1
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Radrizzani S, Kudla G, Izsvák Z, Hurst LD. Selection on synonymous sites: the unwanted transcript hypothesis. Nat Rev Genet 2024; 25:431-448. [PMID: 38297070 DOI: 10.1038/s41576-023-00686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 02/02/2024]
Abstract
Although translational selection to favour codons that match the most abundant tRNAs is not readily observed in humans, there is nonetheless selection in humans on synonymous mutations. We hypothesize that much of this synonymous site selection can be explained in terms of protection against unwanted RNAs - spurious transcripts, mis-spliced forms or RNAs derived from transposable elements or viruses. We propose not only that selection on synonymous sites functions to reduce the rate of creation of unwanted transcripts (for example, through selection on exonic splice enhancers and cryptic splice sites) but also that high-GC content (but low-CpG content), together with intron presence and position, is both particular to functional native mRNAs and used to recognize transcripts as native. In support of this hypothesis, transcription, nuclear export, liquid phase condensation and RNA degradation have all recently been shown to promote GC-rich transcripts and suppress AU/CpG-rich ones. With such 'traps' being set against AU/CpG-rich transcripts, the codon usage of native genes has, in turn, evolved to avoid such suppression. That parallel filters against AU/CpG-rich transcripts also affect the endosomal import of RNAs further supports the unwanted transcript hypothesis of synonymous site selection and explains the similar design rules that have enabled the successful use of transgenes and RNA vaccines.
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Affiliation(s)
- Sofia Radrizzani
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK.
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2
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The Power of Clinical Diagnosis for Deciphering Complex Genetic Mechanisms in Rare Diseases. Genes (Basel) 2023; 14:genes14010196. [PMID: 36672937 PMCID: PMC9858967 DOI: 10.3390/genes14010196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Complex genetic disease mechanisms, such as structural or non-coding variants, currently pose a substantial difficulty in frontline diagnostic tests. They thus may account for most unsolved rare disease patients regardless of the clinical phenotype. However, the clinical diagnosis can narrow the genetic focus to just a couple of genes for patients with well-established syndromes defined by prominent physical and/or unique biochemical phenotypes, allowing deeper analyses to consider complex genetic origin. Then, clinical-diagnosis-driven genome sequencing strategies may expedite the development of testing and analytical methods to account for complex disease mechanisms as well as to advance functional assays for the confirmation of complex variants, clinical management, and the development of new therapies.
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3
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Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept. NPJ Genom Med 2022; 7:74. [PMID: 36577754 PMCID: PMC9797484 DOI: 10.1038/s41525-022-00347-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) is emerging in genetic diagnoses as it provides functional support for the interpretation of variants of uncertain significance. However, the use of amniotic fluid (AF) cells for RNA-seq has not yet been explored. Here, we examined the expression of clinically relevant genes in AF cells (n = 48) compared with whole blood and fibroblasts. The number of well-expressed genes in AF cells was comparable to that in fibroblasts and much higher than that in blood across different disease categories. We found AF cells RNA-seq feasible and beneficial in prenatal diagnosis (n = 4) as transcriptomic data elucidated the molecular consequence leading to the pathogenicity upgrade of variants in CHD7 and COL1A2 and revising the in silico prediction of a variant in MYRF. AF cells RNA-seq could become a reasonable choice for postnatal patients with advantages over fibroblasts and blood as it prevents invasive procedures.
