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Bakhtiar D, Vorechovsky I. Copper-binding proteins and exonic splicing enhancers and silencers. Metallomics 2024; 16:mfae023. [PMID: 38692844 PMCID: PMC11097207 DOI: 10.1093/mtomcs/mfae023] [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: 02/20/2024] [Accepted: 04/21/2024] [Indexed: 05/03/2024]
Abstract
Eukaryotic DNA codes not only for proteins but contains a wealth of information required for accurate splicing of messenger RNA precursors and inclusion of constitutively or alternatively spliced exons in mature transcripts. This "auxiliary" splicing code has been characterized as exonic splicing enhancers and silencers (ESE and ESS). The exact interplay between protein and splicing codes is, however, poorly understood. Here, we show that exons encoding copper-coordinating amino acids in human cuproproteins lack ESEs and/or have an excess of ESSs, yet RNA sequencing and expressed sequence tags data show that they are more efficiently included in mature transcripts by the splicing machinery than average exons. Their largely constitutive inclusion in messenger RNA is facilitated by stronger splice sites, including polypyrimidine tracts, consistent with an important role of the surrounding intron architecture in ensuring high expression of metal-binding residues during evolution. ESE/ESS profiles of codons and entire exons that code for copper-coordinating residues were very similar to those encoding residues that coordinate zinc but markedly different from those that coordinate calcium. Together, these results reveal how the traditional and auxiliary splicing motifs responded to constraints of metal coordination in proteins.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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2
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Tokatly Latzer I, Roullet JB, Afshar-Saber W, Lee HHC, Bertoldi M, McGinty GE, DiBacco ML, Arning E, Tsuboyama M, Rotenberg A, Opladen T, Jeltsch K, García-Cazorla À, Juliá-Palacios N, Gibson KM, Sahin M, Pearl PL. Clinical and molecular outcomes from the 5-Year natural history study of SSADH Deficiency, a model metabolic neurodevelopmental disorder. J Neurodev Disord 2024; 16:21. [PMID: 38658850 PMCID: PMC11044349 DOI: 10.1186/s11689-024-09538-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Succinic semialdehyde dehydrogenase deficiency (SSADHD) represents a model neurometabolic disease at the fulcrum of translational research within the Boston Children's Hospital Intellectual and Developmental Disabilities Research Centers (IDDRC), including the NIH-sponsored natural history study of clinical, neurophysiological, neuroimaging, and molecular markers, patient-derived induced pluripotent stem cells (iPSC) characterization, and development of a murine model for tightly regulated, cell-specific gene therapy. METHODS SSADHD subjects underwent clinical evaluations, neuropsychological assessments, biochemical quantification of γ-aminobutyrate (GABA) and related metabolites, electroencephalography (standard and high density), magnetoencephalography, transcranial magnetic stimulation, magnetic resonance imaging and spectroscopy, and genetic tests. This was parallel to laboratory molecular investigations of in vitro GABAergic neurons derived from induced human pluripotent stem cells (hiPSCs) of SSADHD subjects and biochemical analyses performed on a versatile murine model that uses an inducible and reversible rescue strategy allowing on-demand and cell-specific gene therapy. RESULTS The 62 SSADHD subjects [53% females, median (IQR) age of 9.6 (5.4-14.5) years] included in the study had a reported symptom onset at ∼ 6 months and were diagnosed at a median age of 4 years. Language developmental delays were more prominent than motor. Autism, epilepsy, movement disorders, sleep disturbances, and various psychiatric behaviors constituted the core of the disorder's clinical phenotype. Lower clinical severity scores, indicating worst severity, coincided with older age (R= -0.302, p = 0.03), as well as age-adjusted lower values of plasma γ-aminobutyrate (GABA) (R = 0.337, p = 0.02) and γ-hydroxybutyrate (GHB) (R = 0.360, p = 0.05). While epilepsy and psychiatric behaviors increase in severity with age, communication abilities and motor function tend to improve. iPSCs, which were differentiated into GABAergic neurons, represent the first in vitro neuronal model of SSADHD and express the neuronal marker microtubule-associated protein 2 (MAP2), as well as GABA. GABA-metabolism in induced GABAergic neurons could be reversed using CRISPR correction of the pathogenic variants or mRNA transfection and SSADHD iPSCs were associated with excessive glutamatergic activity and related synaptic excitation. CONCLUSIONS Findings from the SSADHD Natural History Study converge with iPSC and animal model work focused on a common disorder within our IDDRC, deepening our knowledge of the pathophysiology and longitudinal clinical course of a complex neurodevelopmental disorder. This further enables the identification of biomarkers and changes throughout development that will be essential for upcoming targeted trials of enzyme replacement and gene therapy.
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Affiliation(s)
- Itay Tokatly Latzer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
- School of Medicine, Faculty of Medical and Health Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Jean-Baptiste Roullet
- Department of Pharmacotherapy, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Wardiya Afshar-Saber
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Henry H C Lee
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Gabrielle E McGinty
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Melissa L DiBacco
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Erland Arning
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Melissa Tsuboyama
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Alexander Rotenberg
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Thomas Opladen
- Division of Neuropediatrics & Metabolic Medicine, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Kathrin Jeltsch
- Division of Neuropediatrics & Metabolic Medicine, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Àngels García-Cazorla
- Neurometabolic Unit, Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Natalia Juliá-Palacios
- Neurometabolic Unit, Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - K Michael Gibson
- Department of Pharmacotherapy, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Phillip L Pearl
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA.
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3
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Bakhtiar D, Vondraskova K, Pengelly RJ, Chivers M, Kralovicova J, Vorechovsky I. Exonic splicing code and coordination of divalent metals in proteins. Nucleic Acids Res 2024; 52:1090-1106. [PMID: 38055834 PMCID: PMC10853796 DOI: 10.1093/nar/gkad1161] [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: 06/16/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving-Williams series, a universal order of relative stabilities of metal-organic complexes. We show that exons encoding Zn2+-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca2+. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position -3 relative to 3' splice junctions. However, both Ca2+ and Zn2+ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon-intron architecture to ensure adequate metalloprotein expression.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Katarina Vondraskova
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Martin Chivers
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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4
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Perchlik M, Sasse A, Mostafavi S, Fields S, Cuperus JT. Impact on splicing in Saccharomyces cerevisiae of random 50-base sequences inserted into an intron. RNA (NEW YORK, N.Y.) 2023; 30:52-67. [PMID: 37879864 PMCID: PMC10726166 DOI: 10.1261/rna.079752.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023]
Abstract
Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing-5' and 3' splice sites and a branchpoint-are especially well-characterized in Saccharomyces cerevisiae, but our understanding of additional intron features that impact splicing in this organism is incomplete, due largely to its small number of introns. To overcome this limitation, we constructed a library in S. cerevisiae of random 50-nt (N50) elements individually inserted into the intron of a reporter gene and quantified canonical splicing and the use of cryptic splice sites by sequencing analysis. More than 70% of approximately 140,000 N50 elements reduced splicing by at least 20%. N50 features, including higher GC content, presence of GU repeats, and stronger predicted secondary structure of its pre-mRNA, correlated with reduced splicing efficiency. A likely basis for the reduced splicing of such a large proportion of variants is the formation of RNA structures that pair N50 bases-such as the GU repeats-with other bases specifically within the reporter pre-mRNA analyzed. However, multiple models were unable to explain more than a small fraction of the variance in splicing efficiency across the library, suggesting that complex nonlinear interactions in RNA structures are not accurately captured by RNA structure prediction methods. Our results imply that the specific context of a pre-mRNA may determine the bases allowable in an intron to prevent secondary structures that reduce splicing. This large data set can serve as a resource for further exploration of splicing mechanisms.
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Affiliation(s)
- Molly Perchlik
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Alexander Sasse
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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5
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Krzywinska E, Ribeca P, Ferretti L, Hammond A, Krzywinski J. A novel factor modulating X chromosome dosage compensation in Anopheles. Curr Biol 2023; 33:4697-4703.e4. [PMID: 37774706 DOI: 10.1016/j.cub.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 10/01/2023]
Abstract
Dosage compensation (DC), a process countering chromosomal imbalance in individuals with heteromorphic sex chromosomes, has been molecularly characterized only in mammals, Caenorhabditis elegans, and fruit flies.1 In Drosophila melanogaster males, it is achieved by an approximately 2-fold hypertranscription of the monosomic X chromosome mediated by the MSL complex.2,3 The complex is not assembled on female X chromosomes because production of its key protein MSL-2 is prevented due to intron retention and inhibition of translation by Sex-lethal, a female-specific protein operating at the top of the sex determination pathway.4 It remains unclear how DC is mechanistically regulated in other insects. In the malaria mosquito Anopheles gambiae, an approximately 2-fold hypertranscription of the male X also occurs5 by a yet-unknown molecular mechanism distinct from that in D. melanogaster.6 Here we show that a male-specifically spliced gene we call 007, which arose by a tandem duplication in the Anopheles ancestral lineage, is involved in the control of DC in males. Homozygous 007 knockouts lead to a global downregulation of the male X, phenotypically manifested by a slower development compared to wild-type mosquitoes or mutant females-however, without loss of viability or fertility. In females, a 007 intron retention promoted by the sex determination protein Femaleless, known to prevent hypertranscription from both X chromosomes,7 introduces a premature termination codon apparently rendering the female transcripts non-productive. In addition to providing a unique perspective on DC evolution, the 007, with its conserved properties, may represent an important addition to a genetic toolbox for malaria vector control.
