1
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Cotrina-Vinagre FJ, Rodríguez-García ME, Del Pozo-Filíu L, Hernández-Laín A, Arteche-López A, Morte B, Sevilla M, Pérez-Jurado LA, Quijada-Fraile P, Camacho A, Martínez-Azorín F. Expanding the genetic and phenotypic spectrum of congenital myasthenic syndrome: new homozygous VAMP1 splicing variants in 2 novel individuals. J Hum Genet 2024; 69:187-196. [PMID: 38355957 DOI: 10.1038/s10038-024-01228-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
We report the cases of two Spanish pediatric patients with hypotonia, muscle weakness and feeding difficulties at birth. Whole-exome sequencing (WES) uncovered two new homozygous VAMP1 (Vesicle Associated Membrane Protein 1) splicing variants, NM_014231.5:c.129+5 G > A in the boy patient (P1) and c.341-24_341-16delinsAGAAAA in the girl patient (P2). This gene encodes the vesicle-associated membrane protein 1 (VAMP1) that is a component of a protein complex involved in the fusion of synaptic vesicles with the presynaptic membrane. VAMP1 has a highly variable C-terminus generated by alternative splicing that gives rise to three main isoforms (A, B and D), being VAMP1A the only isoform expressed in the nervous system. In order to assess the pathogenicity of these variants, expression experiments of RNA for VAMP1 were carried out. The c.129+5 G > A and c.341-24_341-16delinsAGAAAA variants induced aberrant splicing events resulting in the deletion of exon 2 (r.5_131del; p.Ser2TrpfsTer7) in the three isoforms in the first case, and the retention of the last 14 nucleotides of the 3' of intron 4 (r.340_341ins341-14_341-1; p.Ile114AsnfsTer77) in the VAMP1A isoform in the second case. Pathogenic VAMP1 variants have been associated with autosomal dominant spastic ataxia 1 (SPAX1) and with autosomal recessive presynaptic congenital myasthenic syndrome (CMS). Our patients share the clinical manifestations of CMS patients with two important differences: they do not show the typical electrophysiological pattern that suggests pathology of pre-synaptic neuromuscular junction, and their muscular biopsies present hypertrophic fibers type 1. In conclusion, our data expand both genetic and phenotypic spectrum associated with VAMP1 variants.
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Affiliation(s)
- Francisco Javier Cotrina-Vinagre
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - María Elena Rodríguez-García
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Madrid, Spain
| | - Lucía Del Pozo-Filíu
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Aurelio Hernández-Laín
- Servicio de Anatomía Patológica (Neuropatología), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Ana Arteche-López
- Servicio de Genética, Hospital Universitario 12 de Octubre, E-28041, Madrid, Spain
| | - Beatriz Morte
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Madrid, Spain
- Instituto de Investigaciones Biomedicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Marta Sevilla
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Genetics Service, Hospital del Mar, Barcelona, Spain
| | - Luis Alberto Pérez-Jurado
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Genetics Service, Hospital del Mar, Barcelona, Spain
| | - Pilar Quijada-Fraile
- Unidad Pediátrica de Enfermedades Raras, Enfermedades Mitocondriales y Metabólicas Hereditarias, Hospital 12 de Octubre, Madrid, Spain
| | - Ana Camacho
- Sección de Neurología Infantil, Hospital 12 de Octubre, Universidad Complutense de Madrid, Madrid, Spain
| | - Francisco Martínez-Azorín
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Madrid, Spain.
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2
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Weber AI, Parthasarathy S, Borisova E, Epifanova E, Preußner M, Rusanova A, Ambrozkiewicz MC, Bessa P, Newman A, Müller L, Schaal H, Heyd F, Tarabykin V. Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression. Nucleic Acids Res 2023; 51:10218-10237. [PMID: 37697438 PMCID: PMC10602877 DOI: 10.1093/nar/gkad703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/13/2023] Open
Abstract
The seat of higher-order cognitive abilities in mammals, the neocortex, is a complex structure, organized in several layers. The different subtypes of principal neurons are distributed in precise ratios and at specific positions in these layers and are generated by the same neural progenitor cells (NPCs), steered by a spatially and temporally specified combination of molecular cues that are incompletely understood. Recently, we discovered that an alternatively spliced isoform of the TrkC receptor lacking the kinase domain, TrkC-T1, is a determinant of the corticofugal projection neuron (CFuPN) fate. Here, we show that the finely tuned balance between TrkC-T1 and the better known, kinase domain-containing isoform, TrkC-TK+, is cell type-specific in the developing cortex and established through the antagonistic actions of two RNA-binding proteins, Srsf1 and Elavl1. Moreover, our data show that Srsf1 promotes the CFuPN fate and Elavl1 promotes the callosal projection neuron (CPN) fate in vivo via regulating the distinct ratios of TrkC-T1 to TrkC-TK+. Taken together, we connect spatio-temporal expression of Srsf1 and Elavl1 in the developing neocortex with the regulation of TrkC alternative splicing and transcript stability and neuronal fate choice, thus adding to the mechanistic and functional understanding of alternative splicing in vivo.
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Affiliation(s)
- A Ioana Weber
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Srinivas Parthasarathy
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Ekaterina Borisova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ekaterina Epifanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Alexandra Rusanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Mateusz C Ambrozkiewicz
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Paraskevi Bessa
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew G Newman
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Lisa Müller
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Victor Tarabykin
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
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3
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Borovská I, Vořechovský I, Královičová J. Alu RNA fold links splicing with signal recognition particle proteins. Nucleic Acids Res 2023; 51:8199-8216. [PMID: 37309897 PMCID: PMC10450188 DOI: 10.1093/nar/gkad500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
Transcriptomic diversity in primates was considerably expanded by exonizations of intronic Alu elements. To better understand their cellular mechanisms we have used structure-based mutagenesis coupled with functional and proteomic assays to study the impact of successive primate mutations and their combinations on inclusion of a sense-oriented AluJ exon in the human F8 gene. We show that the splicing outcome was better predicted by consecutive RNA conformation changes than by computationally derived splicing regulatory motifs. We also demonstrate an involvement of SRP9/14 (signal recognition particle) heterodimer in splicing regulation of Alu-derived exons. Nucleotide substitutions that accumulated during primate evolution relaxed the conserved left-arm AluJ structure including helix H1 and reduced the capacity of SRP9/14 to stabilize the closed Alu conformation. RNA secondary structure-constrained mutations that promoted open Y-shaped conformations of the Alu made the Alu exon inclusion reliant on DHX9. Finally, we identified additional SRP9/14 sensitive Alu exons and predicted their functional roles in the cell. Together, these results provide unique insights into architectural elements required for sense Alu exonization, identify conserved pre-mRNA structures involved in exon selection and point to a possible chaperone activity of SRP9/14 outside the mammalian signal recognition particle.
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Affiliation(s)
- Ivana Borovská
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava 840 05, Slovak Republic
| | - Igor Vořechovský
- Faculty of Medicine, University of Southampton, HDH, MP808, Southampton SO16 6YD, United Kingdom
| | - Jana Královičová
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava 840 05, Slovak Republic
- Institute of Zoology, Slovak Academy of Sciences, Bratislava 845 06, Slovak Republic
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4
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García-Ruiz S, Zhang D, Gustavsson EK, Rocamora-Perez G, Grant-Peters M, Fairbrother-Browne A, Reynolds RH, Brenton JW, Gil-Martínez AL, Chen Z, Rio DC, Botia JA, Guelfi S, Collado-Torres L, Ryten M. Splicing accuracy varies across human introns, tissues and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534370. [PMID: 37034741 PMCID: PMC10081249 DOI: 10.1101/2023.03.29.534370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation. We show that mis-splicing occurs at different rates across introns and tissues and that these splicing inaccuracies are primarily affected by the abundance of core components of the spliceosome assembly and its regulators. Using publicly available data on short-hairpin RNA-knockdowns of numerous spliceosomal components and related regulators, we found support for the importance of RNA-binding proteins in mis-splicing. We also demonstrated that age is positively correlated with mis-splicing, and it affects genes implicated in neurodegenerative diseases. This in-depth characterisation of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
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Affiliation(s)
- S García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - D Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - E K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - G Rocamora-Perez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - M Grant-Peters
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - R H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - J W Brenton
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A L Gil-Martínez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Z Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - D C Rio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - J A Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - S Guelfi
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Verge Genomics, South San Francisco, CA, 94080, USA
| | - L Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA , 21205
| | - M Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
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5
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Müller L, Ptok J, Nisar A, Antemann J, Grothmann R, Hillebrand F, Brillen AL, Ritchie A, Theiss S, Schaal H. Modeling splicing outcome by combining 5'ss strength and splicing regulatory elements. Nucleic Acids Res 2022; 50:8834-8851. [PMID: 35947702 PMCID: PMC9410876 DOI: 10.1093/nar/gkac663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/23/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
Correct pre-mRNA processing in higher eukaryotes vastly depends on splice site recognition. Beyond conserved 5'ss and 3'ss motifs, splicing regulatory elements (SREs) play a pivotal role in this recognition process. Here, we present in silico designed sequences with arbitrary a priori prescribed splicing regulatory HEXplorer properties that can be concatenated to arbitrary length without changing their regulatory properties. We experimentally validated in silico predictions in a massively parallel splicing reporter assay on more than 3000 sequences and exemplarily identified some SRE binding proteins. Aiming at a unified 'functional splice site strength' encompassing both U1 snRNA complementarity and impact from neighboring SREs, we developed a novel RNA-seq based 5'ss usage landscape, mapping the competition of pairs of high confidence 5'ss and neighboring exonic GT sites along HBond and HEXplorer score coordinate axes on human fibroblast and endothelium transcriptome datasets. These RNA-seq data served as basis for a logistic 5'ss usage prediction model, which greatly improved discrimination between strong but unused exonic GT sites and annotated highly used 5'ss. Our 5'ss usage landscape offers a unified view on 5'ss and SRE neighborhood impact on splice site recognition, and may contribute to improved mutation assessment in human genetics.