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4
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Jones AN, Graß C, Meininger I, Geerlof A, Klostermann M, Zarnack K, Krappmann D, Sattler M. Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1. SCIENCE ADVANCES 2022; 8:eabp9153. [PMID: 35921415 PMCID: PMC9348792 DOI: 10.1126/sciadv.abp9153] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Alternative splicing plays key roles for cell type-specific regulation of protein function. It is controlled by cis-regulatory RNA elements that are recognized by RNA binding proteins (RBPs). The MALT1 paracaspase is a key factor of signaling pathways that mediate innate and adaptive immune responses. Alternative splicing of MALT1 is critical for controlling optimal T cell activation. We demonstrate that MALT1 splicing depends on RNA structural elements that sequester the splice sites of the alternatively spliced exon7. The RBPs hnRNP U and hnRNP L bind competitively to stem-loop RNA structures that involve the 5' and 3' splice sites flanking exon7. While hnRNP U stabilizes RNA stem-loop conformations that maintain exon7 skipping, hnRNP L disrupts these RNA elements to facilitate recruitment of the essential splicing factor U2AF2, thereby promoting exon7 inclusion. Our data represent a paradigm for the control of splice site selection by differential RBP binding and modulation of pre-mRNA structure.
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Affiliation(s)
- Alisha N. Jones
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, 85748 München, Germany
| | - Carina Graß
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
| | - Isabel Meininger
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Corresponding author. (D.K.); (M.S.)
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, 85748 München, Germany
- Corresponding author. (D.K.); (M.S.)
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5
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Zhang H, Chen C, Wu X, Lou C, Liang Q, Wu W, Wang X, Ding Q. Effects of 14 F9 synonymous codon variants on hemophilia B expression: Alteration of splicing along with protein expression. Hum Mutat 2022; 43:928-939. [PMID: 35391506 DOI: 10.1002/humu.24377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023]
Abstract
There is growing evidence that synonymous codon variants (SCVs) can cause disease through the disruption of different processes of protein production. The aim of the study is to investigate whether the 14 SCVs reported in the F9 variant database were the pathogenic causes of hemophilia B. The impacts of SCVs on splicing and protein expression were detected using a combination of in silico prediction, in vitro minigene splicing assay and cell expression detection. The splicing transcripts were identified and quantified by co-amplification fluorescent PCR. The mechanism of splicing was verified by a modified pU1snRNA and pU7snRNA approach. Aberrant splicing patterns were found in eight SCVs. Five of the 8 SCVs produced almost all aberrant splicing isoforms, which were expected to truncate protein, three of them presented a partial defect on both splicing and protein secretion, the overall effects were consistent with the residual Factor IX activity of the affected cases. Neither the pre-messenger RNA (mRNA) splicing process nor the protein function was impaired in the rest six SCVs. In conclusion, our study firstly revealed the pathogenic mechanism of the 14 F9 SCVs and highlighted the importance of performing mRNA splicing analysis and protein expression studies of SCVs in inherited disorders.
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Affiliation(s)
- Huayang Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Can Lou
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
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6
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Smirnov D, Schlieben LD, Peymani F, Berutti R, Prokisch H. Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes. Hum Mutat 2022; 43:1056-1070. [DOI: 10.1002/humu.24416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Lea D. Schlieben
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Fatemeh Peymani
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
| | - Riccardo Berutti
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Holger Prokisch
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
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7
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Abrahams L, Savisaar R, Mordstein C, Young B, Kudla G, Hurst LD. Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption. Nucleic Acids Res 2021; 49:9665-9685. [PMID: 34469537 PMCID: PMC8464065 DOI: 10.1093/nar/gkab750] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Transcripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exonic cis motifs, such as exonic splice enhancers (ESEs), are disrupted by nonsense mutations. We employ genome-wide transcriptomic and k-mer enrichment methods to scrutinize this model. First, we show that ESEs are prone to disruptive nonsense mutations owing to their purine richness and paucity of TGA, TAA and TAG. The motif model correctly predicts that NAS rates should be low (we estimate 5–30%) and approximately in line with estimates for the rate at which random point mutations disrupt splicing (8–20%). Further, we find that, as expected, NAS-associated PTCs are predictable from nucleotide-based machine learning approaches to predict splice disruption and, at least for pathogenic variants, are enriched in ESEs. Finally, we find that both in and out of frame mutations to TAA, TGA or TAG are associated with exon skipping. While a higher relative frequency of such skip-inducing mutations in-frame than out of frame lends some credence to the scanning model, these results reinforce the importance of considering splice motif modulation to understand the etiology of PTC-associated disease.