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Affiliation(s)
| | - Paolo Ribeca
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; National Infection Service, UK Health Security Agency, Colindale Avenue, London NW9 5EQ, UK
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Andrew Hammond
- Department of Life Sciences, Imperial College, Exhibition Road, London SW7 2AZ, UK; Biocentis, S.r.l., Via Mazzieri, 05100 Terni, Italy
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Joudaki A, Takeda JI, Masuda A, Ode R, Fujiwara K, Ohno K. FexSplice: A LightGBM-Based Model for Predicting the Splicing Effect of a Single Nucleotide Variant Affecting the First Nucleotide G of an Exon. Genes (Basel) 2023; 14:1765. [PMID: 37761905 PMCID: PMC10531444 DOI: 10.3390/genes14091765] [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: 08/02/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Single nucleotide variants (SNVs) affecting the first nucleotide G of an exon (Fex-SNVs) identified in various diseases are mostly recognized as missense or nonsense variants. Their effect on pre-mRNA splicing has been seldom analyzed, and no curated database is available. We previously reported that Fex-SNVs affect splicing when the length of the polypyrimidine tract is short or degenerate. However, we cannot readily predict the splicing effects of Fex-SNVs. We here scrutinized the available literature and identified 106 splicing-affecting Fex-SNVs based on experimental evidence. We similarly identified 106 neutral Fex-SNVs in the dbSNP database with a global minor allele frequency (MAF) of more than 0.01 and less than 0.50. We extracted 115 features representing the strength of splicing cis-elements and developed machine-learning models with support vector machine, random forest, and gradient boosting to discriminate splicing-affecting and neutral Fex-SNVs. Gradient boosting-based LightGBM outperformed the other two models, and the length and nucleotide compositions of the polypyrimidine tract played critical roles in the discrimination. Recursive feature elimination showed that the LightGBM model using 15 features achieved the best performance with an accuracy of 0.80 ± 0.12 (mean and SD), a Matthews Correlation Coefficient (MCC) of 0.57 ± 0.15, an area under the curve of the receiver operating characteristics curve (AUROC) of 0.86 ± 0.08, and an area under the curve of the precision-recall curve (AUPRC) of 0.87 ± 0.09 using a 10-fold cross-validation. We developed a web service program, named FexSplice that accepts a genomic coordinate either on GRCh37/hg19 or GRCh38/hg38 and returns a predicted probability of aberrant splicing of A, C, and T variants.
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Affiliation(s)
- Atefeh Joudaki
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
| | - Jun-ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
| | - Rikumo Ode
- Department of Materials Science and Engineering, Nagoya University Graduate School of Engineering, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.O.); (K.F.)
| | - Koichi Fujiwara
- Department of Materials Science and Engineering, Nagoya University Graduate School of Engineering, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.O.); (K.F.)
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (A.J.); (J.-i.T.); (A.M.)
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7
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Yıldırım B, Vogl C. Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract. J Evol Biol 2023; 36:1295-1312. [PMID: 37564008 PMCID: PMC10946897 DOI: 10.1111/jeb.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 08/12/2023]
Abstract
Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3' splice signal is characterized by over-representation of pyrimidines. If the over-representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, we hypothesize that AG should be the most under-represented dimer. Through the use of DNA-strand asymmetry patterns, we confirm this prediction in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, we quantify the selection strength acting on each motif. Moreover, our inference and simulation method revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3' splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.
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Affiliation(s)
- Burçin Yıldırım
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Claus Vogl
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
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8
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Georgakopoulos-Soares I, Parada GE, Wong HY, Medhi R, Furlan G, Munita R, Miska EA, Kwok CK, Hemberg M. Alternative splicing modulation by G-quadruplexes. Nat Commun 2022; 13:2404. [PMID: 35504902 PMCID: PMC9065059 DOI: 10.1038/s41467-022-30071-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms are incompletely understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold near splice junctions. The importance of G4s in RNA is emphasised by a higher enrichment for the non-template strand. RNA-seq data from mouse and human neurons reveals an enrichment of G4s at exons that were skipped following depolarisation induced by potassium chloride. We validate the formation of stable RNA G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Moreover, we find that sQTLs are enriched at G4s, and a minigene experiment provides further support for their role in promoting exon inclusion. Analysis of >1,800 high-throughput experiments reveals multiple RNA binding proteins associated with G4s. Finally, exploration of G4 motifs across eleven species shows strong enrichment at splice sites in mammals and birds, suggesting an evolutionary conserved splice regulatory mechanism. Here the authors shows that G-quadruplexes, non-canonical DNA/RNA structures, can have a direct impact on alternative splicing and that binding of splicing regulators is affected by their presence.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Guillermo E Parada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5A 1A8, Canada
| | - Hei Yuen Wong
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ragini Medhi
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Giulia Furlan
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Eric A Miska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. .,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK. .,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
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9
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Zeng T, Li YI. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol 2022; 23:103. [PMID: 35449021 PMCID: PMC9022248 DOI: 10.1186/s13059-022-02664-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 04/04/2022] [Indexed: 11/26/2022] Open
Abstract
Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pangolin outperforms state-of-the-art methods for predicting RNA splicing on a variety of prediction tasks. Pangolin improves prediction of the impact of genetic variants on RNA splicing, including common, rare, and lineage-specific genetic variation. In addition, Pangolin identifies loss-of-function mutations with high accuracy and recall, particularly for mutations that are not missense or nonsense, demonstrating remarkable potential for identifying pathogenic variants.
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Affiliation(s)
- Tony Zeng
- The College, University of Chicago, Chicago, 60637, IL, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, 60637, IL, USA.
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10
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Sette C, Paronetto MP. Somatic Mutations in Core Spliceosome Components Promote Tumorigenesis and Generate an Exploitable Vulnerability in Human Cancer. Cancers (Basel) 2022; 14:cancers14071827. [PMID: 35406598 PMCID: PMC8997811 DOI: 10.3390/cancers14071827] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary High throughput exome sequencing approaches have disclosed recurrent cancer-associated mutations in spliceosomal components, which drive aberrant pre-mRNA processing events and support the tumor phenotype. At the same time, mutations in spliceosome genes and aberrant splicing regulation establish a selective vulnerability of cancer cells to splicing-targeting approaches, which could be exploited therapeutically. It is conceivable that a better understanding of the mechanisms and roles of abnormal splicing in tumor metabolism will facilitate the development of a novel generation of tumor-targeting drugs. In this review, we describe recent advances in the elucidation of the biological impact and biochemical effects of somatic mutations in core spliceosome components on splicing choices and their associated targetable vulnerabilities. Abstract Alternative pre-mRNA processing enables the production of distinct mRNA and protein isoforms from a single gene, thus greatly expanding the coding potential of eukaryotic genomes and fine-tuning gene expression programs. Splicing is carried out by the spliceosome, a complex molecular machinery which assembles step-wise on mRNA precursors in the nucleus of eukaryotic cells. In the last decade, exome sequencing technologies have allowed the identification of point mutations in genes encoding splicing factors as a recurrent hallmark of human cancers, with higher incidence in hematological malignancies. These mutations lead to production of splicing factors that reduce the fidelity of the splicing process and yield splicing variants that are often advantageous for cancer cells. However, at the same time, these mutations increase the sensitivity of transformed cells to splicing inhibitors, thus offering a therapeutic opportunity for novel targeted strategies. Herein, we review the recent literature documenting cancer-associated mutations in components of the early spliceosome complex and discuss novel therapeutic strategies based on small-molecule spliceosome inhibitors that exhibit strong anti-tumor effects, particularly against cancer cells harboring mutations in spliceosomal components.
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Affiliation(s)
- Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro De Bosis, 6, 00135 Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, IRCCS, Via del Fosso di Fiorano 64, 00143 Rome, Italy
- Correspondence:
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11
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Laine P, Rowell WJ, Paulin L, Kujawa S, Raterman D, Mayhew G, Wendt J, Burgess DL, Partonen T, Paunio T, Auvinen P, Ekholm JM. Alu element in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder. PLoS One 2021; 16:e0261170. [PMID: 34914762 PMCID: PMC8675739 DOI: 10.1371/journal.pone.0261170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Objective We have used long-read single molecule, real-time (SMRT) sequencing to fully characterize a ~12Mb genomic region on chromosome Xq24-q27, significantly linked to bipolar disorder (BD) in an extended family from a genetic sub-isolate. This family segregates BD in at least four generations with 24 affected individuals. Methods We selected 16 family members for targeted sequencing. The selected individuals either carried the disease haplotype, were non-carriers of the disease haplotype, or served as married-in controls. We designed hybrid capture probes enriching for 5-9Kb fragments spanning the entire 12Mb region that were then sequenced to screen for candidate structural variants (SVs) that could explain the increased risk for BD in this extended family. Results Altogether, 201 variants were detected in the critically linked region. Although most of these represented common variants, three variants emerged that showed near-perfect segregation among all BD type I affected individuals. Two of the SVs were identified in or near genes belonging to the RNA Binding Motif Protein, X-Linked (RBMX) gene family—a 330bp Alu (subfamily AluYa5) deletion in intron 3 of the RBMX2 gene and an intergenic 27bp tandem repeat deletion between the RBMX and G protein-coupled receptor 101 (GPR101) genes. The third SV was a 50bp tandem repeat insertion in intron 1 of the Coagulation Factor IX (F9) gene. Conclusions Among the three genetically linked SVs, additional evidence supported the Alu element deletion in RBMX2 as the leading candidate for contributing directly to the disease development of BD type I in this extended family.
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Affiliation(s)
- Pia Laine
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Steve Kujawa
- Pacific Biosciences, Menlo Park, CA, United States of America
| | - Denise Raterman
- Roche Sequencing Solutions, Madison, WI, United States of America
| | - George Mayhew
- Roche Sequencing Solutions, Madison, WI, United States of America
| | - Jennifer Wendt
- Roche Sequencing Solutions, Madison, WI, United States of America
| | | | - Timo Partonen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Tiina Paunio
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jenny M. Ekholm
- Pacific Biosciences, Menlo Park, CA, United States of America
- * E-mail:
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12
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Borao S, Ayté J, Hümmer S. Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing. Int J Mol Sci 2021; 22:ijms222212444. [PMID: 34830325 PMCID: PMC8624252 DOI: 10.3390/ijms222212444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5' and 3' splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.
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Affiliation(s)
- Sonia Borao
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Correspondence: (J.A.); (S.H.)
| | - Stefan Hümmer
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Translational Molecular Pathology, Vall d’Hebron Research Institute (VHIR), CIBERONC, 08035 Barcelona, Spain
- Correspondence: (J.A.); (S.H.)