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Affiliation(s)
| | | | - Azlan Nisar
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany,Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, Recklinghausen 45665, Germany
| | - Jennifer Antemann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Ramona Grothmann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Frank Hillebrand
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | | | - Heiner Schaal
- To whom correspondence should be addressed. Tel: +49 211 81 12393; Fax: +49 211 81 10856;
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6
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Ramakrishnan M, Rajan KS, Mullasseri S, Palakkal S, Kalpana K, Sharma A, Zhou M, Vinod KK, Ramasamy S, Wei Q. The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1241-1256. [PMID: 35445501 PMCID: PMC9241379 DOI: 10.1111/pbi.13829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 06/01/2023]
Abstract
There is growing evidence that post-transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6-methyladenosine (m6 A) and 5-methylcytosine (m5 C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2'-O-methylation (Nm), in the cell remain unclear due to insufficient advances in high-throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high-throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology InstituteBar‐Ilan University52900Ramat‐GanIsrael
- Department of Chemical and Structural BiologyWeizmann Institute7610001RehovotIsrael
| | - Sileesh Mullasseri
- School of Ocean Science and TechnologyKerala University of Fisheries and Ocean StudiesCochinIndia
| | - Sarin Palakkal
- The Institute for Drug ResearchSchool of PharmacyThe Hebrew University of JerusalemJerusalemIsrael
| | - Krishnan Kalpana
- Department of Plant PathologyAgricultural College and Research InstituteTamilnadu Agricultural University625 104MaduraiTamil NaduIndia
| | - Anket Sharma
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
| | - Mingbing Zhou
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High‐Efficiency UtilizationZhejiang A&F UniversityHangzhouZhejiangChina
| | | | - Subbiah Ramasamy
- Cardiac Metabolic Disease LaboratoryDepartment of BiochemistrySchool of Biological SciencesMadurai Kamaraj UniversityMaduraiTamil NaduIndia
| | - Qiang Wei
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
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7
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Abstract
Alternative splicing enables higher eukaryotes to expand mRNA diversity from a finite number of genes through highly combinatorial splice site selection mechanisms that are influenced by the sequence of competing splice sites, cis-regulatory elements binding trans-acting factors, the length of exons and introns harbouring alternative splice sites and RNA secondary structures at putative splice junctions. To test the hypothesis that the intron definition or exon definition modes of splice site recognition direct the selection of alternative splice patterns, we created a database of alternative splice site usage (ALTssDB). When alternative splice sites are embedded within short introns (intron definition), the 5' and 3' splice sites closest to each other across the intron preferentially pair, consistent with previous observations. However, when alternative splice sites are embedded within large flanking introns (exon definition), the 5' and 3' splice sites closest to each other across the exon are preferentially selected. Thus, alternative splicing decisions are influenced by the intron and exon definition modes of splice site recognition. The results demonstrate that the spliceosome pairs splice sites that are closest in proximity within the unit of initial splice site selection.
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Affiliation(s)
- Francisco Carranza
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
| | - Hossein Shenasa
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
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8
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Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
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Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
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9
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Müller L, Moskorz W, Brillen AL, Hillebrand F, Ostermann PN, Kiel N, Walotka L, Ptok J, Timm J, Lübke N, Schaal H. Altered HIV-1 mRNA Splicing Due to Drug-Resistance-Associated Mutations in Exon 2/2b. Int J Mol Sci 2021; 23:ijms23010156. [PMID: 35008581 PMCID: PMC8745674 DOI: 10.3390/ijms23010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 12/02/2022] Open
Abstract
The underlying molecular mechanism and their general effect on the replication capacity of HIV 1 drug-resistance-associated mutations is often poorly understood. To elucidate the effect of two such mutations located in a region with a high density of spicing regulatory elements on the HIV-1-splicing outcome, bioinformatic predictions were combined with transfection and infection experiments. Results show that the previously described R263K drug-resistance-associated integrase mutation has additionally a severe effect on the ESE2b splicing regulatory element (SRE) in exon 2b, which causes loss of SD2b recognition. This was confirmed by an R263R silent mutation with a similar predicted effect on the exon 2b SRE. In contrast, a V260I mutation and its silent counterpart with a lower effect on ESS2b did not exhibit any differences in the splicing pattern. Since HIV-1 highly relies on a balanced splicing reaction, changes in the splicing outcome can contribute to changes in viral replication and might add to the effect of escape mutations toward antiviral drugs. Thus, a classification of mutations purely addressing proteins is insufficient.
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10
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Holmes BB, Russ JB, Wu YW, Gallagher RC, Gano D. Clinical Reasoning: A 2-Day-Old Boy With Sudden Cardiac Arrest and Encephalopathy. Neurology 2021; 97:e1743-e1746. [PMID: 34158382 PMCID: PMC10513875 DOI: 10.1212/wnl.0000000000012408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Brandon B Holmes
- From the Neurology Residency Program (B.B.H.) and Child Neurology Residency Program (J.B.R.), Department of Neurology, University of California San Francisco; and the Departments of Neurology (Y.W.W., D.G.), and Pediatrics (R.C.G., D.G.), University of California San Francisco.
| | - Jeffrey B Russ
- From the Neurology Residency Program (B.B.H.) and Child Neurology Residency Program (J.B.R.), Department of Neurology, University of California San Francisco; and the Departments of Neurology (Y.W.W., D.G.), and Pediatrics (R.C.G., D.G.), University of California San Francisco
| | - Yvonne W Wu
- From the Neurology Residency Program (B.B.H.) and Child Neurology Residency Program (J.B.R.), Department of Neurology, University of California San Francisco; and the Departments of Neurology (Y.W.W., D.G.), and Pediatrics (R.C.G., D.G.), University of California San Francisco
| | - Renata C Gallagher
- From the Neurology Residency Program (B.B.H.) and Child Neurology Residency Program (J.B.R.), Department of Neurology, University of California San Francisco; and the Departments of Neurology (Y.W.W., D.G.), and Pediatrics (R.C.G., D.G.), University of California San Francisco
| | - Dawn Gano
- From the Neurology Residency Program (B.B.H.) and Child Neurology Residency Program (J.B.R.), Department of Neurology, University of California San Francisco; and the Departments of Neurology (Y.W.W., D.G.), and Pediatrics (R.C.G., D.G.), University of California San Francisco
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11
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Ptok J, Müller L, Ostermann PN, Ritchie A, Dilthey AT, Theiss S, Schaal H. Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code. Comput Struct Biotechnol J 2021; 19:3069-3076. [PMID: 34136105 PMCID: PMC8178101 DOI: 10.1016/j.csbj.2021.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 11/22/2022] Open
Abstract
Codon degeneracy of amino acid sequences permits an additional “mRNP code” layer underlying the genetic code that is related to RNA processing. In pre-mRNA splicing, splice site usage is determined by both intrinsic strength and sequence context providing RNA binding sites for splicing regulatory proteins. In this study, we systematically examined modification of splicing regulatory properties in the neighborhood of a GT site, i.e. potential splice site, without altering the encoded amino acids. We quantified the splicing regulatory properties of the neighborhood around a potential splice site by its Splice Site HEXplorer Weight (SSHW) based on the HEXplorer score algorithm. To systematically modify GT site neighborhoods, either minimizing or maximizing their SSHW, we designed the novel stochastic optimization algorithm ModCon that applies a genetic algorithm with stochastic crossover, insertion and random mutation elements supplemented by a heuristic sliding window approach. To assess the achievable range in SSHW in human splice donors without altering the encoded amino acids, we applied ModCon to a set of 1000 randomly selected Ensembl annotated human splice donor sites, achieving substantial and accurate changes in SSHW. Using ModCon optimization, we successfully switched splice donor usage in a splice site competition reporter containing coding sequences from FANCA, FANCB or BRCA2, while retaining their amino acid coding information. The ModCon algorithm and its R package implementation can assist in reporter design by either introducing novel splice sites, silencing accidental, undesired splice sites, and by generally modifying the entire mRNP code while maintaining the genetic code.
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Key Words
- A, adenine
- F1, filial sequence 1
- G, guanine
- GA, genetic algorithm
- HBS, HBond score
- HBond score
- HEXplorer score
- HZEI, HEXplorer score
- P1, parental sequence 1
- SA, splice acceptor
- SD, splice donor
- SR proteins, serine- and arginine-rich proteins
- SRP, splicing regulatory protein
- SSHW, splice site HEXplorer weight
- SW, sliding window
- Splice donor
- Splicing regulatory proteins
- Splicing reporter
- T, thymine
- eGFP, enhanced green fluorescent protein
- hnRNP, heterogeneous nuclear ribonucleoproteins
- nt, nucleotides
- pre-mRNA splicing
- pre-mRNA, precursor messenger RNA
- snRNA, small nuclear RNA
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Philipp Niklas Ostermann
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Alexander T Dilthey
- Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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12
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Daniels NJ, Hershberger CE, Gu X, Schueger C, DiPasquale WM, Brick J, Saunthararajah Y, Maciejewski JP, Padgett RA. Functional analyses of human LUC7-like proteins involved in splicing regulation and myeloid neoplasms. Cell Rep 2021; 35:108989. [PMID: 33852859 PMCID: PMC8078730 DOI: 10.1016/j.celrep.2021.108989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/12/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Vertebrates have evolved three paralogs, termed LUC7L, LUC7L2, and LUC7L3, of the essential yeast U1 small nuclear RNA (snRNA)-associated splicing factor Luc7p. We investigated the mechanistic and regulatory functions of these putative splicing factors, of which one (LUC7L2) is mutated or deleted in myeloid neoplasms. Protein interaction data show that all three proteins bind similar core but distinct regulatory splicing factors, probably mediated through their divergent arginine-serine-rich domains, which are not present in Luc7p. Knockdown of each factor reveals mostly unique sets of significantly dysregulated alternative splicing events dependent on their binding locations, which are largely non-overlapping. Notably, knockdown of LUC7L2 alone significantly upregulates the expression of multiple spliceosomal factors and downregulates glycolysis genes, possibly contributing to disease pathogenesis. RNA binding studies reveal that LUC7L2 and LUC7L3 crosslink to weak 5' splice sites and to the 5' end of U1 snRNA, establishing an evolutionarily conserved role in 5' splice site selection.