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Affiliation(s)
- Liam Abrahams
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.,Aarhus University, Department of Molecular Biology and Genetics, C F Møllers Allé 3, 8000 Aarhus, Denmark
| | - Bethan Young
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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8
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Lord J, Baralle D. Splicing in the Diagnosis of Rare Disease: Advances and Challenges. Front Genet 2021; 12:689892. [PMID: 34276790 PMCID: PMC8280750 DOI: 10.3389/fgene.2021.689892] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations which affect splicing are significant contributors to rare disease, but are frequently overlooked by diagnostic sequencing pipelines. Greater ascertainment of pathogenic splicing variants will increase diagnostic yields, ending the diagnostic odyssey for patients and families affected by rare disorders, and improving treatment and care strategies. Advances in sequencing technologies, predictive modeling, and understanding of the mechanisms of splicing in recent years pave the way for improved detection and interpretation of splice affecting variants, yet several limitations still prohibit their routine ascertainment in diagnostic testing. This review explores some of these advances in the context of clinical application and discusses challenges to be overcome before these variants are comprehensively and routinely recognized in diagnostics.
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Affiliation(s)
- Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
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9
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Tubeuf H, Charbonnier C, Soukarieh O, Blavier A, Lefebvre A, Dauchel H, Frebourg T, Gaildrat P, Martins A. Large-scale comparative evaluation of user-friendly tools for predicting variant-induced alterations of splicing regulatory elements. Hum Mutat 2020; 41:1811-1829. [PMID: 32741062 DOI: 10.1002/humu.24091] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/11/2020] [Accepted: 07/26/2020] [Indexed: 12/20/2022]
Abstract
Discriminating which nucleotide variants cause disease or contribute to phenotypic traits remains a major challenge in human genetics. In theory, any intragenic variant can potentially affect RNA splicing by altering splicing regulatory elements (SREs). However, these alterations are often ignored mainly because pioneer SRE predictors have proved inefficient. Here, we report the first large-scale comparative evaluation of four user-friendly SRE-dedicated algorithms (QUEPASA, HEXplorer, SPANR, and HAL) tested both as standalone tools and in multiple combined ways based on two independent benchmark datasets adding up to >1,300 exonic variants studied at the messenger RNA level and mapping to 89 different disease-causing genes. These methods display good predictive power, based on decision thresholds derived from the receiver operating characteristics curve analyses, with QUEPASA and HAL having the best accuracies either as standalone or in combination. Still, overall there was a tight race between the four predictors, suggesting that all methods may be of use. Additionally, QUEPASA and HEXplorer may be beneficial as well for predicting variant-induced creation of pseudoexons deep within introns. Our study highlights the potential of SRE predictors as filtering tools for identifying disease-causing candidates among the plethora of variants detected by high-throughput DNA sequencing and provides guidance for their use in genomic medicine settings.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Arnaud Lefebvre
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Hélène Dauchel
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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10
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Dionnet E, Defour A, Da Silva N, Salvi A, Lévy N, Krahn M, Bartoli M, Puppo F, Gorokhova S. Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay. Hum Mutat 2020; 41:1797-1810. [PMID: 32668095 DOI: 10.1002/humu.24083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 01/10/2023]
Abstract
Improving the accuracy of variant interpretation during diagnostic sequencing is a major goal for genomic medicine. To explore an often-overlooked splicing effect of missense variants, we developed the functional assay ("minigene") for the majority of exons of CAPN3, the gene responsible for limb girdle muscular dystrophy. By systematically screening 21 missense variants distributed along the gene, we found that eight clinically relevant missense variants located at a certain distance from the exon-intron borders (deep exonic missense variants) disrupted normal splicing of CAPN3 exons. Several recent machine learning-based computational tools failed to predict splicing impact for the majority of these deep exonic missense variants, highlighting the importance of including variants of this type in the training sets during the future algorithm development. Overall, 24 variants in CAPN3 gene were explored, leading to the change in the American College of Medical Genetics and Genomics classification of seven of them when results of the "minigene" functional assay were considered. Our findings reveal previously unknown splicing impact of several clinically important variants in CAPN3 and draw attention to the existence of deep exonic variants with a disruptive effect on gene splicing that could be overlooked by the current approaches in clinical genetics.
