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Cheng W, Hong C, Zeng F, Liu N, Gao H. Sequence variations affect the 5' splice site selection of plant introns. PLANT PHYSIOLOGY 2023; 193:1281-1296. [PMID: 37394939 DOI: 10.1093/plphys/kiad375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 07/04/2023]
Abstract
Introns are noncoding sequences spliced out of pre-mRNAs by the spliceosome to produce mature mRNAs. The 5' ends of introns mostly begin with GU and have a conserved sequence motif of AG/GUAAGU that could base-pair with the core sequence of U1 snRNA of the spliceosome. Intriguingly, ∼ 1% of introns in various eukaryotic species begin with GC. This occurrence could cause misannotation of genes; however, the underlying splicing mechanism is unclear. We analyzed the sequences around the intron 5' splice site (ss) in Arabidopsis (Arabidopsis thaliana) and found sequences at the GC intron ss are much more stringent than those of GT introns. Mutational analysis at various positions of the intron 5' ss revealed that although mutations impair base pairing, different mutations at the same site can have different effects, suggesting that steric hindrance also affects splicing. Moreover, mutations of 5' ss often activate a hidden ss nearby. Our data suggest that the 5' ss is selected via a competition between the major ss and the nearby minor ss. This work not only provides insights into the splicing mechanism of intron 5' ss but also improves the accuracy of gene annotation and the study of the evolution of intron 5' ss.
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Affiliation(s)
- Wenzhen Cheng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Conghao Hong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Fang Zeng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Nan Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hongbo Gao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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2
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Optimization of Bifunctional Antisense Oligonucleotides for Regulation of Mutually Exclusive Alternative Splicing of PKM Gene. Molecules 2022; 27:molecules27175682. [PMID: 36080449 PMCID: PMC9457596 DOI: 10.3390/molecules27175682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
Oligonucleotide tools, as modulators of alternative splicing, have been extensively studied, giving a rise to new therapeutic approaches. In this article, we report detailed research on the optimization of bifunctional antisense oligonucleotides (BASOs), which are targeted towards interactions with hnRNP A1 protein. We performed a binding screening assay, Kd determination, and UV melting experiments to select sequences that can be used as a high potency binding platform for hnRNP A1. Newly designed BASOs were applied to regulate the mutually exclusive alternative splicing of the PKM gene. Our studies demonstrate that at least three repetitions of regulatory sequence are necessary to increase expression of the PKM1 isoform. On the other hand, PKM2 expression can be inhibited by a lower number of regulatory sequences. Importantly, a novel branched type of BASOs was developed, which significantly increased the efficiency of splicing modulation. Herein, we provide new insights into BASOs design and show, for the first time, the possibility to regulate mutually exclusive alternative splicing via BASOs.
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3
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Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq. NPJ Genom Med 2021; 6:95. [PMID: 34782607 PMCID: PMC8593033 DOI: 10.1038/s41525-021-00258-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is caused by loss-of-function variants in the NF1 gene. Approximately 10% of these variants affect RNA splicing and are either missed by conventional DNA diagnostics or are misinterpreted by in silico splicing predictions. Therefore, a targeted RNAseq-based approach was designed to detect pathogenic RNA splicing and associated pathogenic DNA variants. For this method RNA was extracted from lymphocytes, followed by targeted RNAseq. Next, an in-house developed tool (QURNAs) was used to calculate the enrichment score (ERS) for each splicing event. This method was thoroughly tested using two different patient cohorts with known pathogenic splice-variants in NF1. In both cohorts all 56 normal reference transcript exon splice junctions, 24 previously described and 45 novel non-reference splicing events were detected. Additionally, all expected pathogenic splice-variants were detected. Eleven patients with NF1 symptoms were subsequently tested, three of which have a known NF1 DNA variant with a putative effect on RNA splicing. This effect could be confirmed for all 3. The other eight patients were previously without any molecular confirmation of their NF1-diagnosis. A deep-intronic pathogenic splice variant could now be identified for two of them (25%). These results suggest that targeted RNAseq can be successfully used to detect pathogenic RNA splicing variants in NF1.