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Affiliation(s)
- Noah J Daniels
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Courtney E Hershberger
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaorong Gu
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Caroline Schueger
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - William M DiPasquale
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jonathan Brick
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Richard A Padgett
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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13
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Morais P, Adachi H, Yu YT. Spliceosomal snRNA Epitranscriptomics. Front Genet 2021; 12:652129. [PMID: 33737950 PMCID: PMC7960923 DOI: 10.3389/fgene.2021.652129] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
Small nuclear RNAs (snRNAs) are critical components of the spliceosome that catalyze the splicing of pre-mRNA. snRNAs are each complexed with many proteins to form RNA-protein complexes, termed as small nuclear ribonucleoproteins (snRNPs), in the cell nucleus. snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes. The recognition is achieved primarily by base-pairing interactions (or nucleotide-nucleotide contact) between snRNAs and pre-mRNA. Notably, snRNAs are extensively modified with different RNA modifications, which confer unique properties to the RNAs. Here, we review the current knowledge of the mechanisms and functions of snRNA modifications and their biological relevance in the splicing process.
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Affiliation(s)
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
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14
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Murad NF, Silva-Brandão KL, Brandão MM. Mechanisms behind polyphagia in a pest insect: Responses of Spodoptera frugiperda (J.E. Smith) strains to preferential and alternative larval host plants assessed with gene regulatory networks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194687. [PMID: 33561559 DOI: 10.1016/j.bbagrm.2021.194687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
A dataset of gene expression from Spodoptera frugiperda, a highly generalist pest moth, was used to understand how gene regulation is related to larval host plant preference. Transcriptomic data of corn and rice strains of S. frugiperda larvae, reared on different diets, were analysed with three different approaches of gene network inference, namely co-expression, weighted co-expression and Bayesian networks, since each methodology provides a different visualization of the data. Using these approaches, it was possible to identify two loosely interconnected co-expression networks, one of them responsible for fast response to herbivory and anti-herbivory mechanisms and the other related to housekeeping genes, which present slower response to environmental variations. Integrating different levels of information such as gene expression patterns, gene assembly, transcriptomics, relationship among genes and phenotypes, functional relationships, among other information, enabled a wider visualization of S. frugiperda response to diet stimuli. The biological properties in the proposed networks are here described and discussed, as well as patterns of gene expression related to larval performance attributes.
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Affiliation(s)
- Natália Faraj Murad
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade de Campinas (UNICAMP). Av. Cândido Rondon, 400. CEP 13083-875 Campinas, SP, Brazil
| | - Karina Lucas Silva-Brandão
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade de Campinas (UNICAMP). Av. Cândido Rondon, 400. CEP 13083-875 Campinas, SP, Brazil; Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Av. dos Estados, 5001. CEP 09210-580 Santo André, SP, Brazil
| | - Marcelo Mendes Brandão
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade de Campinas (UNICAMP). Av. Cândido Rondon, 400. CEP 13083-875 Campinas, SP, Brazil.
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15
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Ptok J, Theiss S, Schaal H. VarCon: An R Package for Retrieving Neighboring Nucleotides of an SNV. Cancer Inform 2020; 19:1176935120976399. [PMID: 33281441 PMCID: PMC7691889 DOI: 10.1177/1176935120976399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/01/2020] [Indexed: 11/24/2022] Open
Abstract
Reporting of a single nucleotide variant (SNV) follows the Sequence Variant Nomenclature
(http://varnomen.hgvs.org/), using an unambiguous numbering scheme specific
for coding and noncoding DNA. However, the corresponding sequence neighborhood of a given
SNV, which is required to assess its impact on splicing regulation, is not easily
accessible from this nomenclature. Providing fast and easy access to this neighborhood
just from a given SNV reference, the novel tool VarCon combines information of the Ensembl
human reference genome and the corresponding transcript table for accurate retrieval.
VarCon also displays splice site scores (HBond and MaxEnt scores) and HEXplorer profiles
of an SNV neighborhood, reflecting position-dependent splice enhancing and silencing
properties.
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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16
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Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annu Rev Genet 2020; 54:309-336. [PMID: 32870730 DOI: 10.1146/annurev-genet-112618-043830] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
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Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
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17
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Janin A, Chanavat V, Rollat‐Farnier P, Bardel C, Nguyen K, Chevalier P, Eicher J, Faivre L, Piard J, Albert E, Nony S, Millat G. Whole
MYBPC3
NGS sequencing as a molecular strategy to improve the efficiency of molecular diagnosis of patients with hypertrophic cardiomyopathy. Hum Mutat 2019; 41:465-475. [DOI: 10.1002/humu.23944] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Alexandre Janin
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie EstHospices Civils de Lyon Lyon France
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217Université Claude Bernard Lyon 1, Université de Lyon Lyon France
| | - Valérie Chanavat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie EstHospices Civils de Lyon Lyon France
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217Université Claude Bernard Lyon 1, Université de Lyon Lyon France
| | - Pierre‐Antoine Rollat‐Farnier
- Plateforme NGS‐HCL, Cellule bioinformatique, Centre de Biologie et Pathologie EstHospices Civils de Lyon Lyon France
| | - Claire Bardel
- Plateforme NGS‐HCL, Cellule bioinformatique, Centre de Biologie et Pathologie EstHospices Civils de Lyon Lyon France
- Laboratoire de Biométrie et Biologie EvolutiveUniversité de Lyon, Université Lyon 1, CNRS Villeurbanne France
- Service de Biostatistique‐bioinformatiqueHospices Civils de Lyon Lyon France
| | - Karine Nguyen
- Département de Génétique MédicaleHôpital d'enfants de la Timone Marseille France
| | - Philippe Chevalier
- Service de RythmologieHôpital Cardiologique Louis‐Pradel Bron France
- Université de Lyon Lyon France
| | | | - Laurence Faivre
- Centre de GénétiqueCentre Hospitalier Universitaire Dijon Dijon France
| | - Juliette Piard
- Centre de Génétique HumaineUniversité de Franche‐Comté, CHU Besançon Besançon France
- Unité de recherche en neurosciences intégratives et cognitives EA481Université de Franche‐Comté Besançon France
| | - Emma Albert
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie EstHospices Civils de Lyon Lyon France
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217Université Claude Bernard Lyon 1, Université de Lyon Lyon France
| | - Severine Nony
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie EstHospices Civils de Lyon Lyon France
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217Université Claude Bernard Lyon 1, Université de Lyon Lyon France
| | - Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie EstHospices Civils de Lyon Lyon France
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217Université Claude Bernard Lyon 1, Université de Lyon Lyon France
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18
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Skittrall JP, Ingemarsdotter CK, Gog JR, Lever AML. A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance. PLoS Comput Biol 2019; 15:e1007345. [PMID: 31545786 PMCID: PMC6791557 DOI: 10.1371/journal.pcbi.1007345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/14/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
HIV-1 replicates via a low-fidelity polymerase with a high mutation rate; strong conservation of individual nucleotides is highly indicative of the presence of critical structural or functional properties. Identifying such conservation can reveal novel insights into viral behaviour. We analysed 3651 publicly available sequences for the presence of nucleic acid conservation beyond that required by amino acid constraints, using a novel scale-free method that identifies regions of outlying score together with a codon scoring algorithm. Sequences with outlying score were further analysed using an algorithm for producing local RNA folds whilst accounting for alignment properties. 11 different conserved regions were identified, some corresponding to well-known cis-acting functions of the HIV-1 genome but also others whose conservation has not previously been noted. We identify rational causes for many of these, including cis functions, possible additional reading frame usage, a plausible mechanism by which the central polypurine tract primes second-strand DNA synthesis and a conformational stabilising function of a region at the 5′ end of env. HIV-1 is a very rapidly mutating organism, however some parts of its genetic material change more than others. We looked for coding regions of HIV-1 that change relatively little, by turning the problem of finding such regions into a problem in signal processing, and solving this using a novel analytical approach that we recently described. We investigated why the regions we identified change less, including using the genetic code in the regions we found to prime an algorithm to predict their structures. In some cases there are already known functions for the features we found, in others they provide new insights into the properties of known regions, and in some cases we identify new regions that vary less for as yet unknown functional reasons.