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Affiliation(s)
- Eugénie Dionnet
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Aurélia Defour
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Nathalie Da Silva
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Alexandra Salvi
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Nicolas Lévy
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France.,GIPTIS (Genetics Institute for Patients, Therapies Innovation and Science), Marseille, France
| | - Martin Krahn
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France
| | - Marc Bartoli
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Francesca Puppo
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Svetlana Gorokhova
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France
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11
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Rong S, Buerer L, Rhine CL, Wang J, Cygan KJ, Fairbrother WG. Mutational bias and the protein code shape the evolution of splicing enhancers. Nat Commun 2020; 11:2845. [PMID: 32504065 PMCID: PMC7275064 DOI: 10.1038/s41467-020-16673-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Exonic splicing enhancers (ESEs) are enriched in exons relative to introns and bind splicing activators. This study considers a fundamental question of co-evolution: How did ESE motifs become enriched in exons prior to the evolution of ESE recognition? We hypothesize that the high exon to intron motif ratios necessary for ESE function were created by mutational bias coupled with purifying selection on the protein code. These two forces retain certain coding motifs in exons while passively depleting them from introns. Through the use of simulations, genomic analyses, and high throughput splicing assays, we confirm the key predictions of this hypothesis, including an overlap between protein and splicing information in ESEs. We discuss the implications of mutational bias as an evolutionary driver in other cis-regulatory systems. Splicing is regulated by cis-acting elements in pre-mRNAs such as exonic or intronic splicing enhancers and silencers. Here the authors show that exonic splicing enhancers are enriched in exons compared to introns due to mutational bias coupled with purifying selection on the protein code.
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Affiliation(s)
- Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.,Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA
| | - Luke Buerer
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
| | - Christy L Rhine
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Jing Wang
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Kamil J Cygan
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.,Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - William G Fairbrother
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA. .,Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA. .,Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI, 02912, USA.
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12
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Boschann F, Fischer-Zirnsak B, Wienker TF, Holtgrewe M, Seelow D, Eichhorn B, Döhnert S, Fahsold R, Horn D, Graul-Neumann LM. An intronic splice site alteration in combination with a large deletion affecting VPS13B (COH1) causes Cohen syndrome. Eur J Med Genet 2020; 63:103973. [PMID: 32505691 DOI: 10.1016/j.ejmg.2020.103973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/06/2020] [Accepted: 06/01/2020] [Indexed: 01/15/2023]
Abstract
Cohen syndrome (CS) is a rare, autosomal recessive disorder characterized by intellectual disability, postnatal microcephaly, facial abnormalities, abnormal truncal fat distribution, myopia, and pigmentary retinopathy. It is often considered an underdiagnosed condition, especially in children with developmental delay and intellectual disability. Here we report on four individuals from a large Jordanian family clinically diagnosed with CS. Using Trio Exome Sequencing (Trio-WES) and MLPA analyses we identified a maternally inherited novel intronic nucleotide substitution c.3446-23T>G leading to the activation of a cryptic splice site and a paternally inherited multi-exon deletion in VPS13B (previously termed COH1) in the index patient. Expression analysis showed a strong decrease of VPS13B mRNA levels and direct sequencing of cDNA confirmed splicing at a cryptic upstream splice acceptor site, resulting in the inclusion of 22 intronic bases. This extension results in a frameshift and a premature stop of translation (p.Gly1149Valfs*9). Segregation analysis revealed that three affected maternal cousins were homozygous for the intronic splice site variant. Our data show causality of both alterations and strongly suggest the expansion of the diagnostic strategy to search for intronic splice variants in molecularly unconfirmed patients affected by CS.