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Yang C, Harafuji N, O'Connor AK, Kesterson RA, Watts JA, Majmundar AJ, Braun DA, Lek M, Laricchia KM, Fathy HM, Mane S, Shril S, Hildebrandt F, Guay-Woodford LM. Cystin genetic variants cause autosomal recessive polycystic kidney disease associated with altered Myc expression. Sci Rep 2021; 11:18274. [PMID: 34521872 PMCID: PMC8440558 DOI: 10.1038/s41598-021-97046-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
Mutation of the Cys1 gene underlies the renal cystic disease in the Cys1cpk/cpk (cpk) mouse that phenocopies human autosomal recessive polycystic kidney disease (ARPKD). Cystin, the protein product of Cys1, is expressed in the primary apical cilia of renal ductal epithelial cells. In previous studies, we showed that cystin regulates Myc expression via interaction with the tumor suppressor, necdin. Here, we demonstrate rescue of the cpk renal phenotype by kidney-specific expression of a cystin-GFP fusion protein encoded by a transgene integrated into the Rosa26 locus. In addition, we show that expression of the cystin-GFP fusion protein in collecting duct cells down-regulates expression of Myc in cpk kidneys. Finally, we report the first human patient with an ARPKD phenotype due to homozygosity for a deleterious splicing variant in CYS1. These findings suggest that mutations in Cys1/CYS1 cause an ARPKD phenotype in mouse and human, respectively, and that the renal cystic phenotype in the mouse is driven by overexpression of the Myc proto-oncogene.
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Affiliation(s)
- Chaozhe Yang
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Naoe Harafuji
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Amber K O'Connor
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Jacob A Watts
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hanan M Fathy
- Alexandria Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, CT, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lisa M Guay-Woodford
- Center for Translational Research, Children's National Research Institute, 111 Michigan Ave NW, Washington, DC, 20010, USA.
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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Implications of mosaicism in variant interpretation: A case of a de novo homozygous NF1 variant. Eur J Med Genet 2021; 64:104236. [PMID: 33965620 DOI: 10.1016/j.ejmg.2021.104236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/21/2021] [Accepted: 04/28/2021] [Indexed: 11/23/2022]
Abstract
Neurofibromatosis type 1 is a common multisystem autosomal dominant syndrome caused by pathogenic heterozygous variants in the neurofibromin gene (NF1). It is associated with a substantially increased cancer risk. Mosaicism for NF1 has been clinically well-established for "second hit" variants in skin lesions and tumor tissues. Here, we report on a 3-month-old boy with multiple café au lait macules (CAMs) and juvenile myelomonocytic leukemia (JMML) who was found to carry a previously established pathogenic NF1 variant (c.586+5G>A), as revealed by whole-exome sequencing. Surprisingly, however, this variant was detected in the homozygous state in the patient and was absent in the parents and siblings. Deep sequencing of this variant using blood, buccal swabs and skin samples was performed. As expected for an NF1 gene mutation promoting JMML, the variant was detected in 90.6% of the blood DNA reads, in sharp contrast to the mere 5% and 0.74% of reads in the saliva- and skin fibroblast-derived DNA, respectively. Our analysis, therefore, confirmed postzygotic origin of the variant followed by a mitotic event resulting in its homozygosity, although we could not differentiate between the possibilities of a gene conversion and mitotic crossover. Apparently de novo homozygous variants should trigger a careful investigation into mosaicism to achieve accurate interpretation.
