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Shen A, Hencel K, Parker M, Scott R, Skukan R, Adesina A, Metheringham C, Miska E, Nam Y, Haerty W, Simpson G, Akay A. U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs. Nucleic Acids Res 2024; 52:9139-9160. [PMID: 38808663 PMCID: PMC11347140 DOI: 10.1093/nar/gkae447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 05/30/2024] Open
Abstract
pre-mRNA splicing is a critical feature of eukaryotic gene expression. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that the conserved U6 snRNA m6A methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of METT-10 in C. elegans and METTL16 in humans primarily leads to alternative splicing at 5' splice sites with an adenosine at +4 position. In addition, METT-10 is required for splicing of weak 3' cis- and trans-splice sites. We identified a significant overlap between METT-10 and the conserved splicing factor SNRNP27K in regulating 5' splice sites with +4A. Finally, we show that editing endogenous 5' splice site +4A positions to +4U restores splicing to wild-type positions in a mett-10 mutant background, supporting a direct role for U6 snRNA m6A modification in 5' splice site recognition. We conclude that the U6 snRNA m6A modification is important for accurate and efficient pre-mRNA splicing.
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Affiliation(s)
- Aykut Shen
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Katarzyna Hencel
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Matthew T Parker
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Robyn Scott
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roberta Skukan
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | | | | | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge CB2 1QN, UK
| | - Yunsun Nam
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wilfried Haerty
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gordon G Simpson
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, DD2 5DA, UK
| | - Alper Akay
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
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2
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Elaraby NM, Ahmed HA, Dawoud H, Ashaat NA, Azmy A, Galal ER, Elhusseny Y, Awady HE, Metwally AM, Ashaat EA. Clinical and molecular characterization of myotonia congenita using whole-exome sequencing in Egyptian patients. Mol Biol Rep 2024; 51:766. [PMID: 38877370 DOI: 10.1007/s11033-024-09646-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/16/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Myotonia Congenita (MC) is a rare disease classified into two major forms; Thomsen and Becker disease caused by mutations in the CLCN1 gene, which affects muscle excitability and encodes voltage-gated chloride channels (CLC-1). While, there are no data regarding the clinical and molecular characterization of myotonia in Egyptian patients. METHODS Herein, we report seven Egyptian MC patients from six unrelated families. Following the clinical diagnosis, whole-exome sequencing (WES) was performed for genetic diagnosis. Various in silico prediction tools were utilized to interpret variant pathogenicity. The candidate variants were then validated using Sanger sequencing technique. RESULTS In total, seven cases were recruited. The ages at the examination were ranged from eight months to nineteen years. Clinical manifestations included warm-up phenomenon, hand grip, and percussion myotonia. Electromyography was performed in all patients and revealed myotonic discharges. Molecular genetic analysis revealed five different variants. Of them, we identified two novel variants in the CLCN1 gene ( c.1583G > C; p.Gly528Ala and c.2203_2216del;p.Thr735ValfsTer57) and three known variants in the CLCN1 and SCN4A gene. According to in silico tools, the identified novel variants were predicted to have deleterious effects. CONCLUSIONS As the first study to apply WES among Egyptian MC patients, our findings reported two novel heterozygous variants that expand the CLCN1 mutational spectrum for MC diagnosis. These results further confirm that genetic testing is essential for early diagnosis of MC, which affects follow-up treatment and prognostic assessment in clinical practice.
