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He Z, Chen O, Phillips N, Pasquesi GIM, Sabunciyan S, Florea L. Predicting Alu exonization in the human genome with a deep learning model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574099. [PMID: 38260329 PMCID: PMC10802380 DOI: 10.1101/2024.01.03.574099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alu exonization, or the recruitment of intronic Alu elements into gene sequences, has contributed to functional diversification; however, its extent and the ways in which it influences gene regulation are not fully understood. We developed an unbiased approach to predict Alu exonization events from genomic sequences implemented in a deep learning model, eXAlu, that overcomes the limitations of tissue or condition specificity and the computational burden of RNA-seq analysis. The model captures previously reported characteristics of exonized Alu sequences and can predict sequence elements important for Alu exonization. Using eXAlu, we estimate the number of Alu elements in the human genome undergoing exonization to be between 55-110K, 11-21 fold more than represented in the GENCODE gene database. Using RT-PCR we were able to validate selected predicted Alu exonization events, supporting the accuracy of our method. Lastly, we highlight a potential application of our method to identify polymorphic Alu insertion exonizations in individuals and in the population from whole genome sequencing data.
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Affiliation(s)
- Zitong He
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21205
| | - Ou Chen
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Noelani Phillips
- School of Kinesiology, University of Michigan, Ann Arbor, MI 48109
| | - Giulia Irene Maria Pasquesi
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309 and Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Liliana Florea
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21205
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
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2
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Chu WS, Ng J, Waddington SN, Kurian MA. Gene therapy for neurotransmitter-related disorders. J Inherit Metab Dis 2024; 47:176-191. [PMID: 38221762 PMCID: PMC11108624 DOI: 10.1002/jimd.12697] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024]
Abstract
Inborn errors of neurotransmitter (NT) metabolism are a group of rare, heterogenous diseases with predominant neurological features, such as movement disorders, autonomic dysfunction, and developmental delay. Clinical overlap with other disorders has led to delayed diagnosis and treatment, and some conditions are refractory to oral pharmacotherapies. Gene therapies have been developed and translated to clinics for paediatric inborn errors of metabolism, with 38 interventional clinical trials ongoing to date. Furthermore, efforts in restoring dopamine synthesis and neurotransmission through viral gene therapy have been developed for Parkinson's disease. Along with the recent European Medicines Agency (EMA) and Medicines and Healthcare Products Regulatory Agency (MHRA) approval of an AAV2 gene supplementation therapy for AADC deficiency, promising efficacy and safety profiles can be achieved in this group of diseases. In this review, we present preclinical and clinical advances to address NT-related diseases, and summarise potential challenges that require careful considerations for NT gene therapy studies.
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Affiliation(s)
- Wing Sum Chu
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Genetic Therapy Accelerator Centre, Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Joanne Ng
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Genetic Therapy Accelerator Centre, Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Simon N. Waddington
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Manju A. Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- Department of NeurologyGreat Ormond Street Hospital for ChildrenLondonUK
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3
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Mastrangelo M, Tolve M, Artiola C, Bove R, Carducci C, Carducci C, Angeloni A, Pisani F, Leuzzi V. Phenotypes and Genotypes of Inherited Disorders of Biogenic Amine Neurotransmitter Metabolism. Genes (Basel) 2023; 14:genes14020263. [PMID: 36833190 PMCID: PMC9957200 DOI: 10.3390/genes14020263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Inherited disorders of biogenic amine metabolism are genetically determined conditions resulting in dysfunctions or lack of enzymes involved in the synthesis, degradation, or transport of dopamine, serotonin, adrenaline/noradrenaline, and their metabolites or defects of their cofactor or chaperone biosynthesis. They represent a group of treatable diseases presenting with complex patterns of movement disorders (dystonia, oculogyric crises, severe/hypokinetic syndrome, myoclonic jerks, and tremors) associated with a delay in the emergence of postural reactions, global development delay, and autonomic dysregulation. The earlier the disease manifests, the more severe and widespread the impaired motor functions. Diagnosis mainly depends on measuring neurotransmitter metabolites in cerebrospinal fluid that may address the genetic confirmation. Correlations between the severity of phenotypes and genotypes may vary remarkably among the different diseases. Traditional pharmacological strategies are not disease-modifying in most cases. Gene therapy has provided promising results in patients with DYT-DDC and in vitro models of DYT/PARK-SLC6A3. The rarity of these diseases, combined with limited knowledge of their clinical, biochemical, and molecular genetic features, frequently leads to misdiagnosis or significant diagnostic delays. This review provides updates on these aspects with a final outlook on future perspectives.