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Affiliation(s)
- Felix Boschann
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany; Max-Planck-Institut für Molekulare Genetik, RG Development & Disease, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Björn Fischer-Zirnsak
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany; Max-Planck-Institut für Molekulare Genetik, RG Development & Disease, Ihnestr. 63-73, 14195, Berlin, Germany
| | - Thomas F Wienker
- Max-Planck-Institut für Molekulare Genetik, Dept. Human Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany
| | - Manuel Holtgrewe
- Berliner Institut für Gesundheitsforschung, Core Unit Bioinformatics, Charitéplatz 1, 10117, Berlin, Germany; Charité - Universitätsmedizin Berlin, Charité - Zentrum für Therapieforschung, Charitéplatz 1, 10117, Berlin, Germany
| | - Dominik Seelow
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany; Berliner Institut für Gesundheitsforschung (BIH), RG Bioinformatics and Translational Genetics, Charitéplatz 1, 10117, Berlin, Germany
| | - Birgit Eichhorn
- MVZ Mitteldeutscher Praxisverbund Humangenetik GmbH, Friedrichstrasse 38-40, 01067, Dresden, Germany
| | - Steffi Döhnert
- MVZ Mitteldeutscher Praxisverbund Humangenetik GmbH, Friedrichstrasse 38-40, 01067, Dresden, Germany
| | - Raimund Fahsold
- MVZ Mitteldeutscher Praxisverbund Humangenetik GmbH, Friedrichstrasse 38-40, 01067, Dresden, Germany
| | - Denise Horn
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Luitgard M Graul-Neumann
- Charité - Universitätsmedizin Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany.
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13
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Gauthier L, Stynen B, Serohijos AWR, Michnick SW. Genetics' Piece of the PI: Inferring the Origin of Complex Traits and Diseases from Proteome-Wide Protein-Protein Interaction Dynamics. Bioessays 2019; 42:e1900169. [PMID: 31854021 DOI: 10.1002/bies.201900169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/15/2019] [Indexed: 11/07/2022]
Abstract
How do common and rare genetic polymorphisms contribute to quantitative traits or disease risk and progression? Multiple human traits have been extensively characterized at the genomic level, revealing their complex genetic architecture. However, it is difficult to resolve the mechanisms by which specific variants contribute to a phenotype. Recently, analyses of variant effects on molecular traits have uncovered intermediate mechanisms that link sequence variation to phenotypic changes. Yet, these methods only capture a fraction of genetic contributions to phenotype. Here, in reviewing the field, it is proposed that complex traits can be understood by characterizing the dynamics of biochemical networks within living cells, and that the effects of genetic variation can be captured on these networks by using protein-protein interaction (PPI) methodologies. This synergy between PPI methodologies and the genetics of complex traits opens new avenues to investigate the molecular etiology of human diseases and to facilitate their prevention or treatment.
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Affiliation(s)
- Louis Gauthier
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Bram Stynen
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Adrian W R Serohijos
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Stephen W Michnick
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
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14
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Fontrodona N, Aubé F, Claude JB, Polvèche H, Lemaire S, Tranchevent LC, Modolo L, Mortreux F, Bourgeois CF, Auboeuf D. Interplay between coding and exonic splicing regulatory sequences. Genome Res 2019; 29:711-722. [PMID: 30962178 PMCID: PMC6499313 DOI: 10.1101/gr.241315.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 03/28/2019] [Indexed: 01/24/2023]
Abstract
The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties because of the nonrandomness of the genetic code. Indeed, amino acids sharing similar physicochemical properties correspond to codons that have the same nucleotide composition bias. In particular, we uncover that the TRA2A and TRA2B splicing factors that bind to adenine-rich motifs promote the inclusion of adenine-rich exons coding preferentially for hydrophilic amino acids that correspond to adenine-rich codons. SRSF2 that binds guanine/cytosine-rich motifs promotes the inclusion of GC-rich exons coding preferentially for small amino acids, whereas SRSF3 that binds cytosine-rich motifs promotes the inclusion of exons coding preferentially for uncharged amino acids, like serine and threonine that can be phosphorylated. Finally, coregulated exons encoding amino acids with similar physicochemical properties correspond to specific protein features. In conclusion, the regulation of an exon by a splicing factor that relies on the affinity of this factor for specific nucleotide(s) is tightly interconnected with the exon-encoded physicochemical properties. We therefore uncover an unanticipated bidirectional interplay between the splicing regulatory process and its biological functional outcome.