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Rauschendorf MA, Zimmer AD, Laut A, Demmer P, Rösler B, Happle R, Sartori S, Fischer J. Homozygous intronic MITF mutation causes severe Waardenburg syndrome type 2A. Pigment Cell Melanoma Res 2018; 32:85-91. [PMID: 30117279 DOI: 10.1111/pcmr.12733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marc-Alexander Rauschendorf
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas D Zimmer
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Astrid Laut
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Demmer
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernd Rösler
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rudolf Happle
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Judith Fischer
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Yadegari H, Biswas A, Akhter MS, Driesen J, Ivaskevicius V, Marquardt N, Oldenburg J. Intron retention resulting from a silent mutation in the VWF gene that structurally influences the 5' splice site. Blood 2016; 128:2144-2152. [PMID: 27543438 PMCID: PMC5161009 DOI: 10.1182/blood-2016-02-699686] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/08/2016] [Indexed: 12/26/2022] Open
Abstract
Disease-associated silent mutations are considered to affect the accurate pre-messenger RNA (mRNA) splicing either by influencing regulatory elements, leading to exon skipping, or by creating a new cryptic splice site. This study describes a new molecular pathological mechanism by which a silent mutation inhibits splicing and leads to intron retention. We identified a heterozygous silent mutation, c.7464C>T, in exon 44 of the von Willebrand factor (VWF) gene in a family with type 1 von Willebrand disease. In vivo and ex vivo transcript analysis revealed an aberrantly spliced transcript, with intron 44 retained in the mRNA, implying disruption of the first catalytic step of splicing at the 5' splice site (5'ss). The abnormal transcript with the retained intronic region coded a truncated protein that lacked the carboxy-terminal end of the VWF protein. Confocal immunofluorescence characterizations of blood outgrowth endothelial cells derived from the patient confirmed the presence of the truncated protein by demonstrating accumulation of VWF in the endoplasmic reticulum. In silico pre-mRNA secondary and tertiary structure analysis revealed that this substitution, despite its distal position from the 5'ss (85 bp downstream), induces cis alterations in pre-mRNA structure that result in the formation of a stable hairpin at the 5'ss. This hairpin sequesters the 5'ss residues involved in U1 small nuclear RNA interactions, thereby inhibiting excision of the pre-mRNA intronic region. This study is the first to show the allosteric-like/far-reaching effect of an exonic variation on pre-mRNA splicing that is mediated by structural changes in the pre-mRNA.
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Affiliation(s)
- Hamideh Yadegari
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Arijit Biswas
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Mohammad Suhail Akhter
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Julia Driesen
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Vytautas Ivaskevicius
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Natascha Marquardt
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
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Wang Z, Lin Y, Qiu L, Zheng D, Yan A, Zeng J, Lan F. Hybrid minigene splicing assay verified the pathogenicity of a novel splice site variant in the dystrophin gene of a Chinese patient with typical Duchenne muscular dystrophy phenotype. ACTA ACUST UNITED AC 2016; 54:1435-40. [DOI: 10.1515/cclm-2015-1042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/15/2016] [Indexed: 12/25/2022]
Abstract
AbstractBackground:Duchenne muscular dystrophy (DMD) is typically caused by disrupting the reading frame of the dystrophin gene: approximately 70%–80% of mutational events are represented by deletions or duplications of one or more exons in the dystrophin gene, and the remaining cases by subtle mutations, including point mutations, small indels, small inversions, and complex small rearrangements. The dystrophin gene is the largest known gene with one of the highest known rates of new mutations.Methods:Deletions and duplications were detected in theDMDgene of the proband by using multiple ligation-dependent probe amplification (MLPA). Targeted next-generation sequencing (NGS) was used in the subtle mutation detection, followed by Sanger sequencing confirmation. The effect of the mutation on the splicing of theDMDgene was assessed by bioinformatics prediction and hybrid minigene splicing assay (HMSA).Results:Neither duplication nor deletion was found in theDMDgene of the proband. While a novel splice site mutation c.6762+1G>C was identified in the proband by NGS and Sanger sequencing, and his mother was heterozygous at the same site. Bioinformatics predicted that the 5′ donor splice site of intron 46 disappeared because of the mutation, which would lead to aberrant splicing and introduce premature stop codon. The HMSA results were in agreement with the prediction.Conclusions:The novel splice site mutation caused DMD in the proband by aberrant splicing. We suggested that combined applications of MLPA, NGS, HMSA and bioinformatics are comprehensive and effective methods for diagnosis and aberrant splicing study of DMD.