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Affiliation(s)
- Mario Mastrangelo
- Child Neurology and Psychiatry Unit, Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
| | - Manuela Tolve
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Cristiana Artiola
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Rossella Bove
- Child Neurology and Psychiatry Unit, Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
| | - Claudia Carducci
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Carla Carducci
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Antonio Angeloni
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Francesco Pisani
- Child Neurology and Psychiatry Unit, Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
- Correspondence: ; Tel.: +39-649972930; Fax: +39-64440232
| | - Vincenzo Leuzzi
- Child Neurology and Psychiatry Unit, Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
- Azienda Ospedaliero Universitaria Policlinico Umberto I, 00161 Rome, Italy
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4
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Martínez-Pizarro A, Leal F, Holm LL, Doktor TK, Petersen USS, Bueno M, Thöny B, Pérez B, Andresen BS, Desviat LR. Antisense Oligonucleotide Rescue of Deep-Intronic Variants Activating Pseudoexons in the 6-Pyruvoyl-Tetrahydropterin Synthase Gene. Nucleic Acid Ther 2022; 32:378-390. [PMID: 35833796 PMCID: PMC9595628 DOI: 10.1089/nat.2021.0066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report two new 6-pyruvoyl-tetrahydropterin synthase splicing variants identified through genomic sequencing and transcript analysis in a patient with tetrahydrobiopterin deficiency, presenting with hyperphenylalaninemia and monoamine neurotransmitter deficiency. Variant c.243 + 3A>G causes exon 4 skipping. The deep-intronic c.164-672C>T variant creates a potential 5' splice site that leads to the inclusion of four overlapping pseudoexons, corresponding to exonizations of an antisense short interspersed nuclear element AluSq repeat sequence. Two of the identified pseudoexons have been reported previously, activated by different deep-intronic variants, and were also detected at residual levels in control cells. Interestingly, the predominant pseudoexon is nearly identical to a disease causing activated pseudoexon in the F8 gene, with the same 3' and 5' splice sites. Splice switching antisense oligonucleotides (SSOs) were designed to hybridize with splice sites and/or predicted binding sites for regulatory splice factors. Different SSOs corrected the aberrant pseudoexon inclusion, both in minigenes and in fibroblasts from patients carrying the new variant c.164-672C>T or the previously described c.164-716A>T. With SSO treatment PTPS protein was recovered, illustrating the therapeutic potential of the approach, for patients with different pseudoexon activating variants in the region. In addition, the natural presence of pseudoexons in the wild type context suggests the possibility of applying the antisense strategy in patients with hypomorphic PTS variants with the purpose of upregulating their expression to increase overall protein and activity.
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Affiliation(s)
- Ainhoa Martínez-Pizarro
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), CIBERER, IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fátima Leal
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), CIBERER, IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - María Bueno
- Congenital Metabolic Diseases Unit, Hospital Virgen del Rocio, Sevilla, Spain
| | - Beat Thöny
- Division of Metabolism, University Children's Hospital Zürich, Zürich, Switzerland
| | - Belén Pérez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), CIBERER, IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), CIBERER, IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
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5
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Choi S, Cho N, Kim KK. Non-canonical splice junction processing increases the diversity of RBFOX2 splicing isoforms. Int J Biochem Cell Biol 2022; 144:106172. [PMID: 35124219 DOI: 10.1016/j.biocel.2022.106172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/23/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022]
Abstract
The underlying mechanisms of splicing regulation through non-canonical splice junction processing remain largely unknown. Here, we identified two RBFOX2 splicing isoforms by alternative 3' splice site selection of exon 9; the non-canonical splice junction processed RBFOX2 transcript (RBFOX2-N.C.) was expressed by the selection of the 3' splice GG acceptor sequence. The cytoplasmic localization of RBFOX2-C., a canonical splice junction-processed RBFOX2 transcript, was different from that of RBFOX2-N.C., which showed nuclear localization. In addition, we confirmed that RBFOX2-C. showed a significantly stronger localization into stress granules than RBFOX2-N.C. upon sodium arsenite treatment. Next, we investigated the importance of non-canonical 3' splice GG sequence selection of specific cis-regulatory elements using minigene constructs of the RBFOX2 gene. We found that the non-canonical 3' splice GG sequence and suboptimal branch point site adjacent region were critical for RBFOX2-N.C. expression through a non-canonical 3' splice selection. Our results suggest a regulatory mechanism for the non-canonical 3' splice selection in the RBFOX2 gene, providing a basis for studies related to the regulation of alternative pre-mRNA splicing through non-canonical splice junction processing.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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6
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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7
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Song B, Ma Z, Liu W, Lu L, Jian Y, Yu L, Wan Z, Yue X, Kong Y. Clinical, biochemical and molecular spectrum of mild 6-pyruvoyl-tetrahydropterin synthase deficiency and a case report. Fetal Pediatr Pathol 2021; 40:707-716. [PMID: 32202960 DOI: 10.1080/15513815.2020.1737992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background 6-Pyruvoyl-tetrahydropterin synthase (PTS) is the key enzyme in BH4 synthesis. PTS deficiency is classified as severe type and mild type, and the prognosis and treatment differ for these types. Distinguishing between two types in the early stage is difficult. Reference to reported cases is needed for interpretation of the correlation between genotype and prognosis. Case report: We report a full-term female newborn with mild PTS deficiency. On the day 21 after birth, the phenylalanine level was 859.6 mmol/L (reference range: 30-117 mmol/L). After 1 year of observation, the patient was found to be in a healthy condition without treatment. Conclusions: Although the phenylalanine level is high in mild PTS deficiency patients after birth, some of them may have few symptoms with no treatment. We review 19 cases and find 8 mutations of PTS that may be associated with mild PTS deficiency.