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Affiliation(s)
- Nicolas Fontrodona
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fabien Aubé
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Jean-Baptiste Claude
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Hélène Polvèche
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Sébastien Lemaire
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Léon-Charles Tranchevent
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Laurent Modolo
- LBMC Biocomputing Center, CNRS UMR 5239, INSERM U1210, F-69007, Lyon, France
| | - Franck Mortreux
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Didier Auboeuf
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
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15
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Paolacci S, Li Y, Agolini E, Bellacchio E, Arboleda-Bustos CE, Carrero D, Bertola D, Al-Gazali L, Alders M, Altmüller J, Arboleda G, Beleggia F, Bruselles A, Ciolfi A, Gillessen-Kaesbach G, Krieg T, Mohammed S, Müller C, Novelli A, Ortega J, Sandoval A, Velasco G, Yigit G, Arboleda H, Lopez-Otin C, Wollnik B, Tartaglia M, Hennekam RC. Specific combinations of biallelic POLR3A variants cause Wiedemann-Rautenstrauch syndrome. J Med Genet 2018; 55:837-846. [PMID: 30323018 DOI: 10.1136/jmedgenet-2018-105528] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/28/2018] [Accepted: 09/09/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Wiedemann-Rautenstrauch syndrome (WRS) is a form of segmental progeria presenting neonatally, characterised by growth retardation, sparse scalp hair, generalised lipodystrophy with characteristic local fatty tissue accumulations and unusual face. We aimed to understand its molecular cause. METHODS We performed exome sequencing in two families, targeted sequencing in 10 other families and performed in silico modelling studies and transcript processing analyses to explore the structural and functional consequences of the identified variants. RESULTS Biallelic POLR3A variants were identified in eight affected individuals and monoallelic variants of the same gene in four other individuals. In the latter, lack of genetic material precluded further analyses. Multiple variants were found to affect POLR3A transcript processing and were mostly located in deep intronic regions, making clinical suspicion fundamental to detection. While biallelic POLR3A variants have been previously reported in 4H syndrome and adolescent-onset progressive spastic ataxia, recurrent haplotypes specifically occurring in individuals with WRS were detected. All WRS-associated POLR3A amino acid changes were predicted to perturb substantially POLR3A structure/function. CONCLUSION Biallelic mutations in POLR3A, which encodes for the largest subunit of the DNA-dependent RNA polymerase III, underlie WRS. No isolated functional sites in POLR3A explain the phenotype variability in POLR3A-related disorders. We suggest that specific combinations of compound heterozygous variants must be present to cause the WRS phenotype. Our findings expand the molecular mechanisms contributing to progeroid disorders.