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Affiliation(s)
- Jordan P Skittrall
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Carin K Ingemarsdotter
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Julia R Gog
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Cambridge, United Kingdom
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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19
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Ptok J, Müller L, Theiss S, Schaal H. Context matters: Regulation of splice donor usage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194391. [PMID: 31202784 DOI: 10.1016/j.bbagrm.2019.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 11/16/2022]
Abstract
Elaborate research on splicing, starting in the late seventies, evolved from the discovery that 5' splice sites are recognized by their complementarity to U1 snRNA towards the realization that RNA duplex formation cannot be the sole basis for 5'ss selection. Rather, their recognition is highly influenced by a number of context factors including transcript architecture as well as splicing regulatory elements (SREs) in the splice site neighborhood. In particular, proximal binding of splicing regulatory proteins highly influences splicing outcome. The importance of SRE integrity especially becomes evident in the light of human pathogenic mutations where single nucleotide changes in SREs can severely affect the resulting transcripts. Bioinformatics tools nowadays greatly assist in the computational evaluation of 5'ss, their neighborhood and the impact of pathogenic mutations. Although predictions are already quite robust, computational evaluation of the splicing regulatory landscape still faces challenges to increase future reliability. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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20
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Bohnsack MT, Sloan KE. Modifications in small nuclear RNAs and their roles in spliceosome assembly and function. Biol Chem 2019; 399:1265-1276. [PMID: 29908124 DOI: 10.1515/hsz-2018-0205] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/28/2018] [Indexed: 01/27/2023]
Abstract
Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific ribonucleoproteins (scaRNPs). Modified nucleotides typically cluster in functionally important regions of the snRNAs, suggesting that their presence could optimise the interactions of snRNAs with each other or with pre-mRNAs, or may affect the binding of spliceosomal proteins. snRNA modifications appear to play important roles in snRNP biogenesis and spliceosome assembly, and have also been proposed to influence the efficiency and fidelity of pre-mRNA splicing. Interestingly, alterations in the modification status of snRNAs have recently been observed in different cellular conditions, implying that some snRNA modifications are dynamic and raising the possibility that these modifications may fine-tune the spliceosome for particular functions. Here, we review the current knowledge on the snRNA modification machinery and discuss the timing, functions and dynamics of modifications in snRNAs.
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Affiliation(s)
- Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg August University, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
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21
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Erkelenz S, Theiss S, Kaisers W, Ptok J, Walotka L, Müller L, Hillebrand F, Brillen AL, Sladek M, Schaal H. Ranking noncanonical 5' splice site usage by genome-wide RNA-seq analysis and splicing reporter assays. Genome Res 2018; 28:1826-1840. [PMID: 30355602 PMCID: PMC6280755 DOI: 10.1101/gr.235861.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/20/2018] [Indexed: 01/01/2023]
Abstract
Most human pathogenic mutations in 5' splice sites affect the canonical GT in positions +1 and +2, leading to noncanonical dinucleotides. On the other hand, noncanonical dinucleotides are observed under physiological conditions in ∼1% of all human 5'ss. It is therefore a challenging task to understand the pathogenic mutation mechanisms underlying the conditions under which noncanonical 5'ss are used. In this work, we systematically examined noncanonical 5' splice site selection, both experimentally using splicing competition reporters and by analyzing a large RNA-seq data set of 54 fibroblast samples from 27 subjects containing a total of 2.4 billion gapped reads covering 269,375 exon junctions. From both approaches, we consistently derived a noncanonical 5'ss usage ranking GC > TT > AT > GA > GG > CT. In our competition splicing reporter assay, noncanonical splicing was strictly dependent on the presence of upstream or downstream splicing regulatory elements (SREs), and changes in SREs could be compensated by variation of U1 snRNA complementarity in the competing 5'ss. In particular, we could confirm splicing at different positions (i.e., -1, +1, +5) of a splice site for all noncanonical dinucleotides "weaker" than GC. In our comprehensive RNA-seq data set analysis, noncanonical 5'ss were preferentially detected in weakly used exon junctions of highly expressed genes. Among high-confidence splice sites, they were 10-fold overrepresented in clusters with a neighboring, more frequently used 5'ss. Conversely, these more frequently used neighbors contained only the dinucleotides GT, GC, and TT, in accordance with the above ranking.
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Affiliation(s)
- Steffen Erkelenz
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Center for Biological and Medical Research (BMFZ), Center of Bioinformatics and Biostatistics (CBiBs), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lara Walotka
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Frank Hillebrand
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Michael Sladek
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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22
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Blazquez L, Emmett W, Faraway R, Pineda JMB, Bajew S, Gohr A, Haberman N, Sibley CR, Bradley RK, Irimia M, Ule J. Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing. Mol Cell 2018; 72:496-509.e9. [PMID: 30388411 PMCID: PMC6224609 DOI: 10.1016/j.molcel.2018.09.033] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/24/2018] [Accepted: 09/27/2018] [Indexed: 01/13/2023]
Abstract
Recursive splicing (RS) starts by defining an "RS-exon," which is then spliced to the preceding exon, thus creating a recursive 5' splice site (RS-5ss). Previous studies focused on cryptic RS-exons, and now we find that the exon junction complex (EJC) represses RS of hundreds of annotated, mainly constitutive RS-exons. The core EJC factors, and the peripheral factors PNN and RNPS1, maintain RS-exon inclusion by repressing spliceosomal assembly on RS-5ss. The EJC also blocks 5ss located near exon-exon junctions, thus repressing inclusion of cryptic microexons. The prevalence of annotated RS-exons is high in deuterostomes, while the cryptic RS-exons are more prevalent in Drosophila, where EJC appears less capable of repressing RS. Notably, incomplete repression of RS also contributes to physiological alternative splicing of several human RS-exons. Finally, haploinsufficiency of the EJC factor Magoh in mice is associated with skipping of RS-exons in the brain, with relevance to the microcephaly phenotype and human diseases.
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Affiliation(s)
- Lorea Blazquez
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Warren Emmett
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; University College London Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Rupert Faraway
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Simon Bajew
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Andre Gohr
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Nejc Haberman
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christopher R Sibley
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Jernej Ule
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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23
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Booth KT, Kahrizi K, Najmabadi H, Azaiez H, Smith RJ. Old gene, new phenotype: splice-altering variants in CEACAM16 cause recessive non-syndromic hearing impairment. J Med Genet 2018; 55:555-560. [PMID: 29703829 PMCID: PMC6060001 DOI: 10.1136/jmedgenet-2018-105349] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/03/2018] [Accepted: 04/07/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Hearing loss is a genetically and phenotypically heterogeneous disorder. OBJECTIVES The purpose of this study was to determine the genetic cause underlying the postlingual progressive hearing loss in two Iranian families. METHODS We used OtoSCOPE, a next-generation sequencing platform targeting >150 genes causally linked to deafness, to screen two deaf probands. Data analysis was completed using a custom bioinformatics pipeline, and variants were functionally assessed using minigene splicing assays. RESULTS We identified two homozygous splice-altering variants (c.37G>T and c.662-1G>C) in the CEACAM16 gene, segregating with the deafness in each family. The minigene splicing results revealed the c.37G>T results in complete skipping of exon 2 and loss of the AUG start site. The c.662-1G>C activates a cryptic splice site inside exon 5 resulting in a shift in the mRNA reading frame. CONCLUSIONS These results suggest that loss-of-function mutations in CEACAM16 result in postlingual progressive hearing impairment and further support the role of CEACAM16 in auditory function.
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Affiliation(s)
- Kevin T Booth
- Molecular Otolaryngology Renal Research Laboratories, Department of Otolaryngology-Head Neck Surgery, University of Iowa, Iowa City, Iowa
- The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hela Azaiez
- Molecular Otolaryngology Renal Research Laboratories, Department of Otolaryngology-Head Neck Surgery, University of Iowa, Iowa City, Iowa
| | - Richard J Smith
- Molecular Otolaryngology Renal Research Laboratories, Department of Otolaryngology-Head Neck Surgery, University of Iowa, Iowa City, Iowa
- The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
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24
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Shiraishi Y, Kataoka K, Chiba K, Okada A, Kogure Y, Tanaka H, Ogawa S, Miyano S. A comprehensive characterization of cis-acting splicing-associated variants in human cancer. Genome Res 2018; 28:1111-1125. [PMID: 30012835 PMCID: PMC6071634 DOI: 10.1101/gr.231951.117] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
Abstract
Although many driver mutations are thought to promote carcinogenesis via abnormal splicing, the landscape of splicing-associated variants (SAVs) remains unknown due to the complexity of splicing abnormalities. Here, we developed a statistical framework to systematically identify SAVs disrupting or newly creating splice site motifs and applied it to matched whole-exome and transcriptome sequencing data from 8976 samples across 31 cancer types, generating a catalog of 14,438 SAVs. Such a large collection of SAVs enabled us to characterize their genomic features, underlying mutational processes, and influence on cancer driver genes. In fact, ∼50% of SAVs identified were those disrupting noncanonical splice sites (non-GT-AG dinucleotides), including the third and fifth intronic bases of donor sites, or newly creating splice sites. Mutation signature analysis revealed that tobacco smoking is more strongly associated with SAVs, whereas ultraviolet exposure has less impact. SAVs showed remarkable enrichment of cancer-related genes, and as many as 14.7% of samples harbored at least one SAVs affecting them, particularly in tumor suppressors. In addition to intron retention, whose association with tumor suppressor inactivation has been previously reported, exon skipping and alternative splice site usage caused by SAVs frequently affected tumor suppressors. Finally, we described high-resolution distributions of SAVs along the gene and their splicing outcomes in commonly disrupted genes, including TP53, PIK3R1, GATA3, and CDKN2A, which offers genetic clues for understanding their functional properties. Collectively, our findings delineate a comprehensive portrait of SAVs, novel insights into transcriptional de-regulation in cancer.