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Affiliation(s)
- Boyan Song
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Zhijun Ma
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Wei Liu
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Lihong Lu
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yongjian Jian
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Lu Yu
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Zhihui Wan
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Xiaofei Yue
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yuanyuan Kong
- Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
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8
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Petersen USS, Doktor TK, Andresen BS. Pseudoexon activation in disease by non-splice site deep intronic sequence variation - wild type pseudoexons constitute high-risk sites in the human genome. Hum Mutat 2021; 43:103-127. [PMID: 34837434 DOI: 10.1002/humu.24306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 12/27/2022]
Abstract
Accuracy of pre-messenger RNA (pre-mRNA) splicing is crucial for normal gene expression. Complex regulation supports the spliceosomal distinction between authentic exons and the many seemingly functional splice sites delimiting pseudoexons. Pseudoexons are nonfunctional intronic sequences that can be activated for aberrant inclusion in mRNA, which may cause disease. Pseudoexon activation is very challenging to predict, in particular when activation occurs by sequence variants that alter the splicing regulatory environment without directly affecting splice sites. As pseudoexon inclusion often evades detection due to activation of nonsense-mediated mRNA decay, and because conventional diagnostic procedures miss deep intronic sequence variation, pseudoexon activation is a heavily underreported disease mechanism. Pseudoexon characteristics have mainly been studied based on in silico predicted sequences. Moreover, because recognition of sequence variants that create or strengthen splice sites is possible by comparison with well-established consensus sequences, this type of pseudoexon activation is by far the most frequently reported. Here we review all known human disease-associated pseudoexons that carry functional splice sites and are activated by deep intronic sequence variants located outside splice site sequences. We delineate common characteristics that make this type of wild type pseudoexons distinct high-risk sites in the human genome.
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Affiliation(s)
- Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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9
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Florea L, Payer L, Antonescu C, Yang G, Burns K. Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data. Front Mol Biosci 2021; 8:727537. [PMID: 34568430 PMCID: PMC8460874 DOI: 10.3389/fmolb.2021.727537] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/30/2021] [Indexed: 11/15/2022] Open
Abstract
Alu exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting incorporation of Alu sequences in mRNA transcripts from large scale RNA-seq data sets. The approach detects Alu sequences derived from both fixed and polymorphic Alu elements, including Alu insertions missing from the reference genome. We applied our methods to 117 GTEx human frontal cortex samples to build and characterize a collection of Alu-containing mRNAs. In particular, we detected and characterized Alu exonizations occurring at 870 fixed Alu loci, of which 237 were novel, as well as hundreds of putative events involving Alu elements that are polymorphic variants or rare alleles not present in the reference genome. These methods and annotations represent a unique and valuable resource that can be used to understand the characteristics of Alu-containing mRNAs and their tissue-specific expression patterns.
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Affiliation(s)
- Liliana Florea
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Lindsay Payer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Corina Antonescu
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Guangyu Yang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Kathleen Burns
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
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10
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Himmelreich N, Blau N, Thöny B. Molecular and metabolic bases of tetrahydrobiopterin (BH 4) deficiencies. Mol Genet Metab 2021; 133:123-136. [PMID: 33903016 DOI: 10.1016/j.ymgme.2021.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/09/2021] [Accepted: 04/09/2021] [Indexed: 01/01/2023]
Abstract
Tetrahydrobiopterin (BH4) deficiency is caused by genetic variants in the three genes involved in de novo cofactor biosynthesis, GTP cyclohydrolase I (GTPCH/GCH1), 6-pyruvoyl-tetrahydropterin synthase (PTPS/PTS), sepiapterin reductase (SR/SPR), and the two genes involved in cofactor recycling, carbinolamine-4α-dehydratase (PCD/PCBD1) and dihydropteridine reductase (DHPR/QDPR). Dysfunction in BH4 metabolism leads to reduced cofactor levels and may result in systemic hyperphenylalaninemia and/or neurological sequelae due to secondary deficiency in monoamine neurotransmitters in the central nervous system. More than 1100 patients with BH4 deficiency and 800 different allelic variants distributed throughout the individual genes are tabulated in database of pediatric neurotransmitter disorders PNDdb. Here we provide an update on the molecular-genetic analysis and structural considerations of these variants, including the clinical courses of the genotypes. From a total of 324 alleles, 11 are associated with the autosomal recessive form of GTPCH deficiency presenting with hyperphenylalaninemia (HPA) and neurotransmitter deficiency, 295 GCH1 variant alleles are detected in the dominant form of L-dopa-responsive dystonia (DRD or Segawa disease) while phenotypes of 18 alleles remained undefined. Autosomal recessive variants observed in the PTS (199 variants), PCBD1 (32 variants), and QDPR (141 variants) genes lead to HPA concomitant with central monoamine neurotransmitter deficiency, while SPR deficiency (104 variants) presents without hyperphenylalaninemia. The clinical impact of reported variants is essential for genetic counseling and important for development of precision medicine.