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Affiliation(s)
- Stefano Paolacci
- Department of Experimental Medicine, Sapienza "University of Rome", Rome, Italy
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Emanuele Agolini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Carlos E Arboleda-Bustos
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Dido Carrero
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, and Centro de Investigación Biomédica en Red de Cáncer, Oviedo, Spain
| | - Debora Bertola
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, e Centro de Estudos sobre o Genoma Humano e Células-Tronco do Instituto de Biociências da Universidade de São Paulo, São Paulo, Brazil
| | - Lihadh Al-Gazali
- Department of Paediatric, College of Medicine and Health Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mariel Alders
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Janine Altmüller
- Cologne Centre for Genomics and Centre for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Filippo Beleggia
- Department of Internal Medicine I, University Hospital Cologne, Cologne, Germany
| | - Alessandro Bruselles
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | | | - Thomas Krieg
- Department of Dermatology, University Hospital Cologne, Cologne, Germany
| | | | - Christian Müller
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Antonio Novelli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Jenny Ortega
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Adrian Sandoval
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Gloria Velasco
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, and Centro de Investigación Biomédica en Red de Cáncer, Oviedo, Spain
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Humberto Arboleda
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Carlos Lopez-Otin
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, and Centro de Investigación Biomédica en Red de Cáncer, Oviedo, Spain
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Raoul C Hennekam
- Department of Paediatrics, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands
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16
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Savisaar R, Hurst LD. Exonic splice regulation imposes strong selection at synonymous sites. Genome Res 2018; 28:1442-1454. [PMID: 30143596 PMCID: PMC6169883 DOI: 10.1101/gr.233999.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/31/2018] [Indexed: 01/17/2023]
Abstract
What proportion of coding sequence nucleotides have roles in splicing, and how strong is the selection that maintains them? Despite a large body of research into exonic splice regulatory signals, these questions have not been answered. This is because, to our knowledge, previous investigations have not explicitly disentangled the frequency of splice regulatory elements from the strength of the evolutionary constraint under which they evolve. Current data are consistent both with a scenario of weak and diffuse constraint, enveloping large swaths of sequence, as well as with well-defined pockets of strong purifying selection. In the former case, natural selection on exonic splice enhancers (ESEs) might primarily act as a slight modifier of codon usage bias. In the latter, mutations that disrupt ESEs are likely to have large fitness and, potentially, clinical effects. To distinguish between these scenarios, we used several different methods to determine the distribution of selection coefficients for new mutations within ESEs. The analyses converged to suggest that ∼15%-20% of fourfold degenerate sites are part of functional ESEs. Most of these sites are under strong evolutionary constraint. Therefore, exonic splice regulation does not simply impose a weak bias that gently nudges coding sequence evolution in a particular direction. Rather, the selection to preserve these motifs is a strong force that severely constrains the evolution of a substantial proportion of coding nucleotides. Thus synonymous mutations that disrupt ESEs should be considered as a potentially common cause of single-locus genetic disorders.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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17
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Braun S, Enculescu M, Setty ST, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S, König J, Zarnack K. Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun 2018; 9:3315. [PMID: 30120239 PMCID: PMC6098099 DOI: 10.1038/s41467-018-05748-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/19/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON∆165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.
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Affiliation(s)
- Simon Braun
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Samarth T Setty
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Bernardo P de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.,Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus Gambelas, 8005-139, Faro, Portugal
| | | | - Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Markus Seiler
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
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18
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Fernandez JP, Moreno-Mateos MA, Gohr A, Miao L, Chan SH, Irimia M, Giraldez AJ. RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS Genet 2018; 14:e1007473. [PMID: 29969449 PMCID: PMC6047831 DOI: 10.1371/journal.pgen.1007473] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/16/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
Pre-mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins. The retention and splicing (RES) complex is formed by three different proteins (Bud13p, Pml1p and Snu17p) and is involved in splicing in yeast. However, the importance of the RES complex for vertebrate splicing, the intronic features associated with its activity, and its role in development are unknown. In this study, we have generated loss-of-function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13, snip1 (pml1) and rbmx2 (snu17) mutants revealed a global defect in intron splicing, with strong mis-splicing of a subset of introns. We found these RES-dependent introns were short, rich in GC and flanked by GC depleted exons, all of which are features associated with intron definition. Using these features, we developed and validated a predictive model that classifies RES dependent introns. Altogether, our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.