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Affiliation(s)
- Nesma M Elaraby
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Dokki, Cairo, Egypt.
| | - Hoda A Ahmed
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Heba Dawoud
- Pediatric Department, Tanta University, Gharbia, Egypt
| | - Neveen A Ashaat
- Professor of Human Genetics, Ain Shams University, Cairo, Egypt
| | - Ashraf Azmy
- Child Health Department, Medical Research and Clinical Studies Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Eman Reda Galal
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Yasmine Elhusseny
- Lecturer of Medical Biochemistry and Molecular Biology, School of Medicine, Newgiza University, Giza, Egypt
| | - Heba El Awady
- Pediatric Department, Fayoum University Hospitals, Fayoum, Egypt
| | - Ammal M Metwally
- Community Medicine Research Department/Medical Research, Clinical Studies Institute/National Research Centre (Affiliation ID: 60014618), Dokki, Cairo, Egypt
| | - Engy A Ashaat
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
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3
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Mutation spectrum and health status in skeletal muscle channelopathies in Japan. Neuromuscul Disord 2020; 30:546-553. [PMID: 32660787 DOI: 10.1016/j.nmd.2020.06.001] [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: 10/07/2019] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 11/21/2022]
Abstract
Skeletal muscle channelopathies, including non-dystrophic myotonia and periodic paralysis, are rare hereditary disorders caused by mutations of various ion channel genes. To define the frequency of associated mutations of skeletal muscle channelopathies in Japan, clinical and genetic data of two academic institutions, which provides genetic analysis service, were reviewed. Of 105 unrelated pedigrees genetically confirmed, 66 pedigrees were non-dystrophic myotonias [CLCN1 (n = 30) and SCN4A (n = 36)], 11 were hyperkalemic periodic paralysis (SCN4A), and 28 were hypokalemic periodic paralysis [CACNA1S (n = 16) and SCN4A (n = 12)]. Of the 30 families with myotonia congenita, dominant form (Thomsen type) consisted 67%, and unique mutations, A298T, P480T, T539A, and M560T, not found in Western countries, were commonly identified in CLCN1. Hypokalemic periodic paralysis caused by SCN4A mutations consisted 43% in Japan, which was much higher than previous reports. Furthermore, the quality of life of the patients was assessed using the patient-reported outcome measures, SF-36 and INQoL, for 41 patients. This study indicated that the etiology of skeletal muscle channelopathies in Japan was not identical to previous reports from Western countries, and provided crucial information for genetics as well as future therapeutic interventions.
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Frey K, Pucker B. Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites. Cells 2020; 9:E458. [PMID: 32085510 PMCID: PMC7072748 DOI: 10.3390/cells9020458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 11/17/2022] Open
Abstract
Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5' end and AG at the 3' end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations, which have been known for years. Recently, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here, we expand systematic investigations of non-canonical splice site combinations in plants across eukaryotes by analyzing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences, such as an apparently increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts are a likely explanation for this observation, thus indicating annotation errors. In addition, high numbers of GA-AG splice site combinations were observed in Eurytemoraaffinis and Oikopleuradioica. A variant in one U1 small nuclear RNA (snRNA) isoform might allow the recognition of GA as a 5' splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3' splice site compared to the 5' splice site across animals, fungi, and plants.
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Affiliation(s)
- Katharina Frey
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany;
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615 Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany;
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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Morales F, Pusch M. An Up-to-Date Overview of the Complexity of Genotype-Phenotype Relationships in Myotonic Channelopathies. Front Neurol 2020; 10:1404. [PMID: 32010054 PMCID: PMC6978732 DOI: 10.3389/fneur.2019.01404] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Myotonic disorders are inherited neuromuscular diseases divided into dystrophic myotonias and non-dystrophic myotonias (NDM). The latter is a group of dominant or recessive diseases caused by mutations in genes encoding ion channels that participate in the generation and control of the skeletal muscle action potential. Their altered function causes hyperexcitability of the muscle membrane, thereby triggering myotonia, the main sign in NDM. Mutations in the genes encoding voltage-gated Cl− and Na+ channels (respectively, CLCN1 and SCN4A) produce a wide spectrum of phenotypes, which differ in age of onset, affected muscles, severity of myotonia, degree of hypertrophy, and muscle weakness, disease progression, among others. More than 200 CLCN1 and 65 SCN4A mutations have been identified and described, but just about half of them have been functionally characterized, an approach that is likely extremely helpful to contribute to improving the so-far rather poor clinical correlations present in NDM. The observed poor correlations may be due to: (1) the wide spectrum of symptoms and overlapping phenotypes present in both groups (Cl− and Na+ myotonic channelopathies) and (2) both genes present high genotypic variability. On the one hand, several mutations cause a unique and reproducible phenotype in most patients. On the other hand, some mutations can have different inheritance pattern and clinical phenotypes in different families. Conversely, different mutations can be translated into very similar phenotypes. For these reasons, the genotype-phenotype relationships in myotonic channelopathies are considered complex. Although the molecular bases for the clinical variability present in myotonic channelopathies remain obscure, several hypotheses have been put forward to explain the variability, which include: (a) differential allelic expression; (b) trans-acting genetic modifiers; (c) epigenetic, hormonal, or environmental factors; and (d) dominance with low penetrance. Improvements in clinical tests, the recognition of the different phenotypes that result from particular mutations and the understanding of how a mutation affects the structure and function of the ion channel, together with genetic screening, is expected to improve clinical correlation in NDMs.