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13
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Kadri NK, Mapel XM, Pausch H. The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome. Commun Biol 2021; 4:1206. [PMID: 34675361 PMCID: PMC8531310 DOI: 10.1038/s42003-021-02725-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022] Open
Abstract
The branch point sequence is a cis-acting intronic motif required for mRNA splicing. Despite their functional importance, branch point sequences are not routinely annotated. Here we predict branch point sequences in 179,476 bovine introns and investigate their variability using a catalogue of 29.4 million variants detected in 266 cattle genomes. We localize the bovine branch point within a degenerate heptamer "nnyTrAy". An adenine residue at position 6, that acts as branch point, and a thymine residue at position 4 of the heptamer are more strongly depleted for mutations than coding sequences suggesting extreme purifying selection. We provide evidence that mutations affecting these evolutionarily constrained residues lead to alternative splicing. We confirm evolutionary constraints on branch point sequences using a catalogue of 115 million SNPs established from 3,942 human genomes of the gnomAD database.
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Affiliation(s)
- Naveen Kumar Kadri
- grid.5801.c0000 0001 2156 2780Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Xena Marie Mapel
- grid.5801.c0000 0001 2156 2780Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Hubert Pausch
- grid.5801.c0000 0001 2156 2780Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
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14
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A broad analysis of splicing regulation in yeast using a large library of synthetic introns. PLoS Genet 2021; 17:e1009805. [PMID: 34570750 PMCID: PMC8496845 DOI: 10.1371/journal.pgen.1009805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/07/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
RNA splicing is a key process in eukaryotic gene expression, in which an intron is spliced out of a pre-mRNA molecule to eventually produce a mature mRNA. Most intron-containing genes are constitutively spliced, hence efficient splicing of an intron is crucial for efficient regulation of gene expression. Here we use a large synthetic oligo library of ~20,000 variants to explore how different intronic sequence features affect splicing efficiency and mRNA expression levels in S. cerevisiae. Introns are defined by three functional sites, the 5’ donor site, the branch site, and the 3’ acceptor site. Using a combinatorial design of synthetic introns, we demonstrate how non-consensus splice site sequences in each of these sites affect splicing efficiency. We then show that S. cerevisiae splicing machinery tends to select alternative 3’ splice sites downstream of the original site, and we suggest that this tendency created a selective pressure, leading to the avoidance of cryptic splice site motifs near introns’ 3’ ends. We further use natural intronic sequences from other yeast species, whose splicing machineries have diverged to various extents, to show how intron architectures in the various species have been adapted to the organism’s splicing machinery. We suggest that the observed tendency for cryptic splicing is a result of a loss of a specific splicing factor, U2AF1. Lastly, we show that synthetic sequences containing two introns give rise to alternative RNA isoforms in S. cerevisiae, demonstrating that merely a synthetic fusion of two introns might be suffice to facilitate alternative splicing in yeast. Our study reveals novel mechanisms by which introns are shaped in evolution to allow cells to regulate their transcriptome. In addition, it provides a valuable resource to study the regulation of constitutive and alternative splicing in a model organism. RNA splicing is a process in which parts of a new pre-mRNA are spliced out of the mRNA molecule to produce eventually a mature mRNA. Those RNA segments that are spliced out are termed introns, and they are found in most genes in eukaryotic organisms. Hence regulation of this process has a major role in the control of gene expression. The budding yeast S. cerevisiae is a popular model organism for eukaryotic cell biology, but in terms of splicing it differs, as it has only few intron-containing genes. Nevertheless, this species has been used to study basic principles of splicing regulation based on its ~300 introns. Here we used the technology of a large synthetic genetic library to introduce many new intron-containing genes to the yeast genome, to explore splicing regulation at a wider scope than was possible so far. Reassuringly, our results confirm known regulatory mechanisms, and further expand our understanding of splicing regulation, specifically how the yeast splicing machinery interacts with the end of introns, and how through evolution introns have evolved to avoid unwanted misidentifications of this end. We further demonstrate the potential of the yeast splicing machinery to alternatively splice a two-intron gene, which is common in other eukaryotes but rare in yeast. Our work presents a first-of-its-kind resource for the systematic study of splicing in live cells.
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15
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The role of nuclear organization in trans-splicing based expression of heat shock protein 90 in Giardia lamblia. PLoS Negl Trop Dis 2021; 15:e0009810. [PMID: 34559805 PMCID: PMC8494341 DOI: 10.1371/journal.pntd.0009810] [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: 04/07/2021] [Revised: 10/06/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022] Open
Abstract
Hsp90 gene of G. lamblia has a split nature comprising two ORFs separated by 777 kb on chromosome 5. The ORFs of the split gene on chromosome 5 undergo transcription to generate independent pre-mRNAs that join by a unique trans-splicing reaction that remains partially understood. The canonical cis-acting nucleotide elements such as 5'SS-GU, 3'SS-AG, polypyrimidine tract and branch point adenine are present in the independent pre-mRNAs and therefore trans-splicing of Hsp90 must be assisted by spliceosomes in vivo. Using an approach of RNA-protein pull down, we show that an RNA helicase selectively interacts with HspN pre-mRNA. Our experiments involving high resolution chromosome conformation capture technology as well as DNA FISH show that the trans-spliced genes of Giardia are in three-dimensional spatial proximity in the nucleus. Altogether our study provides a glimpse into the in vivo mechanisms involving protein factors as well as chromatin structure to facilitate the unique inter-molecular post-transcriptional stitching of split genes in G. lamblia.
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16
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Dybus A, Kulig H, Yu YH, Lanckriet R, Proskura W, Cheng YH. CRY1 Gene Polymorphism and Racing Performance of Homing Pigeons. Animals (Basel) 2021; 11:2632. [PMID: 34573598 PMCID: PMC8466513 DOI: 10.3390/ani11092632] [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: 08/24/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
Cryptochromes (CRY) are the family of proteins proposed as the putative magnetoreceptor molecules. In birds, among others in pigeons, CRY1 is widely expressed in a retina. Homing pigeons are known for their navigational abilities, and pigeon racing is a popular sport. So, the purpose of this study was to analyze the variability of the nucleotide sequence of the homing pigeon CRY1 gene, spanning the region coding the two amino acids W320 and W374 of Trp-triad, and estimate the relationship between genotypes and the racing performance. Investigations were carried out on 129 pigeons. Analysis of sequencing results indicated the AG to TT change within the seventh intron of CRY1 gene. Genotypes were determined by the forced PCR-RFLP method. The influence of detected polymorphism on the results of racing pigeons in 100-400 km flights was shown. The AG/TT individuals achieved significantly higher (p ≤ 0.05) mean values of ace points (AP) than the AG/AG ones. Regarding the detected nucleotide change localization, the polymorphism may be involved in CRY1 gene expression modulation. The AG to TT change in CRY1 gene may be considered as a potential genetic marker of racing performance in homing pigeons.
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Affiliation(s)
- Andrzej Dybus
- Department of Genetics, West Pomeranian University of Technology, 70-311 Szczecin, Poland;
| | - Hanna Kulig
- Department of Genetics, West Pomeranian University of Technology, 70-311 Szczecin, Poland;
| | - Yu-Hsiang Yu
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (Y.-H.Y.); (Y.-H.C.)
| | | | - Witold Proskura
- Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 71-270 Szczecin, Poland;
| | - Yeong-Hsiang Cheng
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (Y.-H.Y.); (Y.-H.C.)
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17
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Riolo G, Cantara S, Ricci C. What's Wrong in a Jump? Prediction and Validation of Splice Site Variants. Methods Protoc 2021; 4:62. [PMID: 34564308 PMCID: PMC8482176 DOI: 10.3390/mps4030062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a crucial process to enhance gene expression driving organism development. Interestingly, more than 95% of human genes undergo AS, producing multiple protein isoforms from the same transcript. Any alteration (e.g., nucleotide substitutions, insertions, and deletions) involving consensus splicing regulatory sequences in a specific gene may result in the production of aberrant and not properly working proteins. In this review, we introduce the key steps of splicing mechanism and describe all different types of genomic variants affecting this process (splicing variants in acceptor/donor sites or branch point or polypyrimidine tract, exonic, and deep intronic changes). Then, we provide an updated approach to improve splice variants detection. First, we review the main computational tools, including the recent Machine Learning-based algorithms, for the prediction of splice site variants, in order to characterize how a genomic variant interferes with splicing process. Next, we report the experimental methods to validate the predictive analyses are defined, distinguishing between methods testing RNA (transcriptomics analysis) or proteins (proteomics experiments). For both prediction and validation steps, benefits and weaknesses of each tool/procedure are accurately reported, as well as suggestions on which approaches are more suitable in diagnostic rather than in clinical research.
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Affiliation(s)
| | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.)
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18
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Nosková A, Hiltpold M, Janett F, Echtermann T, Fang ZH, Sidler X, Selige C, Hofer A, Neuenschwander S, Pausch H. Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing. Genetics 2021; 217:6041611. [PMID: 33724408 DOI: 10.1093/genetics/iyaa033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed at a semen collection center. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P = 4.22 × 10-15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1: c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Maya Hiltpold
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Fredi Janett
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Echtermann
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Xaver Sidler
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Stefan Neuenschwander
- Animal Genetics, Institute of Agricultural Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
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19
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Lee HHC, Pearl PL, Rotenberg A. Enzyme Replacement Therapy for Succinic Semialdehyde Dehydrogenase Deficiency: Relevance in γ-Aminobutyric Acid Plasticity. J Child Neurol 2021; 36:1200-1209. [PMID: 33624531 PMCID: PMC8382780 DOI: 10.1177/0883073821993000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Succinic semialdehyde dehydrogenase deficiency (SSADHD) is a rare inborn metabolic disorder caused by the functional impairment of SSADH (encoded by the ALDH5A1 gene), an enzyme essential for metabolism of the inhibitory neurotransmitter γ-aminobutyric acid (GABA). In SSADHD, pathologic accumulation of GABA and its metabolite γ-hydroxybutyrate (GHB) results in broad spectrum encephalopathy including developmental delay, ataxia, seizures, and a heightened risk of sudden unexpected death in epilepsy (SUDEP). Proof-of-concept systemic SSADH restoration via enzyme replacement therapy increased survival of SSADH knockout mice, suggesting that SSADH restoration might be a viable intervention for SSADHD. However, before testing enzyme replacement therapy or gene therapy in patients, we must consider its safety and feasibility in the context of early brain development and unique SSADHD pathophysiology. Specifically, a profound use-dependent downregulation of GABAA receptors in SSADHD indicates a risk that any sudden SSADH restoration might diminish GABAergic tone and provoke seizures. In addition, the tight developmental regulation of GABA circuit plasticity might limit the age window when SSADH restoration is accomplished safely. Moreover, given SSADH expressions are cell type-specific, targeted instead of global restoration might be necessary. We therefore describe 3 key parameters for the clinical readiness of SSADH restoration: (1) rate, (2) timing, and (3) cell type specificity. Our work focuses on the construction of a novel SSADHD mouse model that allows "on-demand" SSADH restoration for the systematic investigation of these key parameters. We aim to understand the impacts of specific SSADH restoration protocols on brain physiology, accelerating bench-to-bedside development of enzyme replacement therapy or gene therapy for SSADHD patients.