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Affiliation(s)
- Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Ai Okada
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasunori Kogure
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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25
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Leighton LJ, Bredy TW. Functional Interplay between Small Non-Coding RNAs and RNA Modification in the Brain. Noncoding RNA 2018; 4:E15. [PMID: 29880782 PMCID: PMC6027130 DOI: 10.3390/ncrna4020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/11/2022] Open
Abstract
Small non-coding RNAs are essential for transcription, translation and gene regulation in all cell types, but are particularly important in neurons, with known roles in neurodevelopment, neuroplasticity and neurological disease. Many small non-coding RNAs are directly involved in the post-transcriptional modification of other RNA species, while others are themselves substrates for modification, or are functionally modulated by modification of their target RNAs. In this review, we explore the known and potential functions of several distinct classes of small non-coding RNAs in the mammalian brain, focusing on the newly recognised interplay between the epitranscriptome and the activity of small RNAs. We discuss the potential for this relationship to influence the spatial and temporal dynamics of gene activation in the brain, and predict that further research in the field of epitranscriptomics will identify interactions between small RNAs and RNA modifications which are essential for higher order brain functions such as learning and memory.
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Affiliation(s)
- Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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26
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Sertznig H, Hillebrand F, Erkelenz S, Schaal H, Widera M. Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet. Virology 2018; 516:176-188. [PMID: 29407375 DOI: 10.1016/j.virol.2018.01.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 01/31/2023]
Abstract
Alternative splicing plays a key role in the HIV-1 life cycle and is essential to maintain an equilibrium of mRNAs that encode viral proteins and polyprotein-isoforms. In particular, since all early HIV-1 proteins are expressed from spliced intronless and late enzymatic and structural proteins from intron containing, i.e. splicing repressed viral mRNAs, cellular splicing factors and splicing regulatory proteins are crucial for the replication capacity. In this review, we will describe the complex network of cis-acting splicing regulatory elements (SREs), which are mainly localized in the neighbourhoods of all HIV-1 splice sites and warrant the proper ratio of individual transcript isoforms. Since SREs represent binding sites for trans-acting cellular splicing factors interacting with the cellular spliceosomal apparatus we will review the current knowledge of interactions between viral RNA and cellular proteins as well as their impact on viral replication. Finally, we will discuss potential therapeutic approaches targeting HIV-1 alternative splicing.
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Affiliation(s)
- Helene Sertznig
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Hillebrand
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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27
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Zhao Y, Dunker W, Yu YT, Karijolich J. The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events. Front Bioeng Biotechnol 2018; 6:8. [PMID: 29473035 PMCID: PMC5809436 DOI: 10.3389/fbioe.2018.00008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022] Open
Abstract
Pseudouridine is the most abundant internal RNA modification in stable noncoding RNAs (ncRNAs). It can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Pseudouridylation impacts both the biochemical and biophysical properties of RNAs and thus influences RNA-mediated cellular processes. The investigation of nuclear-ncRNA pseudouridylation has demonstrated that it is critical for the proper control of multiple stages of gene expression regulation. Here, we review how nuclear-ncRNA pseudouridylation contributes to transcriptional regulation and pre-mRNA splicing.
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Affiliation(s)
- Yang Zhao
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States.,Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
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28
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Brillen AL, Schöneweis K, Walotka L, Hartmann L, Müller L, Ptok J, Kaisers W, Poschmann G, Stühler K, Buratti E, Theiss S, Schaal H. Succession of splicing regulatory elements determines cryptic 5΄ss functionality. Nucleic Acids Res 2017; 45:4202-4216. [PMID: 28039323 PMCID: PMC5397162 DOI: 10.1093/nar/gkw1317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022] Open
Abstract
A critical step in exon definition is the recognition of a proper splice donor (5΄ss) by the 5’ end of U1 snRNA. In the selection of appropriate 5΄ss, cis-acting splicing regulatory elements (SREs) are indispensable. As a model for 5΄ss recognition, we investigated cryptic 5΄ss selection within the human fibrinogen Bβ-chain gene (FGB) exon 7, where we identified several exonic SREs that simultaneously acted on up- and downstream cryptic 5΄ss. In the FGB exon 7 model system, 5΄ss selection iteratively proceeded along an alternating sequence of U1 snRNA binding sites and interleaved SREs which in principle supported different 3’ exon ends. Like in a relay race, SREs either suppressed a potential 5΄ss and passed the splicing baton on or splicing actually occurred. From RNA-Seq data, we systematically selected 19 genes containing exons with silent U1 snRNA binding sites competing with nearby highly used 5΄ss. Extensive SRE analysis by different algorithms found authentic 5΄ss significantly more supported by SREs than silent U1 snRNA binding sites, indicating that our concept may permit generalization to a model for 5΄ss selection and 3’ exon end definition.
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Affiliation(s)
- Anna-Lena Brillen
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Katrin Schöneweis
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Lara Walotka
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Linda Hartmann
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.,Institute for Molecular Medicine, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, 34149 Trieste, Italy
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, 40225
| | - Heiner Schaal
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
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29
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RNA splicing in human disease and in the clinic. Clin Sci (Lond) 2017; 131:355-368. [PMID: 28202748 DOI: 10.1042/cs20160211] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 01/12/2023]
Abstract
Defects at the level of the pre-mRNA splicing process represent a major cause of human disease. Approximately 15-50% of all human disease mutations have been shown to alter functioning of basic and auxiliary splicing elements. These elements are required to ensure proper processing of pre-mRNA splicing molecules, with their disruption leading to misprocessing of the pre-mRNA molecule and disease. The splicing process is a complex process, with much still to be uncovered before we are able to accurately predict whether a reported genomic sequence variant (GV) represents a splicing-associated disease mutation or a harmless polymorphism. Furthermore, even when a mutation is correctly identified as affecting the splicing process, there still remains the difficulty of providing an exact evaluation of the potential impact on disease onset, severity and duration. In this review, we provide a brief overview of splicing diagnostic methodologies, from in silico bioinformatics approaches to wet lab in vitro and in vivo systems to evaluate splicing efficiencies. In particular, we provide an overview of how the latest developments in high-throughput sequencing can be applied to the clinic, and are already changing clinical approaches.
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30
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Analysis of Competing HIV-1 Splice Donor Sites Uncovers a Tight Cluster of Splicing Regulatory Elements within Exon 2/2b. J Virol 2017; 91:JVI.00389-17. [PMID: 28446664 DOI: 10.1128/jvi.00389-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/18/2017] [Indexed: 12/24/2022] Open
Abstract
The HIV-1 accessory protein Vif is essential for viral replication by counteracting the host restriction factor APOBEC3G (A3G), and balanced levels of both proteins are required for efficient viral replication. Noncoding exons 2/2b contain the Vif start codon between their alternatively used splice donors 2 and 2b (D2 and D2b). For vif mRNA, intron 1 must be removed while intron 2 must be retained. Thus, splice acceptor 1 (A1) must be activated by U1 snRNP binding to either D2 or D2b, while splicing at D2 or D2b must be prevented. Here, we unravel the complex interactions between previously known and novel components of the splicing regulatory network regulating HIV-1 exon 2/2b inclusion in viral mRNAs. In particular, using RNA pulldown experiments and mass spectrometry analysis, we found members of the heterogeneous nuclear ribonucleoparticle (hnRNP) A/B family binding to a novel splicing regulatory element (SRE), the exonic splicing silencer ESS2b, and the splicing regulatory proteins Tra2/SRSF10 binding to the nearby exonic splicing enhancer ESE2b. Using a minigene reporter, we performed bioinformatics HEXplorer-guided mutational analysis to narrow down SRE motifs affecting splice site selection between D2 and D2b. Eventually, the impacts of these SREs on the viral splicing pattern and protein expression were exhaustively analyzed in viral particle production and replication experiments. Masking of these protein binding sites by use of locked nucleic acids (LNAs) impaired Vif expression and viral replication.IMPORTANCE Based on our results, we propose a model in which a dense network of SREs regulates vif mRNA and protein expression, crucial to maintain viral replication within host cells with varying A3G levels and at different stages of infection. This regulation is maintained by several serine/arginine-rich splicing factors (SRSF) and hnRNPs binding to those elements. Targeting this cluster of SREs with LNAs may lead to the development of novel effective therapeutic strategies.
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31
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Zhang X, Wu Y, Cai F, Liu S, Bromley-Brits K, Xia K, Song W. A Novel Alzheimer-Associated SNP in Tmp21 Increases Amyloidogenesis. Mol Neurobiol 2017; 55:1862-1870. [PMID: 28233271 DOI: 10.1007/s12035-017-0459-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
Abstract
Recent studies suggest that TMP21 is a selective modulator of γ-secretase and its dysregulation affects APP processing, leading to increased Aβ generation. However, the genetic association between Tmp21 and Alzheimer's disease (AD) remains elusive. In this study, we identified that a novel single-nucleotide polymorphism (SNP) rs12435391 (IVS4-28T>C) in intron 4 of Tmp21 was genetically associated with AD. We found that allele C of the SNP rs12435391 did not affect splicing site recognition, but it significantly increased TMP21 gene expression. The stability of Tmp21 pre-mRNA and the transcription of Tmp21 were not affected by allele C of the SNP rs12435391. However, allele C of the SNP rs12435391 significantly increased the splicing efficiency of Tmp21 pre-mRNA, leading to the elevation of mature mRNA. Furthermore, allele C of the SNP rs12435391 significantly reduced C83 level and increased Aβ generation. Taken together, our study suggests that TMP21 is genetically associated with Alzheimer's disease, with the novel Tmp21 SNP as a risk factor for Alzheimer's pathogenesis.