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Affiliation(s)
- Fernando Morales
- Instituto de Investigaciones en Salud, Universidad de Costa, San José, Costa Rica
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Wong MS, Kinney JB, Krainer AR. Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell 2018; 71:1012-1026.e3. [PMID: 30174293 DOI: 10.1016/j.molcel.2018.07.033] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/18/2018] [Accepted: 07/23/2018] [Indexed: 02/02/2023]
Abstract
Pre-mRNA splicing is an essential step in the expression of most human genes. Mutations at the 5' splice site (5'ss) frequently cause defective splicing and disease due to interference with the initial recognition of the exon-intron boundary by U1 small nuclear ribonucleoprotein (snRNP), a component of the spliceosome. Here, we use a massively parallel splicing assay (MPSA) in human cells to quantify the activity of all 32,768 unique 5'ss sequences (NNN/GYNNNN) in three different gene contexts. Our results reveal that although splicing efficiency is mostly governed by the 5'ss sequence, there are substantial differences in this efficiency across gene contexts. Among other uses, these MPSA measurements facilitate the prediction of 5'ss sequence variants that are likely to cause aberrant splicing. This approach provides a framework to assess potential pathogenic variants in the human genome and streamline the development of splicing-corrective therapies.
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Affiliation(s)
- Mandy S Wong
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin B Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Mani T, Bourguinat C, Prichard RK. G-protein-coupled receptor genes of Dirofilaria immitis. Mol Biochem Parasitol 2018; 222:6-13. [PMID: 29625152 DOI: 10.1016/j.molbiopara.2018.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/28/2018] [Accepted: 04/02/2018] [Indexed: 12/27/2022]
Abstract
The diversity and uniqueness of nematode heterotrimeric G-protein-coupled receptors (GPCRs) provides impetus for identifying ligands that can be used as therapeutics for treating diseases caused by parasitic nematode infections. In human medicine, GPCRs have represented the largest group of 'drugable' targets exploited in the market today. In the filarial nematode Dirofilaria immitis, which causes heartworm disease, the macrocyclic lactones (ML) have been used as the sole preventatives for more than 25 years and now there is confirmed ML resistance in this parasite. A novel anthelmintic emodepside, with antifilarial activity, can act on a GPCR. In view of the ML resistance, there is an urgent need to identify new drug targets and GPCRs of D. immitis may be promising receptors. Knowledge of polymorphism within the GPCR superfamily is of interest. A total of 127 GPCR genes have been identified, so far, in the genome of D. immitis. Whole genome sequencing data from four ML susceptible and four ML loss of efficacy populations was used to identify 393 polymorphic loci in 35 D. immitis GPCR genes. Out of 57 SNPs in exonic regions, 36 of them caused a change in an amino acid, out of which 2 changed the predicted secondary structure of the protein. Knowledge about GPCR genes and their polymorphism is valuable information for drug design processes. Further studies need to be carried out to more fully understand the implications of each of the SNPs identified by this study.