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Affiliation(s)
- Henry Hing Cheong Lee
- FM Kirby Neurobiology Center, Boston Children’s Hospital,Correspondence: Henry Lee () and Alexander Rotenberg ()
| | | | - Alexander Rotenberg
- FM Kirby Neurobiology Center, Boston Children’s Hospital,Department of Neurology, Boston Children’s Hospital,Correspondence: Henry Lee () and Alexander Rotenberg ()
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20
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Castanotto D, Zhang X, Rüger J, Alluin J, Sharma R, Pirrotte P, Joenson L, Ioannou S, Nelson MS, Vikeså J, Hansen BR, Koch T, Jensen MA, Rossi JJ, Stein CA. A Multifunctional LNA Oligonucleotide-Based Strategy Blocks AR Expression and Transactivation Activity in PCa Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:63-75. [PMID: 33335793 PMCID: PMC7723773 DOI: 10.1016/j.omtn.2020.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023]
Abstract
The androgen receptor (AR) plays a critical role in the development of prostate cancer (PCa) through the activation of androgen-induced cellular proliferation genes. Thus, blocking AR-mediated transcriptional activation is expected to inhibit the growth and spread of PCa. Using tailor-made splice-switching locked nucleic acid (LNA) oligonucleotides (SSOs), we successfully redirected splicing of the AR precursor (pre-)mRNA and destabilized the transcripts via the introduction of premature stop codons. Furthermore, the SSOs simultaneously favored production of the AR45 mRNA in lieu of the full-length AR. AR45 is an AR isoform that can attenuate the activity of both full-length and oncogenic forms of AR by binding to their common N-terminal domain (NTD), thereby blocking their transactivation potential. A large screen was subsequently used to identify individual SSOs that could best perform this dual function. The selected SSOs powerfully silence AR expression and modulate the expression of AR-responsive cellular genes. This bi-functional strategy that uses a single therapeutic molecule can be the basis for novel PCa treatments. It might also be customized to other types of therapies that require the silencing of one gene and the simultaneous expression of a different isoform.
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Affiliation(s)
- Daniela Castanotto
- Department of Medical Oncology, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Xiaowei Zhang
- Department of Medical Oncology, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Jacqueline Rüger
- Department of Medical Oncology, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Jessica Alluin
- Department of Molecular and Cellular Biology, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Ritin Sharma
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Lars Joenson
- Roche Innovation Center Copenhagen A/S, Fremtidsvej 3, 2970 Hørsholm, Denmark
| | - Silvia Ioannou
- Science Department, Flintridge Preparatory School, 4543 Crown Avenue, La Cañada Flintridge, CA 91011, USA
| | - Michael S Nelson
- The Light Microscopy and Digital Imaging Core, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte CA 91010
| | - Jonas Vikeså
- Roche Innovation Center Copenhagen A/S, Fremtidsvej 3, 2970 Hørsholm, Denmark
| | - Bo Rode Hansen
- Genevant Sciences, 245 Main Street, Floor 2, Cambridge, MA 02142
| | - Troels Koch
- Frederikskaj 10B, 2nd floor, 2450 Copenhagen SV, Denmark
| | - Mads Aaboe Jensen
- Roche Innovation Center Copenhagen A/S, Fremtidsvej 3, 2970 Hørsholm, Denmark
| | - John J Rossi
- Department of Molecular and Cellular Biology, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Cy A Stein
- Department of Medical Oncology, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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21
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Ferraro NM, Strober BJ, Einson J, Abell NS, Aguet F, Barbeira AN, Brandt M, Bucan M, Castel SE, Davis JR, Greenwald E, Hess GT, Hilliard AT, Kember RL, Kotis B, Park Y, Peloso G, Ramdas S, Scott AJ, Smail C, Tsang EK, Zekavat SM, Ziosi M, Aradhana, Ardlie KG, Assimes TL, Bassik MC, Brown CD, Correa A, Hall I, Im HK, Li X, Natarajan P, Lappalainen T, Mohammadi P, Montgomery SB, Battle A. Transcriptomic signatures across human tissues identify functional rare genetic variation. Science 2020; 369:eaaz5900. [PMID: 32913073 PMCID: PMC7646251 DOI: 10.1126/science.aaz5900] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
Abstract
Rare genetic variants are abundant across the human genome, and identifying their function and phenotypic impact is a major challenge. Measuring aberrant gene expression has aided in identifying functional, large-effect rare variants (RVs). Here, we expanded detection of genetically driven transcriptome abnormalities by analyzing gene expression, allele-specific expression, and alternative splicing from multitissue RNA-sequencing data, and demonstrate that each signal informs unique classes of RVs. We developed Watershed, a probabilistic model that integrates multiple genomic and transcriptomic signals to predict variant function, validated these predictions in additional cohorts and through experimental assays, and used them to assess RVs in the UK Biobank, the Million Veterans Program, and the Jackson Heart Study. Our results link thousands of RVs to diverse molecular effects and provide evidence to associate RVs affecting the transcriptome with human traits.
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Affiliation(s)
- Nicole M Ferraro
- Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA
| | - Benjamin J Strober
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jonah Einson
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Nathan S Abell
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Margot Brandt
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephane E Castel
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Joe R Davis
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Emily Greenwald
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Austin T Hilliard
- Palo Alto Veterans Institute for Research, Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Rachel L Kember
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bence Kotis
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - YoSon Park
- Department of Systems Pharmacology and Translational Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Gina Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Shweta Ramdas
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandra J Scott
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Craig Smail
- Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA
| | - Emily K Tsang
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Seyedeh M Zekavat
- Medical & Population Genomics, Yale School of Medicine and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Aradhana
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Themistocles L Assimes
- Palo Alto Veterans Institute for Research, Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Ira Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Xin Li
- Department of Pathology, Stanford University, Stanford, CA, USA
- Shanghai Institutes for Biological Sciences, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Pejman Mohammadi
- New York Genome Center, New York, NY, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Translational Science Institute, La Jolla, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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22
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Densen P, Ackermann L, Saucedo L, Figueroa JE, Si ZH, Stoltzfus CM. A Point Mutation Creating a 3' Splice Site in C8A Is a Predominant Cause of C8α-γ Deficiency in African Americans. THE JOURNAL OF IMMUNOLOGY 2020; 205:1535-1539. [PMID: 32769119 DOI: 10.4049/jimmunol.2000272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/11/2020] [Indexed: 11/19/2022]
Abstract
C8α-γ deficiency was examined in four unrelated African Americans. Two individuals were compound heterozygotes for a previously reported point mutation in exon 9. mRNA from the remaining six C8A alleles contained a 10 nt insertion between nt 992 and 993 corresponding to the junction between exons 6 and 7. This suggested that C8α-γ deficiency in these individuals was caused by a splicing defect. Genomic sequencing revealed a G→A point mutation in intron 6, upstream of the exon 7 acceptor site. This mutation converts a GG to an AG, generates a consensus 3' splice site that shifts the reading frame, and creates a premature stop codon downstream. To verify that the point mutation caused a splicing defect, we tested wild-type and mutant mRNA substrates, containing 333 nt of the C8α intron 6/exon 7 boundary, in an in vitro splicing assay. This assay generated spliced RNA containing the 10 bp insertion observed in the C8α mRNA of affected patients. In addition, in mutant RNA substrates, the new 3' splice site was preferentially recognized compared with wild-type. Preferential selection of the mutant splice site likely reflects its positioning adjacent to a polypyrimidine tract that is stronger than that adjacent to the wild-type site. In summary, we have identified a G→A mutation in intron 6 of C8A as a predominant cause of C8α-γ deficiency in African Americans. This mutation creates a new and preferred 3' splice site, results in a 10 nt insertion in mRNA, shifts the reading frame, and produces a premature stop codon downstream.