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Affiliation(s)
- Nastassja Himmelreich
- Center for Child and Adolescent Medicine, Dietmar-Hopp Metabolic Center, Division 1, Heidelberg, Germany
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital Zürich, Zürich, Switzerland.
| | - Beat Thöny
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zürich, Zürich, Switzerland.
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11
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Muniz JR, Szeto NWS, Frise R, Lee WH, Wang XS, Thöny B, Himmelreich N, Blau N, Hsiao KJ, Liu TT, Gileadi O, Oppermann U, Von Delft F, Yue WW, Tang NLS. Role of protein structure in variant annotation: structural insight of mutations causing 6-pyruvoyl-tetrahydropterin synthase deficiency. Pathology 2019; 51:274-280. [DOI: 10.1016/j.pathol.2018.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
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12
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Value of genetic analysis for confirming inborn errors of metabolism detected through the Spanish neonatal screening program. Eur J Hum Genet 2019; 27:556-562. [PMID: 30626930 DOI: 10.1038/s41431-018-0330-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/16/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
The present work describes the value of genetic analysis as a confirmatory measure following the detection of suspected inborn errors of metabolism in the Spanish newborn mass spectrometry screening program. One hundred and forty-one consecutive DNA samples were analyzed by next-generation sequencing using a customized exome sequencing panel. When required, the Illumina extended clinical exome panel was used, as was Sanger sequencing or transcriptional profiling. Biochemical tests were used to confirm the results of the genetic analysis. Using the customized panel, the metabolic disease suspected in 83 newborns (59%) was confirmed. In three further cases, two monoallelic variants were detected for two genes involved in the same biochemical pathway. In the remainder, either a single variant or no variant was identified. Given the persistent absence of biochemical alterations, carrier status was assigned in 39 cases. False positives were recorded for 11. In five cases in which the biochemical pattern was persistently altered, further genetic analysis allowed the detection of two variants affecting the function of BCAT2, ACSF3, and DNAJC12, as well as a second, deep intronic variant in ETFDH or PTS. The present results suggest that genetic analysis using extended next-generation sequencing panels can be used as a confirmatory test for suspected inborn errors of metabolism detected in newborn screening programs. Biochemical tests can be very helpful when a diagnosis is unclear. In summary, simultaneous genomic and metabolomic analyses can increase the number of inborn errors of metabolism that can be confirmed following suggestive newborn screening results.
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Jourdy Y, Janin A, Fretigny M, Lienhart A, Négrier C, Bozon D, Vinciguerra C. Reccurrent F8 Intronic Deletion Found in Mild Hemophilia A Causes Alu Exonization. Am J Hum Genet 2018; 102:199-206. [PMID: 29357978 DOI: 10.1016/j.ajhg.2017.12.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/12/2017] [Indexed: 01/12/2023] Open
Abstract
Incorporation of distant intronic sequences in mature mRNA is an underappreciated cause of genetic disease. Several disease-causing pseudoexons have been found to contain repetitive elements such as Alu elements. This study describes an original pathological mechanism by which a small intronic deletion leads to Alu exonization. We identified an intronic deletion, c.2113+461_2113+473del, in the F8 intron 13, in two individuals with mild hemophilia A. In vivo and in vitro transcript analysis found an aberrant transcript, with an insertion of a 122-bp intronic fragment (c.2113_2114ins2113+477_2113+598) at the exon 13-14 junction. This out-of-frame insertion is predicted to lead to truncated protein (p.Gly705Aspfs∗37). DNA sequencing analysis found that the pseudoexon corresponds to antisense AluY element and the deletion removed a part of the poly(T)-tail from the right arm of these AluY. The heterogenous nuclear riboprotein C1/C2 (hnRNP C) is an important antisense Alu-derived cryptic exon silencer and binds to poly(T)-tracts. Disruption of the hnRNP C binding site in AluY T-tract by mutagenesis or hnRNP C knockdown using siRNA in HeLa cells reproduced the effect of c.2113+461_2113+473del. The screening of 114 unrelated families with mild hemophilia A in whom no genetic event was previously identified found a deletion in the poly(T)-tail of AluY in intron 13 in 54% of case subjects (n = 61/114). In conclusion, this study describes a deletion leading to Alu exonization found in 6.1% of families with mild hemophila A in France.
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Affiliation(s)
- Yohann Jourdy
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France; EA 4609 Hémostase et cancer, Lyon (69008), Université Claude Bernard Lyon 1, Univ Lyon, France.