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Affiliation(s)
- Xiaojie Zhang
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Yili Wu
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Fang Cai
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Shengchun Liu
- Department of Surgery, The First Affiliated Hospital, Chongqing Medical University, 1 Friendship Road, Yuzhong District, Chongqing, 410006, China
| | - Kelley Bromley-Brits
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Kun Xia
- The State Key Lab of Medical Genetics of China, School of Life Sciences, Central South University, Changsha, 410000, China.
| | - Weihong Song
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
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32
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Hillebrand F, Peter JO, Brillen AL, Otte M, Schaal H, Erkelenz S. Differential hnRNP D isoform incorporation may confer plasticity to the ESSV-mediated repressive state across HIV-1 exon 3. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:205-217. [PMID: 27919832 DOI: 10.1016/j.bbagrm.2016.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/22/2016] [Accepted: 12/01/2016] [Indexed: 11/27/2022]
Abstract
Even though splicing repression by hnRNP complexes bound to exonic sequences is well-documented, the responsible effector domains of hnRNP proteins have been described for only a select number of hnRNP constituents. Thus, there is only limited information available for possible varying silencer activities amongst different hnRNP proteins and composition changes within possible hnRNP complex assemblies. In this study, we identified the glycine-rich domain (GRD) of hnRNP proteins as a unifying feature in splice site repression. We also show that all four hnRNP D isoforms can act as genuine splicing repressors when bound to exonic positions. The presence of an extended GRD, however, seemed to potentiate the hnRNP D silencer activity of isoforms p42 and p45. Moreover, we demonstrate that hnRNP D proteins associate with the HIV-1 ESSV silencer complex, probably through direct recognition of "UUAG" sequences overlapping with the previously described "UAGG" motifs bound by hnRNP A1. Consequently, this spatial proximity seems to cause mutual interference between hnRNP A1 and hnRNP D. This interplay between hnRNP A1 and D facilitates a dynamic regulation of the repressive state of HIV-1 exon 3 which manifests as fluctuating relative levels of spliced vpr- and unspliced gag/pol-mRNAs.
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Affiliation(s)
- Frank Hillebrand
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Jan Otto Peter
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marianne Otte
- Institute of Evolutionary Genetics, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute of Virology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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33
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Mueller N, Klaver B, Berkhout B, Das AT. Human immunodeficiency virus type 1 splicing at the major splice donor site is controlled by highly conserved RNA sequence and structural elements. J Gen Virol 2016; 96:3389-3395. [PMID: 26385834 DOI: 10.1099/jgv.0.000288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) splicing has to be strictly controlled to ensure the balanced production of the unspliced and all differently spliced viral RNAs. Splicing at the major 59 splice site (59ss) that is used for the synthesis of all spliced RNAs is modulated by the local RNA structure and binding of regulatory SR proteins. Here, we demonstrate that the suboptimal sequence complementarity between this 59ss and U1 small nuclear RNA (snRNA) also contributes to prevent excessive splicing. Analysis of a large set of HIV-1 sequences revealed that all three regulatory features of the 59ss region (RNA structure, SR protein binding and sequence complementarity with U1 snRNA) are highly conserved amongst virus isolates, which supports their importance. Combined mutations that destabilize the local RNA structure, remove binding sites for inhibitory SR proteins and optimize the U1 snRNA complementarity resulted in almost complete splicing and accordingly reduced virus replication.
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Affiliation(s)
- Nancy Mueller
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Exon-skipping and mRNA decay in human liver tissue: molecular consequences of pathogenic bile salt export pump mutations. Sci Rep 2016; 6:24827. [PMID: 27114171 PMCID: PMC4845019 DOI: 10.1038/srep24827] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/05/2016] [Indexed: 12/12/2022] Open
Abstract
The bile salt export pump BSEP mediates bile formation. Over 150 BSEP mutations are associated with progressive familial intrahepatic cholestasis type 2 (PFIC-2), with few characterised specifically. We examined liver tissues from two PFIC-2 patients compound heterozygous for the splice-site mutation c.150 + 3A > C and either c.2783_2787dup5 resulting in a frameshift with a premature termination codon (child 1) or p.R832C (child 2). Splicing was analysed with a minigene system and mRNA sequencing from patients’ livers. Protein expression was shown by immunofluorescence. Using the minigene, c.150 + 3A > C causes complete skipping of exon 3. In liver tissue of child 1, c.2783_2787dup5 was found on DNA but not on mRNA level, implying nonsense-mediated mRNA decay (NMD) when c.2783_2787dup5 is present. Still, BSEP protein as well as mRNA with and without exon 3 were detectable and can be assigned to the c.150 + 3A > C allele. Correctly spliced transcripts despite c.150 + 3A > C were also confirmed in liver of child 2. In conclusion, we provide evidence (1) for effective NMD due to a BSEP frameshift mutation and (2) partial exon-skipping due to c.150 + 3A > C. The results illustrate that the extent of exon-skipping depends on the genomic and cellular context and that regulation of splicing may have therapeutic potential.
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Functional Dissection of an Alternatively Spliced Herpesvirus Gene by Splice Site Mutagenesis. J Virol 2016; 90:4626-4636. [PMID: 26912612 DOI: 10.1128/jvi.02987-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Herpesviruses have large and complex DNA genomes. The largest among the herpesviruses, those of the cytomegaloviruses, include over 170 genes. Although most herpesvirus gene products are expressed from unspliced transcripts, a substantial number of viral transcripts are spliced. Some viral transcripts are subject to alternative splicing, which leads to the expression of several proteins from a single gene. Functional analysis of individual proteins derived from an alternatively spliced gene is difficult, as deletion and nonsense mutagenesis, both common methods used in the generation of viral gene knockout mutants, affect several or all gene products at the same time. Here, we show that individual gene products of an alternatively spliced herpesvirus gene can be inactivated selectively by mutagenesis of the splice donor or acceptor site and by intron deletion or substitution mutagenesis. We used this strategy to dissect the essential M112/113 gene of murine cytomegalovirus (MCMV), which encodes the MCMV Early 1 (E1) proteins. The expression of each of the four E1 protein isoforms was inactivated individually, and the requirement for each isoform in MCMV replication was analyzed in fibroblasts, endothelial cells, and macrophages. We show that the E1 p87 isoform, but not the p33, p36, and p38 isoforms, is essential for viral replication in cell culture. Moreover, the presence of one of the two medium-size isoforms (p36 or p38) and the presence of intron 1, but not its specific sequence, are required for viral replication. This study demonstrates the usefulness of splice site mutagenesis for the functional analysis of alternatively spliced herpesvirus genes. IMPORTANCE Herpesviruses include up to 170 genes in their DNA genomes. The functions of most viral gene products remain poorly defined. The construction of viral gene knockout mutants has thus been an important tool for functional analysis of viral proteins. However, this strategy is of limited use when viral gene transcripts are alternatively spliced, leading to the expression of several proteins from a single gene. In this study, we showed, as a proof of principle, that each protein product of an alternatively spliced gene can be eliminated individually by splice site mutagenesis. Mutant viruses lacking individual protein products displayed different phenotypes, demonstrating that the products of alternatively spliced genes have nonredundant functions.
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Goering W, Schmitt K, Dostert M, Schaal H, Deenen R, Mayer J, Schulz WA. Human endogenous retrovirus HERV-K(HML-2) activity in prostate cancer is dominated by a few loci. Prostate 2015; 75:1958-71. [PMID: 26384005 DOI: 10.1002/pros.23095] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/02/2015] [Indexed: 11/11/2022]
Abstract
BACKGROUND Increased expression of human endogenous retroviruses, especially HERV-K(HML-2) proviruses, has recently been associated with prostate carcinoma progression. In particular, a HML-2 locus in chromosome 22q11.23 (H22q) is upregulated in many cases. We therefore aimed at delineating the extent and repertoire of HML-2 transcription in prostate cancer tissues and cell lines and to define the transcription pattern and biological effects of H22q. METHODS Sanger and high throughput amplicon sequencing was used to define the repertoire of expressed HML-2 in a selected set of samples. qRT-PCR was used to quantify expression of selected proviruses in an extended set of prostate cancer tissues. Transcription factor binding sites (TFBS) were compared bioinformatically using the Transfac database. Expression of H22q was further characterized by siRNA-mediated knockdown, 5' RACE mapping of transcriptional start sites (TSS) and identification of splice sites. Functional effects of H22q knockdown were investigated by viability and apoptosis assays. RESULTS In addition to H22q, a limited number of other proviruses were found expressed by sequencing. Of these, provirus ERVK-5 and to a lesser degree ERVK-15 were frequently upregulated in prostate cancer. In contrast, expression of ERVK-24, predominant in germ cell tumors, was not detectable in prostatic tissues. While HML-2 LTRs contain binding sites for the androgen receptor and cofactors, no consistent differences in transcription factor binding sites were found between expressed and non-expressed proviruses. The H22q locus contains two 5'-LTRs of which the upstream LTR is predominantly used in prostatic cells, with an imprecise TSS. Splicing of H22q transcripts is complex, generating, among others, a transcript with an Np9-like ORF. Knockdown of H22q did not significantly affect proliferation or apoptosis of prostate cancer cells. CONCLUSIONS Our findings further underline that HML-2 expression is commonly highly tissue-specific. In prostate cancer, a limited number of loci become activated, especially H22q and ERVK-5. As expressed and non-expressed proviruses do not differ significantly in TFBS, tissue- and tumor-specific expression may be governed primarily by chromatin context. Overexpression of HML-2 H22q is more likely consequence than cause of prostate cancer progression.