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Affiliation(s)
- Peter Densen
- Department of Internal Medicine, Veteran Affairs Medical Center and University of Iowa College of Medicine, Iowa City, IA 52242;
| | - Laynez Ackermann
- Department of Microbiology and Immunology, University of Iowa College of Medicine, Iowa City, IA 52242
| | - Leslie Saucedo
- Department of Biology, University of Puget Sound, Tacoma, WA 98416
| | - Julio E Figueroa
- Department of Internal Medicine, Section of Infectious Diseases, Louisiana State University, New Orleans, LA 70112; and
| | - Zhi-Hai Si
- Akebia Therapeutics, Cambridge, MA 02142
| | - Conrad Martin Stoltzfus
- Department of Microbiology and Immunology, University of Iowa College of Medicine, Iowa City, IA 52242
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23
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Terkelsen T, Larsen OH, Vang S, Jensen UB, Wikman F. Deleterious mis-splicing of STK11 caused by a novel single-nucleotide substitution in the 3' polypyrimidine tract of intron five. Mol Genet Genomic Med 2020; 8:e1381. [PMID: 32573125 PMCID: PMC7507455 DOI: 10.1002/mgg3.1381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 01/07/2023] Open
Abstract
Background Pathogenic variants in STK11, also designated as LKB1, cause Peutz–Jeghers syndrome, which is a rare autosomal dominant disorder characterized by mucocutaneous pigmentation changes, polyposis, and a high risk of cancer. Methods A male meeting the clinical diagnostic criteria for Peutz–Jeghers syndrome underwent next‐generation sequencing. To validate the predicted splicing impact of a detected STK11 variant, we performed RNA‐Seq on mRNA extracted from patient‐derived Epstein‐Barr virus‐transformed lymphocytes treated with cycloheximide to inhibit nonsense‐mediated decay ex vivo. Results Blood testing identified a novel single‐nucleotide substitution, NM_000455.4:c.735‐10C>A, at the end of the 3′ polypyrimidine tract of intron five in STK11. RNA‐Seq confirmed a predicted eight base pair insertion in the mRNA transcript. Following inhibition of nonsense‐mediated decay, the out‐of‐frame insertion was detected in 50% of all RNA‐Seq reads. This confirmed a strong, deleterious splicing impact of the variant. Conclusion We characterized a novel likely pathogenic germline variant in intron five of STK11 associated with Peutz–Jeghers syndrome. The study highlights RNA‐Seq as a useful supplement in hereditary cancer predisposition testing.
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Affiliation(s)
- Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Ole H Larsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe B Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Friedrik Wikman
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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24
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Rowlands CF, Baralle D, Ellingford JM. Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing. Cells 2019; 8:E1513. [PMID: 31779139 PMCID: PMC6953098 DOI: 10.3390/cells8121513] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022] Open
Abstract
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.
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Affiliation(s)
- Charlie F Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, MP808, Tremona Road, Southampton SO16 6YD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
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25
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Wangensteen T, Felde CN, Ahmed D, Mæhle L, Ariansen SL. Diagnostic mRNA splicing assay for variants in BRCA1 and BRCA2 identified two novel pathogenic splicing aberrations. Hered Cancer Clin Pract 2019; 17:14. [PMID: 31143303 PMCID: PMC6532242 DOI: 10.1186/s13053-019-0113-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/16/2019] [Indexed: 12/15/2022] Open
Abstract
Background Pathogenic variants in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. Screening of these genes has become easily accessible in diagnostic laboratories. Sequencing and copy number analyses are used to detect pathogenic variants, but also lead to identification of variants of unknown clinical significance (VUS). If the effect of a VUS can be clarified, it has direct consequence for the clinical management of the patient and family members. A splicing assay is one of several tools that might help in the classification of VUS. We therefore established mRNA analyses for BRCA1 and BRCA2 in the diagnostic laboratory in 2015. We hereby report the results of mRNA analysis variants in BRCA1 and BRCA2 after three years. Methods Variants predicted to alter splicing and variants within the canonical splice sites were selected for splicing analyses. Splicing assays were performed by reverse transcription-PCR of patient RNA. A biallalic expression analysis was carried out whenever possible. Results Twenty-five variants in BRCA1 and BRCA2 were analyzed by splicing assays; nine showed altered transcripts and 16 showed normal splicing patterns. The two novel pathogenic variants in BRCA1 c.4484 + 3 A > C and c.5407–10G > A were characterized. Conclusions We conclude that mRNA analyses are useful in characterization of variants that may affect splicing. The results can guide classification of variants from unknown clinical significance to pathogenic or benign in a diagnostic laboratory, and thus be of direct clinical importance.
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Affiliation(s)
| | | | - Deeqa Ahmed
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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26
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Wachutka L, Caizzi L, Gagneur J, Cramer P. Global donor and acceptor splicing site kinetics in human cells. eLife 2019; 8:45056. [PMID: 31025937 PMCID: PMC6548502 DOI: 10.7554/elife.45056] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 04/25/2019] [Indexed: 11/13/2022] Open
Abstract
RNA splicing is an essential part of eukaryotic gene expression. Although the mechanism of splicing has been extensively studied in vitro, in vivo kinetics for the two-step splicing reaction remain poorly understood. Here, we combine transient transcriptome sequencing (TT-seq) and mathematical modeling to quantify RNA metabolic rates at donor and acceptor splice sites across the human genome. Splicing occurs in the range of minutes and is limited by the speed of RNA polymerase elongation. Splicing kinetics strongly depends on the position and nature of nucleotides flanking splice sites, and on structural interactions between unspliced RNA and small nuclear RNAs in spliceosomal intermediates. Finally, we introduce the 'yield' of splicing as the efficiency of converting unspliced to spliced RNA and show that it is highest for mRNAs and independent of splicing kinetics. These results lead to quantitative models describing how splicing rates and yield are encoded in the human genome.
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Affiliation(s)
- Leonhard Wachutka
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Livia Caizzi
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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27
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Grymová T, Grodecká L, Souček P, Freiberger T. SERPING1 exon 3 splicing variants using alternative acceptor splice sites. Mol Immunol 2019; 107:91-96. [PMID: 30685616 DOI: 10.1016/j.molimm.2019.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/03/2019] [Accepted: 01/11/2019] [Indexed: 11/26/2022]
Abstract
Mutations in the C1 inhibitor (C1INH) encoding gene, SERPING1, are associated with hereditary angioedema (HAE) which manifests as recurrent submucosal and subcutaneous edema episodes. The major C1INH function is the complement system inhibition, preventing its spontaneous activation. The presented study is focused on SERPING1 exon 3, an alternative and extraordinarily long exon (499 bp). Endogenous expression analysis performed in the HepG2, human liver, and human peripheral blood cells revealed several exon 3 splicing variants alongside exon inclusion: a highly prevalent exon skipping variant and less frequent +38 and -15 variants with alternative 3' splice sites (ss) located 38 and 15 nucleotides downstream and upstream from the authentic 3' ss, respectively. An exon skipping variant introducing a premature stop codon, represented nearly one third of all splicing variants and surprisingly appeared not to be degraded by NMD. The alternative -15 3' ss was used to a small extent, although predicted to be extremely weak. Its use was shown to be independent of its strength and highly sensitive to any changes in the surrounding sequence. -15 3' ss seems to be co-regulated with the authentic 3' ss, whose use is dependent mainly on its strength and less on the presence of intronic regulatory motifs. Subtle SERPING1 exon 3 splicing regulation can contribute to overall C1INH plasma levels and HAE pathogenesis.
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Affiliation(s)
- Tereza Grymová
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Lucie Grodecká
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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28
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Bruijnesteijn J, van der Wiel MKH, de Groot N, Otting N, de Vos-Rouweler AJM, Lardy NM, de Groot NG, Bontrop RE. Extensive Alternative Splicing of KIR Transcripts. Front Immunol 2018; 9:2846. [PMID: 30564240 PMCID: PMC6288254 DOI: 10.3389/fimmu.2018.02846] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
The killer-cell Ig-like receptors (KIR) form a multigene entity involved in modulating immune responses through interactions with MHC class I molecules. The complexity of the KIR cluster is reflected by, for instance, abundant levels of allelic polymorphism, gene copy number variation, and stochastic expression profiles. The current transcriptome study involving human and macaque families demonstrates that KIR family members are also subjected to differential levels of alternative splicing, and this seems to be gene dependent. Alternative splicing may result in the partial or complete skipping of exons, or the partial inclusion of introns, as documented at the transcription level. This post-transcriptional process can generate multiple isoforms from a single KIR gene, which diversifies the characteristics of the encoded proteins. For example, alternative splicing could modify ligand interactions, cellular localization, signaling properties, and the number of extracellular domains of the receptor. In humans, we observed abundant splicing for KIR2DL4, and to a lesser extent in the lineage III KIR genes. All experimentally documented splice events are substantiated by in silico splicing strength predictions. To a similar extent, alternative splicing is observed in rhesus macaques, a species that shares a close evolutionary relationship with humans. Splicing profiles of Mamu-KIR1D and Mamu-KIR2DL04 displayed a great diversity, whereas Mamu-KIR3DL20 (lineage V) is consistently spliced to generate a homolog of human KIR2DL5 (lineage I). The latter case represents an example of convergent evolution. Although just a single KIR splice event is shared between humans and macaques, the splicing mechanisms are similar, and the predicted consequences are comparable. In conclusion, alternative splicing adds an additional layer of complexity to the KIR gene system in primates, and results in a wide structural and functional variety of KIR receptors and its isoforms, which may play a role in health and disease.
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Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marit K H van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Nanine de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Nel Otting
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | | | - Neubury M Lardy
- Department of Immunogenetics, Sanquin, Amsterdam, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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29
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Abstract
Since its discovery in 1977, much has been known about RNA splicing and how it plays a central role in human development, function, and, notably, disease. Defects in RNA splicing account for at least 10% of all genetic disorders, with the number expected to increase as more information is uncovered on the contribution of noncoding genomic regions to disease. Splice modulation through the use of antisense oligonucleotides (AOs) has emerged as a promising avenue for the treatment of these disorders. In fact, two splice-switching AOs have recently obtained approval from the US Food and Drug Administration: eteplirsen (Exondys 51) for Duchenne muscular dystrophy, and nusinersen (Spinraza) for spinal muscular atrophy. These work by exon skipping and exon inclusion, respectively. In this chapter, we discuss the early development of AO-based splice modulation therapy-its invention, first applications, and its evolution into the approach we are now familiar with. We give a more extensive history of exon skipping in particular, as it is the splice modulation approach given the most focus in this book.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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30
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Zhang W, Zhu X, Fu Y, Tsuji J, Weng Z. Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. BMC Bioinformatics 2017; 18:464. [PMID: 29219070 PMCID: PMC5773893 DOI: 10.1186/s12859-017-1875-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order to guide wet experiments, we develop computational methods to predict human splicing branchpoints. Results Considering the fact that an intron may have multiple branchpoints, we transform the branchpoint prediction as the multi-label learning problem, and attempt to predict branchpoint sites from intron sequences. First, we investigate a variety of intron sequence-derived features, such as sparse profile, dinucleotide profile, position weight matrix profile, Markov motif profile and polypyrimidine tract profile. Second, we consider several multi-label learning methods: partial least squares regression, canonical correlation analysis and regularized canonical correlation analysis, and use them as the basic classification engines. Third, we propose two ensemble learning schemes which integrate different features and different classifiers to build ensemble learning systems for the branchpoint prediction. One is the genetic algorithm-based weighted average ensemble method; the other is the logistic regression-based ensemble method. Conclusions In the computational experiments, two ensemble learning methods outperform benchmark branchpoint prediction methods, and can produce high-accuracy results on the benchmark dataset.