| | - Alexandre Janin
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Bron (69500), Hospices Civils de Lyon, France; Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Univ Lyon, France, CNRS UMR 5510, Villeurbanne (69100), France; INSERM U1217, Villeurbanne, France
| | - Mathilde Fretigny
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France
| | - Anne Lienhart
- Unité d'hémostase clinique, Hôpital Cardiologique Louis Pradel, Bron (69500), Hospices Civils de Lyon, France
| | - Claude Négrier
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France; EA 4609 Hémostase et cancer, Lyon (69008), Université Claude Bernard Lyon 1, Univ Lyon, France; Unité d'hémostase clinique, Hôpital Cardiologique Louis Pradel, Bron (69500), Hospices Civils de Lyon, France
| | - Dominique Bozon
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Bron (69500), Hospices Civils de Lyon, France
| | - Christine Vinciguerra
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France; EA 4609 Hémostase et cancer, Lyon (69008), Université Claude Bernard Lyon 1, Univ Lyon, France
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Humphrey J, Emmett W, Fratta P, Isaacs AM, Plagnol V. Quantitative analysis of cryptic splicing associated with TDP-43 depletion. BMC Med Genomics 2017; 10:38. [PMID: 28549443 PMCID: PMC5446763 DOI: 10.1186/s12920-017-0274-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/17/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. METHODS We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. RESULTS We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. CONCLUSIONS Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.
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Affiliation(s)
- Jack Humphrey
- University College London Genetics Institute, Gower Street, London, UK.
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.
| | - Warren Emmett
- University College London Genetics Institute, Gower Street, London, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
- The Francis Crick Institute, Midland Road, London, UK
| | - Pietro Fratta
- Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, Queen Square, London, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
| | - Vincent Plagnol
- University College London Genetics Institute, Gower Street, London, UK
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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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Nozu K, Iijima K, Ohtsuka Y, Fu XJ, Kaito H, Nakanishi K, Vorechovsky I. Alport syndrome caused by a COL4A5 deletion and exonization of an adjacent AluY. Mol Genet Genomic Med 2014; 2:451-3. [PMID: 25333070 PMCID: PMC4190880 DOI: 10.1002/mgg3.89] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/03/2014] [Accepted: 05/09/2014] [Indexed: 11/12/2022] Open
Abstract
Mutation-induced activation of splice sites in intronic repetitive sequences has contributed significantly to the evolution of exon–intron structure and genetic disease. Such events have been associated with mutations within transposable elements, most frequently in mutation hot-spots of Alus. Here, we report a case of Alu exonization resulting from a 367-nt genomic COL4A5 deletion that did not encompass any recognizable transposed element, leading to the Alport syndrome. The deletion brought to proximity the 5′ splice site of COL4A5 exon 33 and a cryptic 3′ splice site in an antisense AluY copy in intron 32. The fusion exon was depleted of purines and purine-rich splicing enhancers, but had low levels of intramolecular secondary structure, was flanked by short introns and had strong 5′ and Alu-derived 3′ splice sites, apparently compensating poor composition and context of the new exon. This case demonstrates that Alu splice sites can be activated by outlying deletions, highlighting Alu versatility in shaping the exon–intron organization and expanding the spectrum of mutational mechanisms that introduce repetitive sequences in mRNAs.
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Affiliation(s)
- Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine Kobe, Japan
| | - Yasufumi Ohtsuka
- Department of Pediatrics, Faculty of Medicine, Saga University Saga, Japan
| | - Xue Jun Fu
- Department of Pediatrics, Kobe University Graduate School of Medicine Kobe, Japan
| | - Hiroshi Kaito
- Department of Pediatrics, Kobe University Graduate School of Medicine Kobe, Japan
| | - Koichi Nakanishi
- Department of Pediatrics, Wakayama Medical University Wakayama, Japan
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17
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Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe N, Ule J. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 2013; 152:453-66. [PMID: 23374342 PMCID: PMC3629564 DOI: 10.1016/j.cell.2012.12.023] [Citation(s) in RCA: 337] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 09/22/2012] [Accepted: 12/12/2012] [Indexed: 11/26/2022]
Abstract
There are ~650,000 Alu elements in transcribed regions of the human genome. These elements contain cryptic splice sites, so they are in constant danger of aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about the molecular mechanisms preventing their inclusion. Here, we present a mechanism for protecting the human transcriptome from the aberrant exonization of transposable elements. Quantitative iCLIP data show that the RNA-binding protein hnRNP C competes with the splicing factor U2AF65 at many genuine and cryptic splice sites. Loss of hnRNP C leads to formation of previously suppressed Alu exons, which severely disrupt transcript function. Minigene experiments explain disease-associated mutations in Alu elements that hamper hnRNP C binding. Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease.
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Affiliation(s)
- Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julian König
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Mojca Tajnik
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1104 Ljubljana, Slovenia
| | - Iñigo Martincorena
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Isabelle Stévant
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alejandro Reyes
- EMBL, Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simon Anders
- EMBL, Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nicholas M. Luscombe
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, Gower Street, London WC1E 6BT, UK
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- Okinawa Institute for Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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18
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Retroelements in human disease. Gene 2013; 518:231-41. [PMID: 23333607 DOI: 10.1016/j.gene.2013.01.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/28/2012] [Accepted: 01/02/2013] [Indexed: 12/16/2022]
Abstract
Retroelements are an abundant class of noncoding DNAs present in about half of the human genome. Among them, L1, Alu and SVA are currently active. They "jump" by retrotransposition, shuffle genomic regions by 5' and 3' transduction, and promote or inhibit gene transcription by providing alternative promoters or generating antisense and/or regulatory noncoding RNAs. Recent data also suggest that retroelement insertions into exons and introns of genes induce different types of genetic disease, including cancer. Retroelements interfere with the expression of genes by inducing alternative splicing via exon skipping and exonization using cryptic splice sites, and by providing polyadenylation signals. Here we summarize our current understanding of the molecular mechanisms of retroelement-induced mutagenesis which causes fifty different types of human disease. We categorize these mutagenic effects according to eleven different mechanisms and show that most of them may be explained either by traditional exon definition or transcriptional interference, a previously unrecognized molecular mechanism. In summary, this review gives an overview of retroelement insertions in genes that cause significant changes in their transcription and cotranscriptional splicing and show a remarkable level of complexity.