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Affiliation(s)
- Wolfgang Goering
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Katja Schmitt
- Institute of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany
| | - Melanie Dostert
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - René Deenen
- GTL, Biomedical Research Center, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens Mayer
- Institute of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Jung H, Lee D, Lee J, Park D, Kim YJ, Park WY, Hong D, Park PJ, Lee E. Intron retention is a widespread mechanism of tumor-suppressor inactivation. Nat Genet 2015; 47:1242-8. [PMID: 26437032 DOI: 10.1038/ng.3414] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 09/08/2015] [Indexed: 12/14/2022]
Abstract
A substantial fraction of disease-causing mutations are pathogenic through aberrant splicing. Although genome profiling studies have identified somatic single-nucleotide variants (SNVs) in cancer, the extent to which these variants trigger abnormal splicing has not been systematically examined. Here we analyzed RNA sequencing and exome data from 1,812 patients with cancer and identified ∼900 somatic exonic SNVs that disrupt splicing. At least 163 SNVs, including 31 synonymous ones, were shown to cause intron retention or exon skipping in an allele-specific manner, with ∼70% of the SNVs occurring on the last base of exons. Notably, SNVs causing intron retention were enriched in tumor suppressors, and 97% of these SNVs generated a premature termination codon, leading to loss of function through nonsense-mediated decay or truncated protein. We also characterized the genomic features predictive of such splicing defects. Overall, this work demonstrates that intron retention is a common mechanism of tumor-suppressor inactivation.
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Affiliation(s)
- Hyunchul Jung
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Donghoon Lee
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Jongkeun Lee
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Cancer Immunology Branch, Division of Cancer Biology, National Cancer Center, Gyeonggi-do, South Korea
| | - Donghyun Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology, Samsung Electronics Company, Ltd., Seoul, South Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology, Samsung Electronics Company, Ltd., Seoul, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Dongwan Hong
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Cancer Immunology Branch, Division of Cancer Biology, National Cancer Center, Gyeonggi-do, South Korea
| | - Peter J Park
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Eunjung Lee
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
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ROORYCK CAROLINE, KYNDT FLORENCE, BOZON DOMINIQUE, ROUX-BUISSON NATHALIE, SACHER FREDERIC, PROBST VINCENT, THAMBO JEANBENOIT. New Family With Catecholaminergic Polymorphic Ventricular Tachycardia Linked to the Triadin Gene. J Cardiovasc Electrophysiol 2015. [DOI: 10.1111/jce.12763] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- CAROLINE ROORYCK
- Univ. Bordeaux; Maladies Rares: Génétique et Métabolisme (MRGM); Bordeaux France
- LIRYC, L'Institut de rythmologie et modélisation cardiaque; Université de Bordeaux INSERM; France
- Service des cardiopathies congénitales; Hôpital Cardiologique du Haut-Lévêque; CHU Bordeaux; Bordeaux France
| | - FLORENCE KYNDT
- Institut du thorax, Clinique Cardiologique Inserm; CHU de Nantes; France
| | - DOMINIQUE BOZON
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est; Hospices Civils de Lyon; France
| | - NATHALIE ROUX-BUISSON
- INSERM U836, Grenoble Institut des Neurosciences; Equipe Muscle et Pathologies; Grenoble France
| | - FREDERIC SACHER
- LIRYC, L'Institut de rythmologie et modélisation cardiaque; Université de Bordeaux INSERM; France
| | - VINCENT PROBST
- Institut du thorax, Clinique Cardiologique Inserm; CHU de Nantes; France
| | - JEAN-BENOIT THAMBO
- LIRYC, L'Institut de rythmologie et modélisation cardiaque; Université de Bordeaux INSERM; France
- Service des cardiopathies congénitales; Hôpital Cardiologique du Haut-Lévêque; CHU Bordeaux; Bordeaux France
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Millat G, Lafont E, Nony S, Rouvet I, Bozon D. Functional Characterization of Putative Novel Splicing Mutations in the Cardiomyopathy-Causing Genes. DNA Cell Biol 2015; 34:489-96. [DOI: 10.1089/dna.2015.2842] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est–Hospices Civils de Lyon, Bron, France
- EA4612, Université Claude Bernard Lyon 1, Lyon, France
| | - Estèle Lafont
- EA4612, Université Claude Bernard Lyon 1, Lyon, France
| | - Séverine Nony
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est–Hospices Civils de Lyon, Bron, France
| | - Isabelle Rouvet
- Centre de Biotechnologie Cellulaire, CBPE–Hospices Civils de Lyon, Bron, France
| | - Dominique Bozon
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est–Hospices Civils de Lyon, Bron, France
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Mueller N, Berkhout B, Das AT. HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5' splice site. J Gen Virol 2015; 96:1906-17. [PMID: 25779589 DOI: 10.1099/vir.0.000122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The 5' leader region of the human immunodeficiency virus 1 (HIV-1) RNA genome contains the major 5' splice site (ss) that is used in the production of the many spliced viral RNAs. This splice-donor (SD) region can fold into a stable stem-loop structure and the thermodynamic stability of this RNA hairpin influences splicing efficiency. In addition, splicing may be modulated by binding of splicing regulatory (SR) proteins, in particular SF2/ASF (SRSF1), SC35 (SRSF2), SRp40 (SRSF5) and SRp55 (SRSF6), to sequence elements in the SD region. The role of RNA structure and SR protein binding in splicing control was previously studied by functional analysis of mutant SD sequences. The interpretation of these studies was complicated by the fact that most mutations simultaneously affect both structure and sequence elements. We therefore tried to disentangle the contribution of these two variables by designing more precise SD region mutants with a single effect on either the sequence or the structure. The current analysis indicates that HIV-1 splicing at the major 5'ss is modulated by both the stability of the local RNA structure and the binding of splicing regulatory proteins.
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Affiliation(s)
- Nancy Mueller
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
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41
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Kaisers W, Schaal H, Schwender H. rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples. ACTA ACUST UNITED AC 2015; 31:1663-4. [PMID: 25563331 DOI: 10.1093/bioinformatics/btu846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/19/2014] [Indexed: 11/14/2022]
Abstract
The open source environment R isf the most widely used software to statistically explore biological data sets including sequence alignments. BAM is the de facto standard file format for sequence alignment. With rbamtools, we provide now a full spectrum of accessibility to BAM for R users such as reading, writing, extraction of subsets and plotting of alignment depth where the script syntax closely follows the SAM/BAM format. Additionally, rbamtools enables fast accumulative tabulation of splicing events over multiple BAM files.
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Affiliation(s)
- Wolfgang Kaisers
- Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Schwender
- Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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42
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Mueller N, van Bel N, Berkhout B, Das AT. HIV-1 splicing at the major splice donor site is restricted by RNA structure. Virology 2014; 468-470:609-620. [PMID: 25305540 DOI: 10.1016/j.virol.2014.09.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/11/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Abstract
The 5' leader region of the HIV-1 RNA contains the major 5' splice site (ss) that is used in the production of all spliced viral RNAs. This splice-donor (SD) region can fold a stem-loop structure. We demonstrate that whereas stabilization of this SD hairpin reduces splicing efficiency, destabilization increases splicing. Both stabilization and destabilization reduce viral fitness. These results demonstrate that the stability of the SD hairpin can modulate the level of splicing, most likely by controlling the accessibility of the 5'ss for the splicing machinery. The natural stability of the SD hairpin restricts splicing and this stability seems to be fine-tuned to reach the optimal balance between unspliced and spliced RNAs for efficient virus replication. The 5'ss region of different HIV-1 isolates and the related SIVmac239 can fold a similar structure. This evolutionary conservation supports the importance of this structure in viral replication.
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Affiliation(s)
- Nancy Mueller
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Nikki van Bel
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
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Erkelenz S, Theiss S, Otte M, Widera M, Peter JO, Schaal H. Genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Nucleic Acids Res 2014; 42:10681-97. [PMID: 25147205 PMCID: PMC4176321 DOI: 10.1093/nar/gku736] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Effective splice site selection is critically controlled by flanking splicing regulatory elements (SREs) that can enhance or repress splice site use. Although several computational algorithms currently identify a multitude of potential SRE motifs, their predictive power with respect to mutation effects is limited. Following a RESCUE-type approach, we defined a hexamer-based ‘HEXplorer score’ as average Z-score of all six hexamers overlapping with a given nucleotide in an arbitrary genomic sequence. Plotted along genomic regions, HEXplorer score profiles varied slowly in the vicinity of splice sites. They reflected the respective splice enhancing and silencing properties of splice site neighborhoods beyond the identification of single dedicated SRE motifs. In particular, HEXplorer score differences between mutant and reference sequences faithfully represented exonic mutation effects on splice site usage. Using the HIV-1 pre-mRNA as a model system highly dependent on SREs, we found an excellent correlation in 29 mutations between splicing activity and HEXplorer score. We successfully predicted and confirmed five novel SREs and optimized mutations inactivating a known silencer. The HEXplorer score allowed landscaping of splicing regulatory regions, provided a quantitative measure of mutation effects on splice enhancing and silencing properties and permitted calculation of the mutationally most effective nucleotide.