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Affiliation(s)
- Wen Zhang
- School of Computer, Wuhan University, Wuhan, 430072, China.
| | - Xiaopeng Zhu
- School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Yu Fu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Junko Tsuji
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
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31
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Wen J, Wang J, Zhang Q, Guo D. A heuristic model for computational prediction of human branch point sequence. BMC Bioinformatics 2017; 18:459. [PMID: 29065858 PMCID: PMC5655975 DOI: 10.1186/s12859-017-1864-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 10/09/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Pre-mRNA splicing is the removal of introns from precursor mRNAs (pre-mRNAs) and the concurrent ligation of the flanking exons to generate mature mRNA. This process is catalyzed by the spliceosome, where the splicing factor 1 (SF1) specifically recognizes the seven-nucleotide branch point sequence (BPS) and the U2 snRNP later displaces the SF1 and binds to the BPS. In mammals, the degeneracy of BPS motifs together with the lack of a large set of experimentally verified BPSs complicates the task of BPS prediction in silico. RESULTS In this paper, we develop a simple and yet efficient heuristic model for human BPS prediction based on a novel scoring scheme, which quantifies the splicing strength of putative BPSs. The candidate BPS is restricted exclusively within a defined BPS search region to avoid the influences of other elements in the intron and therefore the prediction accuracy is improved. Moreover, using two types of relative frequencies for human BPS prediction, we demonstrate our model outperformed other current implementations on experimentally verified human introns. CONCLUSION We propose that the binding energy contributes to the molecular recognition involved in human pre-mRNA splicing. In addition, a genome-wide human BPS prediction is carried out. The characteristics of predicted BPSs are in accordance with experimentally verified human BPSs, and branch site positions relative to the 3'ss and the 5'end of the shortened AGEZ are consistent with the results of published papers. Meanwhile, a webserver for BPS predictor is freely available at http://biocomputer.bio.cuhk.edu.hk/BPS .
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Affiliation(s)
- Jia Wen
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jue Wang
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Qing Zhang
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Dianjing Guo
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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32
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Ohno K, Takeda JI, Masuda A. Rules and tools to predict the splicing effects of exonic and intronic mutations. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [DOI: 10.1002/wrna.1451] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Jun-ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
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33
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Lu J, Williams JA, Luke J, Zhang F, Chu K, Kay MA. A 5' Noncoding Exon Containing Engineered Intron Enhances Transgene Expression from Recombinant AAV Vectors in vivo. Hum Gene Ther 2017; 28:125-134. [PMID: 27903072 DOI: 10.1089/hum.2016.140] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We previously developed a mini-intronic plasmid (MIP) expression system in which the essential bacterial elements for plasmid replication and selection are placed within an engineered intron contained within a universal 5' UTR noncoding exon. Like minicircle DNA plasmids (devoid of bacterial backbone sequences), MIP plasmids overcome transcriptional silencing of the transgene. However, in addition MIP plasmids increase transgene expression by 2 and often >10 times higher than minicircle vectors in vivo and in vitro. Based on these findings, we examined the effects of the MIP intronic sequences in a recombinant adeno-associated virus (AAV) vector system. Recombinant AAV vectors containing an intron with a bacterial replication origin and bacterial selectable marker increased transgene expression by 40 to 100 times in vivo when compared with conventional AAV vectors. Therefore, inclusion of this noncoding exon/intron sequence upstream of the coding region can substantially enhance AAV-mediated gene expression in vivo.
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Affiliation(s)
- Jiamiao Lu
- 1 Department of Pediatrics, Stanford University , Palo Alto, California.,2 Department of Genetics, Stanford University , Palo Alto, California
| | | | - Jeremy Luke
- 3 Nature Technology Corporation , Lincoln, Nebraska
| | - Feijie Zhang
- 1 Department of Pediatrics, Stanford University , Palo Alto, California.,2 Department of Genetics, Stanford University , Palo Alto, California
| | - Kirk Chu
- 1 Department of Pediatrics, Stanford University , Palo Alto, California.,2 Department of Genetics, Stanford University , Palo Alto, California
| | - Mark A Kay
- 1 Department of Pediatrics, Stanford University , Palo Alto, California.,2 Department of Genetics, Stanford University , Palo Alto, California
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34
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Recognition of the 3' splice site RNA by the U2AF heterodimer involves a dynamic population shift. Proc Natl Acad Sci U S A 2016; 113:E7169-E7175. [PMID: 27799531 DOI: 10.1073/pnas.1605873113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3' splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3' splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein-RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3' splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.
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35
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Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Sci Rep 2016; 6:32406. [PMID: 27617755 PMCID: PMC5019111 DOI: 10.1038/srep32406] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/03/2016] [Indexed: 12/23/2022] Open
Abstract
Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.
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Affiliation(s)
- Pedro G. Ferreira
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Instituto de Investigação e Inovação em Saúde, (i3S) Universidade do Porto, 4200-625 Porto, Portugal
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-625 Porto, Portugal
| | - Martin Oti
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
| | - Matthias Barann
- Institute of Clinical Molecular Biology, Christians-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Suzana Ezquina
- Center for Human Genome and Stem-cell research (HUG-CELL), University of São Paulo (USP), 05508090 São Paulo, Brazil
| | - Marc R. Friedländer
- Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Manuel A. Rivas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Anna Esteve-Codina
- Centre Nacional d’Anàlisi Genòmica, 08028 Barcelona, Catalonia, Spain
- Center for Research in Agricultural Genomics (CRAG), Autonome University of Barcelona, 08193 Bellaterra, Catalonia, Spain
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christians-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Tuuli Lappalainen
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Pompeu Fabra University (UPF), 08003 Barcelona, Catalonia, Spain
| | - Michael Sammeth
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
- National Center of Scientific Computing (LNCC), 2233-6000 Petrópolis, Rio de Janeiro, Brazil
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36
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Kralovicova J, Vorechovsky I. Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons. Nucleic Acids Res 2016; 45:417-434. [PMID: 27566151 PMCID: PMC5224494 DOI: 10.1093/nar/gkw733] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 12/30/2022] Open
Abstract
The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3′ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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37
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Van Der Steen N, Giovannetti E, Pauwels P, Peters GJ, Hong DS, Cappuzzo F, Hirsch FR, Rolfo C. cMET Exon 14 Skipping: From the Structure to the Clinic. J Thorac Oncol 2016; 11:1423-32. [PMID: 27223456 DOI: 10.1016/j.jtho.2016.05.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 12/28/2022]
Abstract
The abnormal stimulation of the multiple signal transduction pathways downstream of the receptor tyrosine kinase mesenchymal-epithelial transition factor (cMET) promotes cellular transformation, tumor motility, and invasion. Therefore, cMET has been the focus of prognostic and therapeutic studies in different tumor types, including non-small cell lung cancer. In particular, several cMET inhibitors have been developed as innovative therapeutic candidates and are currently under investigation in clinical trials. However, one of the challenges in establishing effective targeted treatments against cMET remains the accurate identification of biomarkers for the selection of responsive subsets of patients. Recently, splice site mutations have been discovered in cMET that lead to the skipping of exon 14, impairing the breakdown of the receptor. Patients with NSCLC who are carrying this splice variant typically overexpress the cMET receptor and show a response to small molecule inhibitors of cMET. Here, we review the main differences at the structural level between the wild-type and the splice variants of cMET and their influence on cMET signaling. We clarify the reason why this variant responds to small molecule inhibitors and their prognostic/predictive role.
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Affiliation(s)
- Nele Van Der Steen
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; Department of Pathology, Antwerp University Hospital, Edegem, Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; Cancer Pharmacology Lab, Italian Association for Cancer Research Start-Up Unit, University of Pisa, Hospital of Cisanello, Pisa, Italy
| | - Patrick Pauwels
- Department of Pathology, Antwerp University Hospital, Edegem, Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - David S Hong
- Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | | | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado, Aurora, Colorado
| | - Christian Rolfo
- Center for Oncological Research, University of Antwerp, Wilrijk, Antwerp, Belgium; Phase I Early Clinical Trials Unit, Oncology Department, Antwerp University Hospital, Antwerp, Belgium.
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38
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Correcting the NLRP3 inflammasome deficiency in macrophages from autoimmune NZB mice with exon skipping antisense oligonucleotides. Immunol Cell Biol 2016; 94:520-4. [PMID: 26833024 DOI: 10.1038/icb.2016.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 12/22/2022]
Abstract
Inflammasomes are molecular complexes activated by infection and cellular stress, leading to caspase-1 activation and subsequent interleukin-1β (IL-1β) processing and cell death. The autoimmune NZB mouse strain does not express NLRP3, a key inflammasome initiator mediating responses to a wide variety of stimuli including endogenous danger signals, environmental irritants and a range of bacterial, fungal and viral pathogens. We have previously identified an intronic point mutation in the Nlrp3 gene from NZB mice that generates a splice acceptor site. This leads to inclusion of a pseudoexon that introduces an early termination codon and is proposed to be the cause of NLRP3 inflammasome deficiency in NZB cells. Here we have used exon skipping antisense oligonucleotides (AONs) to prevent aberrant splicing of Nlrp3 in NZB macrophages, and this restored both NLRP3 protein expression and NLRP3 inflammasome activity. Thus, the single point mutation leading to aberrant splicing is the sole cause of NLRP3 inflammasome deficiency in NZB macrophages. The NZB mouse provides a model for addressing a splicing defect in macrophages and could be used to further investigate AON design and delivery of AONs to macrophages in vivo.