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19
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Chiu YH, Chang YC, Chang YH, Niu DM, Yang YL, Ye J, Jiang J, Okano Y, Lee DH, Pangkanon S, Kuptanon C, Hock NL, Chiong MA, Cavan BV, Hsiao KJ, Liu TT. Mutation spectrum of and founder effects affecting the PTS gene in East Asian populations. J Hum Genet 2012; 57:145-52. [DOI: 10.1038/jhg.2011.146] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Roque JB, O'Leary CA, Kyaw-Tanner M, Duffy DL, Gharahkhani P, Vogelnest L, Mason K, Shipstone M. PTPN22 polymorphisms may indicate a role for this gene in atopic dermatitis in West Highland white terriers. BMC Res Notes 2011; 4:571. [PMID: 22208456 PMCID: PMC3271996 DOI: 10.1186/1756-0500-4-571] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/30/2011] [Indexed: 12/20/2022] Open
Abstract
Background Canine atopic dermatitis is an allergic inflammatory skin disease common in West Highland white terriers. A genome-wide association study for atopic dermatitis in a population of West Highland white terriers identified a 1.3 Mb area of association on CFA17 containing canine protein tyrosine phosphatase non-receptor type 22 (lymphoid) PTPN22. This gene is a potential candidate gene for canine atopic dermatitis as it encodes a lymphoid-specific signalling mediator that regulates T-cell and possibly B-cell activity. Findings Sequencing of PTPN22 in three atopic and three non-atopic West Highland white terriers identified 18 polymorphisms, including five genetic variants with a bioinformatically predicted functional effect. An intronic polymorphic repeat sequence variant was excluded as the cause of the genome-wide association study peak signal, by large-scale genotyping in 72 West Highland white terriers (gene-dropping simulation method, P = 0.01). Conclusions This study identified 18 genetic variants in PTPN22 that might be associated with atopic dermatitis in West Highland white terriers. This preliminary data may direct further study on the role of PTPN22 in this disease. Large scale genotyping and complementary genomic and proteomic assays would be required to assess this possibility.
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Affiliation(s)
- Joana Barros Roque
- Centre for Companion Animal Health, School of Veterinary Science, The University of Queensland, St Lucia, Queensland, 4069, Australia.
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21
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Coutinho MF, da Silva Santos L, Lacerda L, Quental S, Wibrand F, Lund AM, Johansen KB, Prata MJ, Alves S. Alu-Alu Recombination Underlying the First Large Genomic Deletion in GlcNAc-Phosphotransferase Alpha/Beta (GNPTAB) Gene in a MLII Alpha/Beta Patient. JIMD Rep 2011; 4:117-24. [PMID: 23430906 PMCID: PMC3509902 DOI: 10.1007/8904_2011_83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 02/01/2023] Open
Abstract
Mucolipidosis type II α/β is a severe, autosomal recessive lysosomal storage disorder, caused by a defect in the GNPTAB gene that codes for the α/β subunits of the GlcNAc-phosphotransferase. To date, over 100 different mutations have been identified in MLII α/β patients, but no large deletions have been reported. Here we present the first case of a large homozygous intragenic GNPTAB gene deletion (c.3435-386_3602 + 343del897) encompassing exon 19, identified in a ML II α/β patient. Long-range PCR and sequencing methodologies were used to refine the characterization of this rearrangement, leading to the identification of a 21 bp repetitive motif in introns 18 and 19. Further analysis revealed that both the 5' and 3' breakpoints were located within highly homologous Alu elements (Alu-Sz in intron 18 and Alu-Sq2, in intron 19), suggesting that this deletion has probably resulted from Alu-Alu unequal homologous recombination. RT-PCR methods were used to further evaluate the consequences of the alteration for the processing of the mutant pre mRNA GNPTAB, revealing the production of three abnormal transcripts: one without exon 19 (p.Lys1146_Trp1201del); another with an additional loss of exon 20 (p.Arg1145Serfs*2), and a third in which exon 19 was substituted by a pseudoexon inclusion consisting of a 62 bp fragment from intron 18 (p.Arg1145Serfs*16). Interestingly, this 62 bp fragment corresponds to the Alu-Sz element integrated in intron 18.This represents the first description of a large deletion identified in the GNPTAB gene and contributes to enrich the knowledge on the molecular mechanisms underlying causative mutations in ML II.