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Affiliation(s)
- Thangadurai Mani
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Catherine Bourguinat
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Roger K Prichard
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada.
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8
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Polymorphism in ion channel genes of Dirofilaria immitis: Relevant knowledge for future anthelmintic drug design. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2016; 6:343-355. [PMID: 27682347 PMCID: PMC5196487 DOI: 10.1016/j.ijpddr.2016.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/22/2016] [Indexed: 11/24/2022]
Abstract
Dirofilaria immitis, a filarial parasite, causes cardiopulmonary dirofilariasis in dogs, cats and wild canids. The macrocyclic lactone (ML) class of drugs has been used to prevent heartworm infection. There is confirmed ML resistance in D. immitis and thus there is an urgent need to find new anthelmintics that could prevent and/or control the disease. Targeting ion channels of D. immitis for drug design has obvious advantages. These channels, present in the nematode nervous system, control movement, feeding, mating and respond to environmental cues which are necessary for survival of the parasite. Any new drug that targets these ion channels is likely to have a motility phenotype and should act to clear the worms from the host. Many of the successful anthelmintics in the past have targeted these ion channels and receptors. Knowledge about genetic variability of the ion channel and receptor genes should be useful information for drug design as receptor polymorphism may affect responses to a drug. Such information may also be useful for anticipation of possible resistance development. A total of 224 ion channel genes/subunits have been identified in the genome of D. immitis. Whole genome sequencing data of parasites from eight different geographical locations, four from ML-susceptible populations and the other four from ML-loss of efficacy (LOE) populations, were used for polymorphism analysis. We identified 1762 single nucleotide polymorphic (SNP) sites (1508 intronic and 126 exonic) in these 224 ion channel genes/subunits with an overall polymorphic rate of 0.18%. Of the SNPs found in the exon regions, 129 of them caused a non-synonymous type of polymorphism. Fourteen of the exonic SNPs caused a change in predicted secondary structure. A few of the SNPs identified may have an effect on gene expression, function of the protein and resistance selection processes. In the Dirofilaria immitis genome, 126 ion channel genes were identified. Within 126 ion channel genes, 1762 polymorphic loci were identified. Fourteen exonic SNPs caused a change in predicted secondary structure. SNPs may effect gene expression, protein function or resistance selection. D. immitis populations have low genetic variability among ion channel genes.
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Tan J, Ho JXJ, Zhong Z, Luo S, Chen G, Roca X. Noncanonical registers and base pairs in human 5' splice-site selection. Nucleic Acids Res 2016; 44:3908-21. [PMID: 26969736 PMCID: PMC4856993 DOI: 10.1093/nar/gkw163] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/27/2022] Open
Abstract
Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5' splice sites are mainly recognized by canonical base-pairing to the 5' end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5' splice site/U1 helix contributes to the recognition of certain 5' splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5' splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5' splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences.
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Affiliation(s)
- Jiazi Tan
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Jia Xin Jessie Ho
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zhensheng Zhong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Shufang Luo
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Gang Chen
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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10
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Abstract
Familial disorders of skeletal muscle excitability were initially described early in the last century and are now known to be caused by mutations of voltage-gated ion channels. The clinical manifestations are often striking, with an inability to relax after voluntary contraction (myotonia) or transient attacks of severe weakness (periodic paralysis). An essential feature of these disorders is fluctuation of symptoms that are strongly impacted by environmental triggers such as exercise, temperature, or serum K(+) levels. These phenomena have intrigued physiologists for decades, and in the past 25 years the molecular lesions underlying these disorders have been identified and mechanistic studies are providing insights for therapeutic strategies of disease modification. These familial disorders of muscle fiber excitability are "channelopathies" caused by mutations of a chloride channel (ClC-1), sodium channel (NaV1.4), calcium channel (CaV1.1), and several potassium channels (Kir2.1, Kir2.6, and Kir3.4). This review provides a synthesis of the mechanistic connections between functional defects of mutant ion channels, their impact on muscle excitability, how these changes cause clinical phenotypes, and approaches toward therapeutics.