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AbuQattam A, Gallego J, Rodríguez-Navarro S. An intronic RNA structure modulates expression of the mRNA biogenesis factor Sus1. RNA (NEW YORK, N.Y.) 2016; 22:75-86. [PMID: 26546116 PMCID: PMC4691836 DOI: 10.1261/rna.054049.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/03/2015] [Indexed: 06/05/2023]
Abstract
Sus1 is a conserved protein involved in chromatin remodeling and mRNA biogenesis. Unlike most yeast genes, the SUS1 pre-mRNA of Saccharomyces cerevisiae contains two introns and is alternatively spliced, retaining one or both introns in response to changes in environmental conditions. SUS1 splicing may allow the cell to control Sus1 expression, but the mechanisms that regulate this process remain unknown. Using in silico analyses together with NMR spectroscopy, gel electrophoresis, and UV thermal denaturation experiments, we show that the downstream intron (I2) of SUS1 forms a weakly stable, 37-nucleotide stem-loop structure containing the branch site near its apical loop and the 3' splice site after the stem terminus. A cellular assay revealed that two of four mutants containing altered I2 structures had significantly impaired SUS1 expression. Semiquantitative RT-PCR experiments indicated that all mutants accumulated unspliced SUS1 pre-mRNA and/or induced distorted levels of fully spliced mRNA relative to wild type. Concomitantly, Sus1 cellular functions in histone H2B deubiquitination and mRNA export were affected in I2 hairpin mutants that inhibited splicing. This work demonstrates that I2 structure is relevant for SUS1 expression, and that this effect is likely exerted through modulation of splicing.
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Affiliation(s)
- Ali AbuQattam
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain Facultad de Medicina, Universidad Católica de Valencia, Valencia 46001, Spain
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, Valencia 46001, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
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40
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Denisov S, Bazykin G, Favorov A, Mironov A, Gelfand M. Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals. PLoS One 2015; 10:e0144388. [PMID: 26642327 PMCID: PMC4671708 DOI: 10.1371/journal.pone.0144388] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/17/2015] [Indexed: 12/26/2022] Open
Abstract
Splice sites (SSs)--short nucleotide sequences flanking introns--are under selection for spliceosome binding, and adhere to consensus sequences. However, non-consensus nucleotides, many of which probably reduce SS performance, are frequent. Little is known about the mechanisms maintaining such apparently suboptimal SSs. Here, we study the correlations between strengths of nucleotides occupying different positions of the same SS. Such correlations may arise due to epistatic interactions between positions (i.e., a situation when the fitness effect of a nucleotide in one position depends on the nucleotide in another position), their evolutionary history, or to other reasons. Within both the intronic and the exonic parts of donor SSs, nucleotides that increase (decrease) SS strength tend to co-occur with other nucleotides increasing (respectively, decreasing) it, consistent with positive epistasis. Between the intronic and exonic parts of donor SSs, the correlations of nucleotide strengths tend to be negative, consistent with negative epistasis. In the course of evolution, substitutions at a donor SS tend to decrease the strength of its exonic part, and either increase or do not change the strength of its intronic part. In acceptor SSs, the situation is more complicated; the correlations between adjacent positions appear to be driven mainly by avoidance of the AG dinucleotide which may cause aberrant splicing. In summary, both the content and the evolution of SSs is shaped by a complex network of interdependences between adjacent nucleotides that respond to a range of sometimes conflicting selective constraints.
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Affiliation(s)
- Stepan Denisov
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
| | - Georgii Bazykin
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Favorov
- Division of Oncology Biostatistics, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, United States of America
- Laboratory of System Biology and Computational Genetics, Department of Computational System Biology, N. I. Vavilov Institute of General Genetics, Moscow, Russia
- Laboratory of Bioinformatics, State Research Institute of Genetics and Selection of Industrial Microorganism (GosNIIGenetika), Moscow, Russia
| | - Andrey Mironov
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Gelfand
- A. A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
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41
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Darman R, Seiler M, Agrawal A, Lim K, Peng S, Aird D, Bailey S, Bhavsar E, Chan B, Colla S, Corson L, Feala J, Fekkes P, Ichikawa K, Keaney G, Lee L, Kumar P, Kunii K, MacKenzie C, Matijevic M, Mizui Y, Myint K, Park E, Puyang X, Selvaraj A, Thomas M, Tsai J, Wang J, Warmuth M, Yang H, Zhu P, Garcia-Manero G, Furman R, Yu L, Smith P, Buonamici S. Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point. Cell Rep 2015; 13:1033-45. [DOI: 10.1016/j.celrep.2015.09.053] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/21/2015] [Accepted: 09/18/2015] [Indexed: 10/22/2022] Open
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Fraser HI, Howlett S, Clark J, Rainbow DB, Stanford SM, Wu DJ, Hsieh YW, Maine CJ, Christensen M, Kuchroo V, Sherman LA, Podolin PL, Todd JA, Steward CA, Peterson LB, Bottini N, Wicker LS. Ptpn22 and Cd2 Variations Are Associated with Altered Protein Expression and Susceptibility to Type 1 Diabetes in Nonobese Diabetic Mice. THE JOURNAL OF IMMUNOLOGY 2015; 195:4841-52. [PMID: 26438525 PMCID: PMC4635565 DOI: 10.4049/jimmunol.1402654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 09/04/2015] [Indexed: 01/08/2023]
Abstract
By congenic strain mapping using autoimmune NOD.C57BL/6J congenic mice, we demonstrated previously that the type 1 diabetes (T1D) protection associated with the insulin-dependent diabetes (Idd)10 locus on chromosome 3, originally identified by linkage analysis, was in fact due to three closely linked Idd loci: Idd10, Idd18.1, and Idd18.3. In this study, we define two additional Idd loci—Idd18.2 and Idd18.4—within the boundaries of this cluster of disease-associated genes. Idd18.2 is 1.31 Mb and contains 18 genes, including Ptpn22, which encodes a phosphatase that negatively regulates T and B cell signaling. The human ortholog of Ptpn22, PTPN22, is associated with numerous autoimmune diseases, including T1D. We, therefore, assessed Ptpn22 as a candidate for Idd18.2; resequencing of the NOD Ptpn22 allele revealed 183 single nucleotide polymorphisms with the C57BL/6J (B6) allele—6 exonic and 177 intronic. Functional studies showed higher expression of full-length Ptpn22 RNA and protein, and decreased TCR signaling in congenic strains with B6-derived Idd18.2 susceptibility alleles. The 953-kb Idd18.4 locus contains eight genes, including the candidate Cd2. The CD2 pathway is associated with the human autoimmune disease, multiple sclerosis, and mice with NOD-derived susceptibility alleles at Idd18.4 have lower CD2 expression on B cells. Furthermore, we observed that susceptibility alleles at Idd18.2 can mask the protection provided by Idd10/Cd101 or Idd18.1/Vav3 and Idd18.3. In summary, we describe two new T1D loci, Idd18.2 and Idd18.4, candidate genes within each region, and demonstrate the complex nature of genetic interactions underlying the development of T1D in the NOD mouse model.
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Affiliation(s)
- Heather I Fraser
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Sarah Howlett
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Jan Clark
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Daniel B Rainbow
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Stephanie M Stanford
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; La Jolla Institute for Allergy and Immunology, Type 1 Diabetes Research Center, La Jolla, CA 92037
| | - Dennis J Wu
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; La Jolla Institute for Allergy and Immunology, Type 1 Diabetes Research Center, La Jolla, CA 92037
| | - Yi-Wen Hsieh
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Christian J Maine
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037
| | - Mikkel Christensen
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Vijay Kuchroo
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Linda A Sherman
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037
| | - Patricia L Podolin
- Department of Pharmacology, Merck Research Laboratories, Rahway, NJ 07065; and
| | - John A Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Charles A Steward
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, United Kingdom
| | - Laurence B Peterson
- Department of Pharmacology, Merck Research Laboratories, Rahway, NJ 07065; and
| | - Nunzio Bottini
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; La Jolla Institute for Allergy and Immunology, Type 1 Diabetes Research Center, La Jolla, CA 92037
| | - Linda S Wicker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom;
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Otterpohl KL, Gould KA. Genetic dissection of the Mom5 modifier locus and evaluation of Mom5 candidate genes. Mamm Genome 2015; 26:235-47. [PMID: 25976411 DOI: 10.1007/s00335-015-9567-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/02/2015] [Indexed: 10/23/2022]
Abstract
Germline mutations in the adenomatous polyposis coli (APC) gene cause familial adenomatous polyposis (FAP), a hereditary colon cancer syndrome in which affected individuals may develop 100-1000s of colonic adenomas. In families affected by FAP, adenoma number can vary markedly between individuals, despite the fact that these individuals carry the same APC mutation. In at least some FAP pedigrees, evidence suggests that these phenotypic differences are caused by segregating modifier alleles that impact adenoma number. However, identifying these modifiers in the human population is difficult, therefore mouse models are essential. Using the Apc (Min/+) mouse colon cancer model, we previously mapped one such modifier, Mom5, to a 25 Mbp region of chromosome 5 that contains hundreds of genes. The purpose of the present study was to refine the Mom5 interval and evaluate candidate genes for the Mom5 modifier of intestinal neoplasia. Recombinant mice were used to narrow the Mom5 interval to 8.1 Mbp containing 70 genes. In silico and gene expression analyses were utilized to identify and evaluate potential candidate genes that reside within this interval. These analyses identified seven genes within the Mom5 interval that contain variants between the B6 and 129P2 strains. These genes represent the most likely candidates for the Mom5 modifier.