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Affiliation(s)
| | | | - Lúcia Lacerda
- Biochemical Genetics Unit, Department of Genetics, CGMJM, INSA, Porto, Portugal
| | | | - Flemming Wibrand
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Allan M. Lund
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | | | - Maria João Prata
- IPATIMUP/ Department of Biology, Faculty of Sciences, Porto, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Genetics, CGMJM, INSA, Porto, Portugal
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22
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Brasil S, Viecelli HM, Meili D, Rassi A, Desviat LR, Pérez B, Ugarte M, Thöny B. Pseudoexon exclusion by antisense therapy in 6-pyruvoyl-tetrahydropterin synthase deficiency. Hum Mutat 2011; 32:1019-27. [PMID: 21542064 DOI: 10.1002/humu.21529] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 04/21/2011] [Indexed: 11/11/2022]
Abstract
Antisense oligonucleotide therapy to modulate splicing mutations in inherited diseases is emerging as a treatment option also for metabolic defects. In this article, we report the effect of cellular antisense therapy to suppress pseudoexon activation in primary dermal fibroblasts from patients with mutations in the PTS gene encoding 6-pyruvoyltetrahydropterin synthase (PTPS), which leads to tetrahydrobiopterin and monoamine neurotransmitter deficiency. Pathogenic inclusion of SINE or LINE-derived cryptic exons in different PTPS patients due to the intronic mutations c.84-322A>T, c.163 + 695_163 + 751del57, or c.164-712A>T was demonstrated by transcript analysis in fibroblasts and minigene ex vivo assays. Antisense morpholino oligonucleotides (AMOs) directed to the pseudoexons 3' or 5' splice sites were designed with the aim of preventing the pathological pseudoexon inclusion. At the time of AMO transfection, we investigated patients' cells for correct PTS-mRNA splicing and functional recovery of the PTPS protein. Transcriptional profiling after 24 hr posttransfection revealed a dose- and sequence-specific recovery of normal splicing. Furthermore, PTPS enzyme activity in all three patients' fibroblasts and the pterin profile were close to normal values after antisense treatment. Our results demonstrate proof-of-concept for pseudoexon exclusion therapy using AMO in inherited metabolic disease.
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Affiliation(s)
- Sandra Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad Autónoma de Madrid, Madrid, Spain
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Lim HT, Zhong T, Cho IC, Seo BY, Kim JH, Lee SS, Ko MS, Park HB, Kim BW, Lee JH, Jeon JT. Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrossed population of Landrace and Korean Native pigs. Anim Genet 2011; 42:451-5. [PMID: 21749430 DOI: 10.1111/j.1365-2052.2011.02225.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The KIT locus has been suggested to be a strong candidate region linked with whole-body roan in the F(2) population produced by intercrosses between Landrace and Korean Native pigs. In this manuscript, we report the finding of a novel alternative splicing event in the porcine KIT gene that results in the skipping of exon 5 in the I(Rn) allele. KIT mRNAs that lack exon 5 were identified in the large intestine and skin, suggesting that the mechanism responsible for the skipping of exon 5 may be tissue specific. A U(26) repeat in intron 5 showed complete linkage (LOD = 11.8) with the roan phenotype and absolute association with the black phenotype of the Korean Native pig (KNP) population samples, inferring that the repeat pattern may alter the complementary base-pairing-mediated looping-out of introns 4 and 5, which may mediate the exon 5-skipping event. Although the sample size in our study was relatively small, we speculate that the R3 allele containing the U(26) repeat is a causative element for the roan phenotype via alternative control of the exon skipping in our roan pedigree.
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Affiliation(s)
- H T Lim
- Division of Applied Life Science, BK21 Program, Graduate School of Gyeongsang National University, Jinju, Korea. s_htim @gnu.ac.kr
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Carboni N, Floris M, Mateddu A, Porcu M, Marrosu G, Solla E, Cocco E, Mura M, Marini S, Maioli MA, Piras R, Aste R, Marrosu MG. Aberrant splicing in the LMNA gene caused by a novel mutation on the polypyrimidine tract of intron 5. Muscle Nerve 2011; 43:688-93. [PMID: 21462202 DOI: 10.1002/mus.21937] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2010] [Indexed: 11/06/2022]
Abstract
INTRODUCTION Familial dilated cardiomyopathy with conduction system defects variably associated with skeletal muscle abnormalities is frequently caused by LMNA gene mutations. METHODS A family affected by cardiac abnormalities, either isolated or variably associated with skeletal muscle compromise, was identified. LMNA gene analysis was applied to all family members. RESULTS A novel intron 5 (c.937-11 C > G) mutation was identified. mRNA transcription analysis was subsequently performed, and cDNA was obtained from mutated patients. It displayed an aberrant splice product featuring the insertion of 40 nucleotides from intron 5, leading to a frameshift. Computational predictions identified a cryptic splice site 40 bp upstream from the canonical site; this alternative splicing event was elicited by intronic mutation, which seems to interfere with the polypyrimidine tract of the canonical site. CONCLUSIONS We have described the first mutation on the LMNA gene interfering with the polypyrimidine tract. Our findings underline the importance of including introns in the search for mutations.