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Carroll C, Hunley TE, Guo Y, Cortez D. A novel splice site mutation in SMARCAL1 results in aberrant exon definition in a child with Schimke immunoosseous dysplasia. Am J Med Genet A 2015; 167A:2260-4. [PMID: 25943327 DOI: 10.1002/ajmg.a.37146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/20/2015] [Indexed: 12/30/2022]
Abstract
Schimke Immunoosseous Dysplasia (SIOD) is a rare, autosomal recessive disorder of childhood characterized by spondyloepiphyseal dysplasia, focal segmental glomerulosclerosis and renal failure, T-cell immunodeficiency, and cancer in certain instances. Approximately half of patients with SIOD are reported to have biallelic mutations in SMARCAL1 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin, subfamily a-like 1), which encodes a DNA translocase that localizes to sites of DNA replication and repairs damaged replication forks. We present a novel mutation (NM_014140.3:c.2070+2insT) that results in defective SMARCAL1 mRNA splicing in a child with SIOD. This mutation, within the donor site of intron 12, results in the skipping of exon 12, which encodes part of a critical hinge region connecting the two lobes of the ATPase domain. This mutation was not recognized as deleterious by diagnostic SMARCAL1 sequencing, but discovered through next generation sequencing and found to result in absent SMARCAL1 expression in patient-derived lymphoblasts. The splicing defect caused by this mutation supports the concept of exon definition. Furthermore, it illustrates the need to broaden the search for SMARCAL1 mutations in patients with SIOD lacking coding sequence variants.
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Affiliation(s)
- Clinton Carroll
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee.,Division of Pediatric Hematology/Oncology, Vanderbilt University School of Medicine, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, Tennessee
| | - Tracy E Hunley
- Division of Pediatric Nephrology, Vanderbilt University School of Medicine, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, Tennessee
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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10
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Functional characterization of the spf/ash splicing variation in OTC deficiency of mice and man. PLoS One 2015; 10:e0122966. [PMID: 25853564 PMCID: PMC4390381 DOI: 10.1371/journal.pone.0122966] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/16/2015] [Indexed: 12/27/2022] Open
Abstract
The spf/ash mouse model of ornithine transcarbamylase (OTC) deficiency, a severe urea cycle disorder, is caused by a mutation (c.386G>A; p.R129H) in the last nucleotide of exon 4 of the Otc gene, affecting the 5' splice site and resulting in partial use of a cryptic splice site 48 bp into the adjacent intron. The equivalent nucleotide change and predicted amino acid change is found in OTC deficient patients. Here we have used liver tissue and minigene assays to dissect the transcriptional profile resulting from the "spf/ash" mutation in mice and man. For the mutant mouse, we confirmed liver transcripts corresponding to partial intron 4 retention by the use of the c.386+48 cryptic site and to normally spliced transcripts, with exon 4 always containing the c.386G>A (p.R129H) variant. In contrast, the OTC patient exhibited exon 4 skipping or c.386G>A (p.R129H)-variant exon 4 retention by using the natural or a cryptic splice site at nucleotide position c.386+4. The corresponding OTC tissue enzyme activities were between 3-6% of normal control in mouse and human liver. The use of the cryptic splice sites was reproduced in minigenes carrying murine or human mutant sequences. Some normally spliced transcripts could be detected in minigenes in both cases. Antisense oligonucleotides designed to block the murine cryptic +48 site were used in minigenes in an attempt to redirect splicing to the natural site. The results highlight the relevance of in depth investigations of the molecular mechanisms of splicing mutations and potential therapeutic approaches. Notably, they emphasize the fact that findings in animal models may not be applicable for human patients due to the different genomic context of the mutations.