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Affiliation(s)
- Juan Pablo Fernandez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | | | - Andre Gohr
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Shun Hang Chan
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, United States of America
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, United States of America
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19
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Booth KT, Azaiez H, Kahrizi K, Wang D, Zhang Y, Frees K, Nishimura C, Najmabadi H, Smith RJ. Exonic mutations and exon skipping: Lessons learned from DFNA5. Hum Mutat 2018; 39:433-440. [PMID: 29266521 PMCID: PMC5805621 DOI: 10.1002/humu.23384] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/27/2017] [Accepted: 12/12/2017] [Indexed: 02/06/2023]
Abstract
Dysregulation of splicing is a common factor underlying many inherited diseases including deafness. For one deafness-associated gene, DFNA5, perturbation of exon 8 splicing results in a constitutively active truncated protein. To date, only intronic mutations have been reported to cause exon 8 skipping in patients with DFNA5-related deafness. In five families with postlingual progressive autosomal dominant non-syndromic hearing loss, we employed two next-generation sequencing platforms-OtoSCOPE and whole exome sequencing-followed by variant filtering and prioritization based on both minor allele frequency and functional consequence using a customized bioinformatics pipeline to identify three novel and two recurrent mutations in DFNA5 that segregated with hearing loss in these families. The three novel mutations are all missense variants within exon 8 that are predicted computationally to decrease splicing efficiency or abolish it completely. We confirmed their functional impact in vitro using mini-genes carrying each mutant DFNA5 exon 8. In so doing, we present the first exonic mutations in DFNA5 to cause deafness, expand the mutational spectrum of DFNA5-related hearing loss, and highlight the importance of assessing the effect of coding variants on splicing.
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Affiliation(s)
- Kevin T Booth
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
- The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Hela Azaiez
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Donghong Wang
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Yuzhou Zhang
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Kathy Frees
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Carla Nishimura
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Richard J Smith
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
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20
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Nagata K, Takahashi M, Kiryu-Seo S, Kiyama H, Saido TC. Distinct functional consequences of ECEL1/DINE missense mutations in the pathogenesis of congenital contracture disorders. Acta Neuropathol Commun 2017; 5:83. [PMID: 29132416 PMCID: PMC5683451 DOI: 10.1186/s40478-017-0486-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/26/2017] [Indexed: 11/10/2022] Open
Abstract
Endothelin-converting enzyme-like 1 (ECEL1, also termed DINE in rodents), a membrane-bound metalloprotease, has been identified as a gene responsible for distal arthrogryposis (DA). ECEL1-mutated DA is generally characterized by ocular phenotypes in addition to the congenital limb contractures that are common to all DA subtypes. Until now, the consequences of the identified pathogenic mutations have remained incompletely understood because of a lack of detailed phenotypic analyses in relevant mouse models. In this study, we generated a new knock-in mouse strain that carries an ECEL1/DINE pathogenic G607S missense mutation, based on a previous study reporting atypical DA hindlimb phenotypes in two siblings with the mutation. We compared the morphological phenotypes of G607S knock-in mice with C760R knock-in mice that we previously established. Both C760R and G607S knock-in mouse embryos showed similar axonal arborization defects with normal trajectory patterns from the spinal cord to the target hindlimb muscles, as well as axon guidance defects of the abducens nerves. Intriguingly, distinct phenotypes in DINE protein localization and mRNA expression were identified in these knock-in mouse lines. For G607S, DINE mRNA and protein expression was decreased or almost absent in motor neurons. In the C760R mutant mice DINE was expressed and localized in the somata of motor neurons but not in axons. Our mutant mouse data suggest that ECEL1/DINE G607S and C760R mutations both lead to motor innervation defects as primary causes in ECEL1-mutated congenital contracture disorders. However, the functional consequences of the two mutations are distinct, with loss of axonal transport of ECEL1/DINE in C760R mutants and mRNA expression deficits in G607S mutants.
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