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Affiliation(s)
- Stephen C Cannon
- Department of Physiology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
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Matos L, Canals I, Dridi L, Choi Y, Prata MJ, Jordan P, Desviat LR, Pérez B, Pshezhetsky AV, Grinberg D, Alves S, Vilageliu L. Therapeutic strategies based on modified U1 snRNAs and chaperones for Sanfilippo C splicing mutations. Orphanet J Rare Dis 2014; 9:180. [PMID: 25491247 PMCID: PMC4279800 DOI: 10.1186/s13023-014-0180-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutations affecting RNA splicing represent more than 20% of the mutant alleles in Sanfilippo syndrome type C, a rare lysosomal storage disorder that causes severe neurodegeneration. Many of these mutations are localized in the conserved donor or acceptor splice sites, while few are found in the nearby nucleotides. METHODS In this study we tested several therapeutic approaches specifically designed for different splicing mutations depending on how the mutations affect mRNA processing. For three mutations that affect the donor site (c.234 + 1G > A, c.633 + 1G > A and c.1542 + 4dupA), different modified U1 snRNAs recognizing the mutated donor sites, have been developed in an attempt to rescue the normal splicing process. For another mutation that affects an acceptor splice site (c.372-2A > G) and gives rise to a protein lacking four amino acids, a competitive inhibitor of the HGSNAT protein, glucosamine, was tested as a pharmacological chaperone to correct the aberrant folding and to restore the normal trafficking of the protein to the lysosome. RESULTS Partial correction of c.234 + 1G > A mutation was achieved with a modified U1 snRNA that completely matches the splice donor site suggesting that these molecules may have a therapeutic potential for some splicing mutations. Furthermore, the importance of the splice site sequence context is highlighted as a key factor in the success of this type of therapy. Additionally, glucosamine treatment resulted in an increase in the enzymatic activity, indicating a partial recovery of the correct folding. CONCLUSIONS We have assayed two therapeutic strategies for different splicing mutations with promising results for the future applications.
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Affiliation(s)
- Liliana Matos
- Department of Human Genetics, Research and Development Unit, INSA, Porto, Portugal. .,Department of Biology, Faculty of Sciences, Porto, Portugal.
| | - Isaac Canals
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Larbi Dridi
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada.
| | - Yoo Choi
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada.
| | - Maria João Prata
- Department of Biology, Faculty of Sciences, Porto, Portugal. .,IPATIMUP, Porto, Portugal.
| | - Peter Jordan
- Department of Human Genetics, Research and Development Unit, INSA, Lisbon, Portugal.
| | - Lourdes R Desviat
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Belén Pérez
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Alexey V Pshezhetsky
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada. .,Department of Anatomy and Cell Biology, Faculty of Medicine, McGill University, Montreal, Canada.
| | - Daniel Grinberg
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Sandra Alves
- Department of Human Genetics, Research and Development Unit, INSA, Porto, Portugal.