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Sobacchi C, Pangrazio A, Lopez AGM, Gomez DPV, Caldana ME, Susani L, Vezzoni P, Villa A. As little as needed: the extraordinary case of a mild recessive osteopetrosis owing to a novel splicing hypomorphic mutation in the TCIRG1 gene. J Bone Miner Res 2014; 29:1646-50. [PMID: 24535816 PMCID: PMC4258090 DOI: 10.1002/jbmr.2203] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/23/2014] [Accepted: 02/09/2014] [Indexed: 01/22/2023]
Abstract
Mutations in the TCIRG1 gene, coding for a subunit of the osteoclast proton pump, are responsible for more than 50% of cases of human malignant autosomal recessive osteopetrosis (ARO), a rare inherited bone disease with increased bone density owing to a failure in bone resorption. A wide variety of mutations has been described, including missense, nonsense, small deletions/insertions, splice-site mutations, and large genomic deletions, all leading to a similar severe presentation. So far, to the best of our knowledge, no report of a mild phenotype owing to recessive TCIRG1 mutations is present neither in our series of more than 100 TCIRG1-dependent ARO patients nor in the literature. Here we describe an 8-year-old patient referred to us with a clinical diagnosis of ARO, based on radiological findings; of note, no neurological or hematological defects were present in this girl. Surprisingly, we identified a novel nucleotide change in intron 15 of the TCIRG1 gene at the homozygous state, leading to the production of multiple aberrant transcripts, but also, more importantly, of a limited amount of the normal transcript. Our results show that a low level of normal TCIRG1 protein can dampen the clinical presentation of TCIRG1-dependent ARO. On this basis, a small amount of protein might be sufficient to rescue, at least partially, the severe ARO phenotype, and this is particularly important when gene therapy approaches are considered. In addition, we would also recommend that the TCIRG1 gene be included in the molecular diagnosis of mild forms of human ARO.
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Affiliation(s)
- Cristina Sobacchi
- Unitá Operativa di Supporto (UOS)/Institute of Genetic and Biomedical Research (IRGB), Milan Unit, National Research Council (CNR), Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Italy
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12
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Fletcher S, Meloni PL, Johnsen RD, Wong BL, Muntoni F, Wilton SD. Antisense suppression of donor splice site mutations in the dystrophin gene transcript. Mol Genet Genomic Med 2013; 1:162-73. [PMID: 24498612 PMCID: PMC3865583 DOI: 10.1002/mgg3.19] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 12/02/2022] Open
Abstract
We describe two donor splice site mutations, affecting dystrophin exons 16 and 45 that led to Duchenne muscular dystrophy (DMD), through catastrophic inactivation of the mRNA. These gene lesions unexpectedly resulted in the retention of the downstream introns, thereby increasing the length of the dystrophin mRNA by 20.2 and 36 kb, respectively. Splice-switching antisense oligomers targeted to exon 16 excised this in-frame exon and the following intron from the patient dystrophin transcript very efficiently in vitro, thereby restoring the reading frame and allowing synthesis of near-normal levels of a putatively functional dystrophin isoform. In contrast, targeting splice-switching oligomers to exon 45 in patient cells promoted only modest levels of an out-of-frame dystrophin transcript after transfection at high oligomer concentrations, whereas dual targeting of exons 44 and 45 or 45 and 46 resulted in more efficient exon skipping, with concomitant removal of intron 45. The splice site mutations reported here appear highly amenable to antisense oligomer intervention. We suggest that other splice site mutations may need to be evaluated for oligomer interventions on a case-by-case basis.
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Affiliation(s)
- Sue Fletcher
- Centre for Comparative Genomics, Murdoch University South St, 6150, Perth, Western Australia, Australia ; Centre for Neuromuscular and Neurological Disorders, University of Western Australia Perth 6009, Western Australia, Australia
| | - Penny L Meloni
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia Perth 6009, Western Australia, Australia
| | - Russell D Johnsen
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia Perth 6009, Western Australia, Australia
| | - Brenda L Wong
- Department of Pediatrics, Cincinnati Children's Hospital Medical Centre and University of Cincinnati College of Medicine Cincinnati, 45229-3039, Ohio
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, University College London Institute of Child Health London London, WC1N 1EH, United Kingdom
| | - Stephen D Wilton
- Centre for Comparative Genomics, Murdoch University South St, 6150, Perth, Western Australia, Australia ; Centre for Neuromuscular and Neurological Disorders, University of Western Australia Perth 6009, Western Australia, Australia
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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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De Conti L, Baralle M, Buratti E. Exon and intron definition in pre-mRNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:49-60. [DOI: 10.1002/wrna.1140] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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