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Affiliation(s)
- Steffen Erkelenz
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Marianne Otte
- Institute of Evolutionary Genetics, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Marek Widera
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Jan Otto Peter
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Heiner Schaal
- Institute for Virology, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
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Molecular events accompanying rous sarcoma virus rescue from rodent cells and the role of viral gene complementation. J Virol 2014; 88:3505-15. [PMID: 24403579 DOI: 10.1128/jvi.02761-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Transformation of rodent cells with avian Rous sarcoma virus (RSV) opened new ways to studying virus integration and expression in nonpermissive cells. We were interested in (i) the molecular changes accompanying fusion of RSV-transformed mammalian cells with avian cells leading to virus rescue and (ii) enhancement of this process by retroviral gene products. The RSV-transformed hamster RSCh cell line was characterized as producing only a marginal amount of env mRNA, no envelope glycoprotein, and a small amount of unprocessed Gag protein. Egress of viral unspliced genomic RNA from the nucleus was hampered, and its stability decreased. Cell fusion of the chicken DF-1 cell line with RSCh cells led to production of env mRNA, envelope glycoprotein, and processed Gag and virus-like particle formation. Proteosynthesis inhibition in DF-1 cells suppressed steps leading to virus rescue. Furthermore, new aberrantly spliced env mRNA species were found in the RSCh cells. Finally, we demonstrated that virus rescue efficiency can be significantly increased by complementation with the env gene and the highly expressed gag gene and can be increased the most by a helper virus infection. In summary, Env and Gag synthesis is increased after RSV-transformed hamster cell fusion with chicken fibroblasts, and both proteins provided in trans enhance RSV rescue. We conclude that the chicken fibroblast yields some factor(s) needed for RSV replication, particularly Env and Gag synthesis, in nonpermissive rodent cells. IMPORTANCE One of the important issues in retrovirus heterotransmission is related to cellular factors that prevent virus replication. Rous sarcoma virus (RSV), a member of the avian sarcoma and leukosis family of retroviruses, is able to infect and transform mammalian cells; however, such transformed cells do not produce infectious virus particles. Using the well-defined model of RSV-transformed rodent cells, we established that the lack of virus replication is due to the absence of chicken factor(s), which can be supplemented by cell fusion. Cell fusion with permissive chicken cells led to an increase in RNA splicing and nuclear export of specific viral mRNAs, as well as synthesis of respective viral proteins and production of virus-like particles. RSV rescue by cell fusion can be potentiated by in trans expression of viral genes in chicken cells. We conclude that rodent cells lack some chicken factor(s) required for proper viral RNA processing and viral protein synthesis.
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In silico tools for splicing defect prediction: a survey from the viewpoint of end users. Genet Med 2013; 16:497-503. [PMID: 24263461 PMCID: PMC4029872 DOI: 10.1038/gim.2013.176] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/09/2013] [Indexed: 12/31/2022] Open
Abstract
RNA splicing is the process during which introns are excised and exons are spliced. The precise recognition of splicing signals is critical to this process and mutations affecting splicing comprise a considerable proportion of genetic disease etiology. Analysis of RNA samples from the patient is the most straightforward and reliable method to detect splicing defects. However, currently the technical limitation prohibits its use in routine clinical practice. In silico tools that predict potential consequences of splicing mutations may be useful in daily diagnostic activities. In this review, we provide medical geneticists with some basic insights into some of the most popular in silico tools for splicing defect prediction, from the viewpoint of end-users. Bioinformaticians in relevant areas who are working on huge datasets may also benefit from this review. Specifically, we focus on those tools whose primary goal is to predict the impact of mutations within the 5′ and 3′ splicing consensus regions: the algorithms used by different tools as well as their major advantages and disadvantages are briefly introduced; the formats of their input and output are summarized; and the interpretation, evaluation, and prospection are also discussed.
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Bezzi M, Teo SX, Muller J, Mok WC, Sahu SK, Vardy LA, Bonday ZQ, Guccione E. Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery. Genes Dev 2013; 27:1903-16. [PMID: 24013503 PMCID: PMC3778243 DOI: 10.1101/gad.219899.113] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/26/2013] [Indexed: 01/08/2023]
Abstract
The tight control of gene expression at the level of both transcription and post-transcriptional RNA processing is essential for mammalian development. We here investigate the role of protein arginine methyltransferase 5 (PRMT5), a putative splicing regulator and transcriptional cofactor, in mammalian development. We demonstrate that selective deletion of PRMT5 in neural stem/progenitor cells (NPCs) leads to postnatal death in mice. At the molecular level, the absence of PRMT5 results in reduced methylation of Sm proteins, aberrant constitutive splicing, and the alternative splicing of specific mRNAs with weak 5' donor sites. Intriguingly, the products of these mRNAs are, among others, several proteins regulating cell cycle progression. We identify Mdm4 as one of these key mRNAs that senses the defects in the spliceosomal machinery and transduces the signal to activate the p53 response, providing a mechanistic explanation of the phenotype observed in vivo. Our data demonstrate that PRMT5 is a master regulator of splicing in mammals and uncover a new role for the Mdm4 pre-mRNA, which could be exploited for anti-cancer therapy.
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Affiliation(s)
- Marco Bezzi
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
| | - Shun Xie Teo
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Julius Muller
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Wei Chuen Mok
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Sanjeeb Kumar Sahu
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Leah A. Vardy
- Institute of Medical Biology (IMB), A*STAR, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zahid Q. Bonday
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Ernesto Guccione
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
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Roca X, Krainer AR, Eperon IC. Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev 2013; 27:129-44. [PMID: 23348838 DOI: 10.1101/gad.209759.112] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Splice site selection is fundamental to pre-mRNA splicing and the expansion of genomic coding potential. 5' Splice sites (5'ss) are the critical elements at the 5' end of introns and are extremely diverse, as thousands of different sequences act as bona fide 5'ss in the human transcriptome. Most 5'ss are recognized by base-pairing with the 5' end of the U1 small nuclear RNA (snRNA). Here we review the history of research on 5'ss selection, highlighting the difficulties of establishing how base-pairing strength determines splicing outcomes. We also discuss recent work demonstrating that U1 snRNA:5'ss helices can accommodate noncanonical registers such as bulged duplexes. In addition, we describe the mechanisms by which other snRNAs, regulatory proteins, splicing enhancers, and the relative positions of alternative 5'ss contribute to selection. Moreover, we discuss mechanisms by which the recognition of numerous candidate 5'ss might lead to selection of a single 5'ss and propose that protein complexes propagate along the exon, thereby changing its physical behavior so as to affect 5'ss selection.
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Affiliation(s)
- Xavier Roca
- School of Biological Sciences, Division of Molecular Genetics and Cell Biology, Nanyang Technological University, Singapore.
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48
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An intronic G run within HIV-1 intron 2 is critical for splicing regulation of vif mRNA. J Virol 2012; 87:2707-20. [PMID: 23255806 DOI: 10.1128/jvi.02755-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Within target T lymphocytes, human immunodeficiency virus type I (HIV-1) encounters the retroviral restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), which is counteracted by the HIV-1 accessory protein Vif. Vif is encoded by intron-containing viral RNAs that are generated by splicing at 3' splice site (3'ss) A1 but lack splicing at 5'ss D2, which results in the retention of a large downstream intron. Hence, the extents of activation of 3'ss A1 and repression of D2, respectively, determine the levels of vif mRNA and thus the ability to evade A3G-mediated antiviral effects. The use of 3'ss A1 can be enhanced or repressed by splicing regulatory elements that control the recognition of downstream 5'ss D2. Here we show that an intronic G run (G(I2)-1) represses the use of a second 5'ss, termed D2b, that is embedded within intron 2 and, as determined by RNA deep-sequencing analysis, is normally inefficiently used. Mutations of G(I2)-1 and activation of D2b led to the generation of transcripts coding for Gp41 and Rev protein isoforms but primarily led to considerable upregulation of vif mRNA expression. We further demonstrate, however, that higher levels of Vif protein are actually detrimental to viral replication in A3G-expressing T cell lines but not in A3G-deficient cells. These observations suggest that an appropriate ratio of Vif-to-A3G protein levels is required for optimal virus replication and that part of Vif level regulation is effected by the novel G run identified here.
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Asang C, Erkelenz S, Schaal H. The HIV-1 major splice donor D1 is activated by splicing enhancer elements within the leader region and the p17-inhibitory sequence. Virology 2012; 432:133-45. [PMID: 22749061 DOI: 10.1016/j.virol.2012.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 04/05/2012] [Accepted: 06/07/2012] [Indexed: 11/25/2022]
Abstract
Usage of the HIV-1 major 5' splice site D1 is a prerequisite for generation of all spliced viral mRNAs encoding essential regulatory and structural proteins. We set out to determine whether flanking sequences ensure D1-activation. We found that an exonic splicing enhancer function is exerted by the region upstream of D1, which is crucially required for its activation. Additionally, we identified an intronic splicing regulatory element within the p17-instability element of the Gag-ORF enhancing D1-activation. Furthermore, our experimental data demonstrated that sequence motifs displaying high similarity to consensus binding sites for SR protein SC35 (SRSF2) overlapping with D1 fine-tune its activation. Our results reveal that D1-activation is safe-guarded by the interplay of upstream and downstream located splicing enhancer elements ensuring usage of D1 even if its strength is decreased upon mutation. The identification of sequence elements activating D1-usage sheds further light on the balanced expression of alternatively spliced HIV-1 mRNAs.
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Affiliation(s)
- Corinna Asang
- Institut für Virologie, Universitätsklinikum Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany.
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50
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Abstract
The predominate form of DNA diagnostics remains nucleic acid sequencing in the research and clinical setting. While DNA sequencing allows a mutation to be correctly identified, only RNA sequencing can confirm the effect of that mutation on the resulting mRNA transcript. In the absence of RNA sequencing, predictions are reliant on either experimental studies or bioinformatic modelling. While each of these approaches provides insights into cellular splicing choices, of which exon skipping is but one, both possess inherent weaknesses. A method which is able to integrate and appropriately weigh the various factors influencing cellular splicing choices into an accurate, comprehensive modelling tool still remains elusive.In this overview chapter, the current methods utilised for DNA diagnostics and the impact of the emerging next-generation sequencing techniques are considered. We explore why RNA remains a problematic medium with which to work. To understand how exon skipping can be predicted from a DNA sequence, the key cis-acting elements influencing splicing are reviewed. Finally, the current methods used to predict exon skipping including RNA-based studies, experimental studies, and bioinformatic modelling approaches are outlined.
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