| | - Lluïsa Vilageliu
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
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The maternal ITPK1 gene polymorphism is associated with neural tube defects in a high-risk Chinese population. PLoS One 2014; 9:e86145. [PMID: 24465924 PMCID: PMC3896452 DOI: 10.1371/journal.pone.0086145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 12/05/2013] [Indexed: 01/05/2023] Open
Abstract
Background Epidemiological surveys and animal studies have revealed that inositol metabolism is associated with NTDs, but the mechanisms are not clear. Inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) is a pivotal regulatory enzyme in inositol metabolic pathway. The objective was to assess the potential impact of the maternal ITPK1 genotypes on the inositol parameter and on the NTD risk in a NTD high-risk area in China. Methodology/Results A case-control study of pregnant women affected with NTDs (n = 200) and controls (n = 320) was carried out. 13 tag SNPs of ITPK1 were selected and genotyped by the Sequenom MassArray system. We found that 4 tag SNPs were statistically significant in spina bifida group (P<0.05). MACH was used to impute the un-genotyped SNPs in ITPK1 locus and showed that 3 meaningful SNPs in the non-coding regions were significant. We also predicted the binding capacity of transcription factors in the positive SNPs using the bioinformatics method and found that only rs3783903 was located in the conserved sequence of activator protein-1 (AP-1). To further study the association between biochemical values and genotypes, maternal plasma inositol hexakisphosphate (IP6) levels were also assessed using LC-MS. The maternal plasma IP6 concentrations in the spina bifida subgroup were 7.1% lower than control (136.67 vs. 147.05 ng mL−1, P<0.05), and significantly lower in rs3783903 GG genotype than others (P<0.05). EMSA showed a different allelic binding capacity of AP-1 in rs3783903, which was affected by an A→G exchange. The RT-PCR suggested the ITPK1 expression was decreased significantly in mutant-type of rs3783903 compared with wild-type in the 60 healthy pregnancies (P<0.05). Conclusions/Significance These results suggested that the maternal rs3783903 of ITPK1 might be associated with spina bifida, and the allele G of rs3783903 might affect the binding of AP-1 and the decrease of maternal plasma IP6 concentration in this Chinese population.
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Roca X, Krainer AR, Eperon IC. Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev 2013; 27:129-44. [PMID: 23348838 DOI: 10.1101/gad.209759.112] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Splice site selection is fundamental to pre-mRNA splicing and the expansion of genomic coding potential. 5' Splice sites (5'ss) are the critical elements at the 5' end of introns and are extremely diverse, as thousands of different sequences act as bona fide 5'ss in the human transcriptome. Most 5'ss are recognized by base-pairing with the 5' end of the U1 small nuclear RNA (snRNA). Here we review the history of research on 5'ss selection, highlighting the difficulties of establishing how base-pairing strength determines splicing outcomes. We also discuss recent work demonstrating that U1 snRNA:5'ss helices can accommodate noncanonical registers such as bulged duplexes. In addition, we describe the mechanisms by which other snRNAs, regulatory proteins, splicing enhancers, and the relative positions of alternative 5'ss contribute to selection. Moreover, we discuss mechanisms by which the recognition of numerous candidate 5'ss might lead to selection of a single 5'ss and propose that protein complexes propagate along the exon, thereby changing its physical behavior so as to affect 5'ss selection.
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Affiliation(s)
- Xavier Roca
- School of Biological Sciences, Division of Molecular Genetics and Cell Biology, Nanyang Technological University, Singapore.
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14
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Roca X, Akerman M, Gaus H, Berdeja A, Bennett CF, Krainer AR. Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides. Genes Dev 2012; 26:1098-109. [PMID: 22588721 DOI: 10.1101/gad.190173.112] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An established paradigm in pre-mRNA splicing is the recognition of the 5' splice site (5'ss) by canonical base-pairing to the 5' end of U1 small nuclear RNA (snRNA). We recently reported that a small subset of 5'ss base-pair to U1 in an alternate register that is shifted by 1 nucleotide. Using genetic suppression experiments in human cells, we now demonstrate that many other 5'ss are recognized via noncanonical base-pairing registers involving bulged nucleotides on either the 5'ss or U1 RNA strand, which we term "bulge registers." By combining experimental evidence with transcriptome-wide free-energy calculations of 5'ss/U1 base-pairing, we estimate that 10,248 5'ss (∼5% of human 5'ss) in 6577 genes use bulge registers. Several of these 5'ss occur in genes with mutations causing genetic diseases and are often associated with alternative splicing. These results call for a redefinition of an essential element for gene expression that incorporates these registers, with important implications for the molecular classification of splicing mutations and for alternative splicing.