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Affiliation(s)
- Karla L Otterpohl
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE, 68198-5805, USA
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44
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Xie BB, Li D, Shi WL, Qin QL, Wang XW, Rong JC, Sun CY, Huang F, Zhang XY, Dong XW, Chen XL, Zhou BC, Zhang YZ, Song XY. Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum. BMC Genomics 2015; 16:54. [PMID: 25652134 PMCID: PMC4324775 DOI: 10.1186/s12864-015-1251-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 01/15/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive. RESULTS The transcriptome of the filamentous fungus Trichoderma longibrachiatum was deep sequenced using Illumina Solexa technology. A total of 14305 splice junctions were discovered. Analyses of alternative splicing events revealed that the number of all alternative splicing events (10034), intron retentions (IR, 9369), alternative 5' splice sites (A5SS, 167), and alternative 3' splice sites (A3SS, 302) is 7.3, 7.4, 5.1, and 5.9-fold higher, respectively, than those observed in the fungus Aspergillus oryzae using Illumina Solexa technology. This unexpectedly high ratio of alternative splicing suggests that alternative splicing is important to the transcriptome diversity of T. longibrachiatum. Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. Further analysis demonstrated that the isoform relative frequencies were correlated with the splice site scores of the isoforms. Moreover, comparative transcriptomics determined that most enzymes related to glycolysis and the citrate cycle and glyoxylate cycle as well as a few carbohydrate-active enzymes are transcriptionally regulated. CONCLUSIONS This study, consisting of a comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum, revealed an unexpectedly high ratio of alternative splicing events and provided new insights into transcriptome diversity in fungi.
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Affiliation(s)
- Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. .,Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China.
| | - Dan Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Wei-Ling Shi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. .,Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China.
| | - Xiao-Wei Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Jin-Cheng Rong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Cai-Yun Sun
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Feng Huang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China.
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. .,Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China.
| | - Xiao-Wei Dong
- Technology Center, Shandong Tobacco Industry Corporation, Jinan, 250013, China.
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. .,Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China.
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. .,Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China.
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China. .,Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China. .,Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, 250100, China.
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Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Genome-wide discovery of human splicing branchpoints. Genome Res 2015; 25:290-303. [PMID: 25561518 PMCID: PMC4315302 DOI: 10.1101/gr.182899.114] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During the splicing reaction, the 5′ intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3′ splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron–exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.
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Affiliation(s)
- Tim R Mercer
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Michael B Clark
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Stacey B Andersen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marion E Brunck
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; Illumina, Inc., San Diego, California 92122, USA; School of Medicine and Health Services, Department of Integrated Systems Biology and Department of Pediatrics, George Washington University, Washington DC 20037, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia;
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Boddu R, Yang C, O’Connor AK, Hendrickson RC, Boone B, Cui X, Garcia-Gonzalez M, Igarashi P, Onuchic LF, Germino GG, Guay-Woodford LM. Intragenic motifs regulate the transcriptional complexity of Pkhd1/PKHD1. J Mol Med (Berl) 2014; 92:1045-56. [PMID: 24984783 PMCID: PMC4197071 DOI: 10.1007/s00109-014-1185-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/05/2014] [Accepted: 06/16/2014] [Indexed: 11/26/2022]
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) results from mutations in the human PKHD1 gene. Both this gene, and its mouse ortholog, Pkhd1, are primarily expressed in renal and biliary ductal structures. The mouse protein product, fibrocystin/polyductin complex (FPC), is a 445-kDa protein encoded by a 67-exon transcript that spans >500 kb of genomic DNA. In the current study, we observed multiple alternatively spliced Pkhd1 transcripts that varied in size and exon composition in embryonic mouse kidney, liver, and placenta samples, as well as among adult mouse pancreas, brain, heart, lung, testes, liver, and kidney. Using reverse transcription PCR and RNASeq, we identified 22 novel Pkhd1 kidney transcripts with unique exon junctions. Various mechanisms of alternative splicing were observed, including exon skipping, use of alternate acceptor/donor splice sites, and inclusion of novel exons. Bioinformatic analyses identified, and exon-trapping minigene experiments validated, consensus binding sites for serine/arginine-rich proteins that modulate alternative splicing. Using site-directed mutagenesis, we examined the functional importance of selected splice enhancers. In addition, we demonstrated that many of the novel transcripts were polysome bound, thus likely translated. Finally, we determined that the human PKHD1 R760H missense variant alters a splice enhancer motif that disrupts exon splicing in vitro and is predicted to truncate the protein. Taken together, these data provide evidence of the complex transcriptional regulation of Pkhd1/PKHD1 and identified motifs that regulate its splicing. Our studies indicate that Pkhd1/PKHD1 transcription is modulated, in part by intragenic factors, suggesting that aberrant PKHD1 splicing represents an unappreciated pathogenic mechanism in ARPKD. Key messages: Multiple mRNA transcripts are generated for Pkhd1 in renal tissues Pkhd1 transcription is modulated by standard splice elements and effectors Mutations in splice motifs may alter splicing to generate nonfunctional peptides.
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Affiliation(s)
- Ravindra Boddu
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chaozhe Yang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Center for Translational Science, Children’s National Medical Center, Washington, DC 20010, USA
| | - Amber K. O’Connor
- Center for Translational Science, Children’s National Medical Center, Washington, DC 20010, USA
| | | | - Braden Boone
- Hudson Alpha Institute, Huntsville, AL 35806, USA
| | - Xiangqin Cui
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Miguel Garcia-Gonzalez
- Complexo Hospitalario de Santiago de Compostela, Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Peter Igarashi
- Department of Medicine, University of Texas Southwestern School of Medicine, Dallas, TX 75235, USA
| | - Luiz F. Onuchic
- Department of Medicine, University of Sao Paulo, Sao Paulo, Brazil 01246-903
| | - Gregory G. Germino
- Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa M. Guay-Woodford
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Center for Translational Science, Children’s National Medical Center, Washington, DC 20010, USA
- Children’s National Medical Center, 6th Floor Main Hospital, Center 6, 111 Michigan Ave NW, Washington, DC 20010, USA
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Mattioli C, Pianigiani G, De Rocco D, Bianco AMR, Cappelli E, Savoia A, Pagani F. Unusual splice site mutations disrupt FANCA exon 8 definition. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1052-8. [DOI: 10.1016/j.bbadis.2014.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 01/23/2023]
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Panunzi LG, Agüero F. A genome-wide analysis of genetic diversity in Trypanosoma cruzi intergenic regions. PLoS Negl Trop Dis 2014; 8:e2839. [PMID: 24784238 PMCID: PMC4006747 DOI: 10.1371/journal.pntd.0002839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 03/20/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi is the causal agent of Chagas Disease. Recently, the genomes of representative strains from two major evolutionary lineages were sequenced, allowing the construction of a detailed genetic diversity map for this important parasite. However this map is focused on coding regions of the genome, leaving a vast space of regulatory regions uncharacterized in terms of their evolutionary conservation and/or divergence. METHODOLOGY Using data from the hybrid CL Brener and Sylvio X10 genomes (from the TcVI and TcI Discrete Typing Units, respectively), we identified intergenic regions that share a common evolutionary ancestry, and are present in both CL Brener haplotypes (TcII-like and TcIII-like) and in the TcI genome; as well as intergenic regions that were conserved in only two of the three genomes/haplotypes analyzed. The genetic diversity in these regions was characterized in terms of the accumulation of indels and nucleotide changes. PRINCIPAL FINDINGS Based on this analysis we have identified i) a core of highly conserved intergenic regions, which remained essentially unchanged in independently evolving lineages; ii) intergenic regions that show high diversity in spite of still retaining their corresponding upstream and downstream coding sequences; iii) a number of defined sequence motifs that are shared by a number of unrelated intergenic regions. A fraction of indels explains the diversification of some intergenic regions by the expansion/contraction of microsatellite-like repeats.
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Affiliation(s)
- Leonardo G. Panunzi
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
- * E-mail: ;
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Neurofibromatosis type 1 alternative splicing is a key regulator of Ras signaling in neurons. Mol Cell Biol 2014; 34:2188-97. [PMID: 24710274 DOI: 10.1128/mcb.00019-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Neurofibromatosis type I (Nf1) is a GTPase-activating protein (GAP) that inactivates the oncoprotein Ras and plays important roles in nervous system development and learning. Alternative exon 23a falls within the Nf1 GAP domain coding sequence and is tightly regulated in favor of skipping in neurons; however, its biological function is not fully understood. Here we generated mouse embryonic stem (ES) cells with a constitutive endogenous Nf1 exon 23a inclusion, termed Nf1 23aIN/23aIN cells, by mutating the splicing signals surrounding the exon to better match consensus sequences. We also made Nf1 23aΔ/23aΔ cells lacking the exon. Active Ras levels are high in wild-type (WT) and Nf1 23aIN/23aIN ES cells, where the Nf1 exon 23a inclusion level is high, and low in Nf1 23aΔ/23aΔ cells. Upon neuronal differentiation, active Ras levels are high in Nf1 23aIN/23aIN cells, where the exon inclusion level remains high, but Ras activation is low in the other two genotypes, where the exon is skipped. Signaling downstream of Ras is significantly elevated in Nf1 23aIN/23aIN neurons. These results suggest that exon 23a suppresses the Ras-GAP activity of Nf1. Therefore, regulation of Nf1 exon 23a inclusion serves as a mechanism for providing appropriate levels of Ras signaling and may be important in modulating Ras-related neuronal functions.
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50
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Grodecká L, Lockerová P, Ravčuková B, Buratti E, Baralle FE, Dušek L, Freiberger T. Exon first nucleotide mutations in splicing: evaluation of in silico prediction tools. PLoS One 2014; 9:e89570. [PMID: 24586880 PMCID: PMC3931810 DOI: 10.1371/journal.pone.0089570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/21/2014] [Indexed: 12/20/2022] Open
Abstract
Mutations in the first nucleotide of exons (E+1) mostly affect pre-mRNA splicing when found in AG-dependent 3′ splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primary sequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 3′ splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E+1 variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it. Among the computational tools tested, the best performance was achieved using the Maximum Entropy Model and Position-Specific Scoring Matrix. As a result of this study, we have now established preliminary discriminative cut-off values showing sensitivity up to 95% and specificity up to 90%. This is expected to improve our ability to detect splicing-affecting variants in a clinical genetic setting.
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Affiliation(s)
- Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavla Lockerová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Barbora Ravčuková
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Ladislav Dušek
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Clinical Immunology and Allergology, St. Anne’s University Hospital and Masaryk University, Brno, Czech Republic
- * E-mail:
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