352&type=93 |
Year(s) Of Engagement Activity | 2020 |
URL | https://devneuro.org/cdn/news-detail.php?NewsID=352&type=93 |
Description | CDN press release |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | We participated in drafting a press release on our recently published paper in Molecular Cell. The press release was published on CDN web site: https://devneuro.org/cdn/news-detail.php?NewsID=469&type=93 |
Year(s) Of Engagement Activity | 2023 |
URL | https://devneuro.org/cdn/news-detail.php?NewsID=469&type=93 |
Description | Hosting a Wellcome Trust-supported undergraduate project |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | We hosted a 2-month research project for an undergraduate student from King's College London supported by a Wellcome Trust Biomedical Vacation Scholarship. The activity provided the student with an opportunity to apply for research funding and acquire a set of practical skills in molecular and cellular biology. We are convinced that this experience promoted student's interest in science and expanded his career possibilities in this field. |
Year(s) Of Engagement Activity | 2018 |
Description | Hosting a summer research project for a student from University California Irvine |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | We hosted a summer research project for an undergraduate student from University California Irvine participating in a Minority Science Program. The purpose of this activity was to allow the student to participate in biomedical research and learn new molecular and cellular biology techniques. The student enjoyed his experience and subsequently presented the results obtained in our lab in several meetings including an AAAS Conference in 2017 (https://aaas.confex.com/aaas/2017/webprogram/Paper20152.html) and Minority Science Program meeting in 2016 (https://www.bio.uci.edu/events/2016-minority-science-programs-msp-research-symposium-day-1/). This experience encouraged the student to continue his scientific education at the postgraduate level. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.bio.uci.edu/events/2016-minority-science-programs-msp-research-symposium-day-1/ |
Description | Hosting an undergraduate summer research project |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | We hosted a 2-month research project for an undergraduate student from King's College London. This activity provided the student with an opportunity to participate in biomedical research and also allowed him to acquire a set of practical skills in molecular and cellular biology. We are convinced that this experience promoted student's interest in science and expanded his career possibilities in this field. |
Year(s) Of Engagement Activity | 2017 |
Description | Hosting research projects for students from the Judd School, Kent |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Our lab hosted 2-month research projects for two Judd pupils. This expanded pupils' knowledge in molecular and cellular biology and provided them with a unique opportunity to participate in biomedical research. We are convinced that this experience promoted pupils' interest in science and technology and expanded their possibilities for further education in this area. |
Year(s) Of Engagement Activity | 2015,2016 |
Description | Organization of symposium on gene expression in health and disease |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | We co-organized a one-day symposium on "Gene expression in health and disease", an event designed to allow mainly students and postdocs to present their research data to an international audience from Estonia Finland and the UK. Three postdoctoral fellows involved in our BBSRC-supported research have been selected to give 15-min presentations. This is an excellent framework for sharing scientific knowledge, fostering future collaborations and improving presentation skills of young scientists. |
Year(s) Of Engagement Activity | 2018 |
Description | Organizing RNA UK 2020 meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | We co-organized the RNA UK 2020 meeting attended by researchers, post-graduate students, and business/media sponsors. Approximately 160 people from the UK, the Netherlands, Australia, Denmark and Italy attended this 3-day event to discuss recent progress in the RNA field. The event was well received by the RNA community and plans were made to organize the next meeting in 2022. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.rnasociety.org/Conferences/rna-uk-2020/ |
Description | Participation in "Glow in the dark science" public outreach program in London primary schools |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | This project is a part of the British Science Week event (https://www.britishscienceweek.org/). It introduces primary school children to science in a playful manner. The project is based on activity stations where the pupils learn the basis of how fluorescence works and observe fluorescently labelled fish and fruit flies, among others. Most pupils attending this event clearly enjoyed the program and asked relevant questions. We believe this project should helped the pupils develop interest in life sciences and biomedical medical research. |
Year(s) Of Engagement Activity | 2016,2017,2018 |
URL | https://devneuro.org/cdn/news-detail.php?NewsID=210&type=91 |
Description | Participation in DevNeuro Academy |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Members of the Makeyev lab participated in the DevNeuro Academy project consisting of a regular program of activities designed to improve the progression and success of school students currently under-represented at our university and other institutes of higher education. The project combines a series of four in-school interactive 'Discovery workshops' with a two-week laboratory summer research work experience at the Centre for Developmental Neurobiology, KCL. |
Year(s) Of Engagement Activity | 2018,2022,2023 |
URL | https://devneuro.org/cdn/public-engagement-dna.php |
Description | Press release article by Molecular Cell highlighting our publication |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | A highlight article showcasing our publication in the same issue of Molecular Cell |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.ncbi.nlm.nih.gov/pubmed/30388407 |
Description | Press release for the Cell Rep. 2016 publication |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | We participated in a press release for our Cell Reports paper explaining significance of this work to the general public. The press release was published on the following science news websites: https://www.sciencedaily.com/releases/2016/04/160428131939.htm https://www.eurekalert.org/pub_releases/2016-04/kcl-coa042016.php https://medicalxpress.com/news/2016-04-co-expression-alternative-gene-products-neurons.html https://www.follownews.com/coexpression-of-alternative-gene-products-helps-neurons-take-shape-16knr http://braintoolsnews.com/wp/feed-items/co-expression-of-alternative-gene-products-helps-neurons-take-shape-2/ http://www.hitechdays.com/news/8570/co-expression-of-alternative-gene-products-helps-neurons-take-shape/ https://scifeeds.com/news/co-expression-of-alternative-gene-products-helps-neurons-take-shape/ |
Year(s) Of Engagement Activity | 2016 |
Description | Press release on a KCL website |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | We participated in a drafting a press release highlighting significance of our work. The press release was published on the Centre for Developmental Neurobiology website: https://devneuro.org/cdn/news-detail.php?NewsID=298&type=93 |
Year(s) Of Engagement Activity | 2018 |
URL | https://devneuro.org/cdn/news-detail.php?NewsID=298&type=93 |
Description | School student research internship |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | We organized and hosted a one-week summer research attachment for a student from the Bullers Wood School (Chislehurst BR7 5LJ). The student learned new scientific concepts and experimental techniques. Based on our discussions with the student and the parents this experience appears to have sparked student's interest in biomedical research. |
Year(s) Of Engagement Activity | 2019,2022,2023 |