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Affiliation(s)
- Xavier Roca
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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15
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Kokunai Y, Goto K, Kubota T, Fukuoka T, Sakoda S, Ibi T, Doyu M, Mochizuki H, Sahashi K, Takahashi MP. A sodium channel myotonia due to a novel SCN4A mutation accompanied by acquired autoimmune myasthenia gravis. Neurosci Lett 2012; 519:67-72. [PMID: 22617007 DOI: 10.1016/j.neulet.2012.05.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/19/2012] [Accepted: 05/07/2012] [Indexed: 10/28/2022]
Abstract
Mutations of the voltage gated sodium channel gene (SCN4A) are responsible for non-dystrophic myotonia including hyperkalemic periodic paralysis, paramyotonia congenita, and sodium channel myotonia, as well as congenital myasthenic syndrome. In vitro functional analyses have demonstrated the non-dystrophic mutants to show a gain-of-function defect of the channel; a disruption of fast inactivation, an enhancement of activation, or both, while the myasthenic mutation presents a loss-of function defect. This report presents a case of non-dystrophic myotonia that is incidentally accompanied with acquired myasthenia. The patient presented a marked warm-up phenomenon of myotonia but the repeated short exercise test suggested mutations of the sodium channel. The genetic analysis identified a novel mutation, G1292D, of SCN4A. A functional study of the mutant channel revealed marked enhancement of activation and slight impairment of fast inactivation, which should induce muscle hyperexcitability. The effects of the alteration of channel function to the myasthenic symptoms were explored by using stimulation of repetitive depolarization pulses. A use-dependent channel inactivation was reduced in the mutant in comparison to normal channel, thus suggesting an opposing effect to myasthenia.
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Affiliation(s)
- Yosuke Kokunai
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
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16
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Abstract
The nondystrophic myotonias and primary periodic paralyses are an important group of genetic muscle diseases characterized by dysfunction of ion channels that regulate membrane excitability. Clinical manifestations vary and include myotonia, hyperkalemic and hypokalemic periodic paralysis, progressive myopathy, and cardiac arrhythmias. The severity of myotonia ranges from severe neonatal presentation causing respiratory compromise through to mild later-onset disease. It remains unclear why the frequency of attacks of paralysis varies greatly or why many patients develop a severe permanent fixed myopathy. Recent detailed characterizations of human genetic mutations in voltage-gated muscle sodium (gene: SCN4A), chloride (gene: CLCN1), calcium (gene: CACNA1S), and inward rectifier potassium (genes: KCNJ2, KCNJ18) channels have resulted in new insights into disease mechanisms, clinical phenotypic variation, and therapeutic options.
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Lehmann-Horn F, Orth M, Kuhn M, Jurkat-Rott K. A novel N440K sodium channel mutation causes myotonia with exercise-induced weakness--exclusion of CLCN1 exon deletion/duplication by MLPA. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2011; 30:133-7. [PMID: 22106717 PMCID: PMC3235863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report a 4-generation Turkish family with 10 affected members presenting with myotonia and potassium- and exercise-induced paralytic attacks. The clinical presentation was neither typical for the chloride channel myotonias Thomsen and Becker nor for the separate sodium channel myotonia entities potassium-aggravated myotonia, paramyotonia congenita, and hyperkalemic periodic paralysis. It is best described by a combination of potassium-aggravated myotonia and hyperkalemic periodic paralysis. We excluded exonic chloride channel mutations including CLCN1 exon deletion/duplication by MLPA. Instead we identified a novel p.N440K sodium channel mutation that is located at the inner end of segment S6 of repeat I. We discuss the genotype phenotype relation.
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Affiliation(s)
- F. Lehmann-Horn
- Address for correspondence: Frank Lehmann-Horn, Division of Neurophysiology, Ulm University, 89081 Ulm, Albert-Einstein-Allee 11, Germany. Tel. +49 731 500 23250. Fax +49 731 500 23260. E-mail:
| | - M. Orth
- Department of Neurology, Ulm University, Ulm, Germany
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