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Affiliation(s)
- Nicola Carboni
- Neuromuscular Unit, Multiple Sclerosis Centre, University of Cagliari, Via Is Guaddazonis 2, Cagliari 09124, Sardinia, Italy.
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Pérez B, Rodríguez-Pascau L, Vilageliu L, Grinberg D, Ugarte M, Desviat LR. Present and future of antisense therapy for splicing modulation in inherited metabolic disease. J Inherit Metab Dis 2010; 33:397-403. [PMID: 20577904 DOI: 10.1007/s10545-010-9135-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 05/12/2010] [Accepted: 05/17/2010] [Indexed: 12/28/2022]
Abstract
The number of mutations identified deep in introns which activate or create novel splice sites resulting in pathogenic pseudoexon inclusion in mRNA continues to grow for inherited metabolic disease (IMD) and other human genetic diseases. A common characteristic is that the native splice sites remain intact thus retaining the potential for normal splicing. Antisense oligonucleotides (AO) have been shown to modulate the splicing pattern by steric hindrance of the recognition and binding of the splicing apparatus to the selected sequences. In the case of pseudoexons, AO force the use of the natural splice sites, recovering normally spliced transcripts encoding functional protein. This review summarizes the present knowledge of antisense splicing modulation as a molecular therapy approach for pseudoexon-activating mutations, with a focus in IMD. Although the feasibility of treatment for patients with IMD has yet to be proven, it appears to be clinically promising, as positive results have been reported in cellular and animal models of disease, and antisense therapy for splicing modulation is currently in the clinical trials phase for Duchenne muscular dystrophy patients. Here, we review the most recent advances in AO stability, targeting and delivery, and other issues to be considered for an effective treatment in the clinical setting. Although the number of patients who can be potentially treated is low for each IMD, it represents an excellent therapeutical option as a type of personalized molecular medicine which is especially relevant for diseases for which there is, to date, no efficient treatment.
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Affiliation(s)
- Belen Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, 28049, Madrid, Spain
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Dhir A, Buratti E. Alternative splicing: role of pseudoexons in human disease and potential therapeutic strategies. FEBS J 2010; 277:841-55. [PMID: 20082636 DOI: 10.1111/j.1742-4658.2009.07520.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
What makes a nucleotide sequence an exon (or an intron) is a question that still lacks a satisfactory answer. Indeed, most eukaryotic genes are full of sequences that look like perfect exons, but which are nonetheless ignored by the splicing machinery (hence the name 'pseudoexons'). The existence of these pseudoexons has been known since the earliest days of splicing research, but until recently the tendency has been to view them as an interesting, but rather rare, curiosity. In recent years, however, the importance of pseudoexons in regulating splicing processes has been steadily revalued. Even more importantly, clinically oriented screening studies that search for splicing mutations are beginning to uncover a situation where aberrant pseudoexon inclusion as a cause of human disease is more frequent than previously thought. Here we aim to provide a review of the mechanisms that lead to pseudoexon activation in human genes and how the various cis- and trans-acting cellular factors regulate their inclusion. Moreover, we list the potential therapeutic approaches that are being tested with the aim of inhibiting their inclusion in the final mRNA molecules.
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Affiliation(s)
- Ashish Dhir
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Vorechovsky I. Transposable elements in disease-associated cryptic exons. Hum Genet 2009; 127:135-54. [PMID: 19823873 DOI: 10.1007/s00439-009-0752-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/27/2009] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon-intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.
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Affiliation(s)
- Igor Vorechovsky
- Division of Human Genetics, University of Southampton School of Medicine, MP808, Tremona Road, Southampton SO16 6YD, UK.
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Divina P, Kvitkovicova A, Buratti E, Vorechovsky I. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet 2009; 17:759-65. [PMID: 19142208 DOI: 10.1038/ejhg.2008.257] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mutations that affect splicing of precursor messenger RNAs play a major role in the development of hereditary diseases. Most splicing mutations have been found to eliminate GT or AG dinucleotides that define the 5' and 3' ends of introns, leading to exon skipping or cryptic splice-site activation. Although accurate description of the mis-spliced transcripts is critical for predicting phenotypic consequences of these alterations, their exact nature in affected individuals cannot often be determined experimentally. Using a comprehensive collection of exons that sustained cryptic splice-site activation or were skipped as a result of splice-site mutations, we have developed a multivariate logistic discrimination procedure that distinguishes the two aberrant splicing outcomes from DNA sequences. The new algorithm was validated using an independent sample of exons and implemented as a free online utility termed CRYP-SKIP (http://www.dbass.org.uk/cryp-skip/). The web application takes up one or more mutated alleles, each consisting of one exon and flanking intronic sequences, and provides a list of important predictor variables and their values, the overall probability of activating cryptic splice vs exon skipping, and the location and intrinsic strength of predicted cryptic splice sites in the input sequence. These results will facilitate phenotypic prediction of splicing mutations and provide further insights into splicing enhancer and silencer elements and their relative importance for splice-site selection in vivo.
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Affiliation(s)
- Petr Divina
- Division of Human Genetics, University of Southampton School of Medicine, Southampton, UK
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