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Spangsberg Petersen US, Dembic M, Martínez-Pizarro A, Richard E, Holm LL, Havelund JF, Doktor TK, Larsen MR, Færgeman NJ, Desviat LR, Andresen BS. Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102101. [PMID: 38204914 PMCID: PMC10776996 DOI: 10.1016/j.omtn.2023.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Pseudoexons are nonfunctional intronic sequences that can be activated by deep-intronic sequence variation. Activation increases pseudoexon inclusion in mRNA and interferes with normal gene expression. The PCCA c.1285-1416A>G variation activates a pseudoexon and causes the severe metabolic disorder propionic acidemia by deficiency of the propionyl-CoA carboxylase enzyme encoded by PCCA and PCCB. We characterized this pathogenic pseudoexon activation event in detail and identified hnRNP A1 to be important for normal repression. The PCCA c.1285-1416A>G variation disrupts an hnRNP A1-binding splicing silencer and simultaneously creates a splicing enhancer. We demonstrate that blocking this region of regulation with splice-switching antisense oligonucleotides restores normal splicing and rescues enzyme activity in patient fibroblasts and in a cellular model created by CRISPR gene editing. Interestingly, the PCCA pseudoexon offers an unexploited potential to upregulate gene expression because healthy tissues show relatively high inclusion levels. By blocking inclusion of the nonactivated wild-type pseudoexon, we can increase both PCCA and PCCB protein levels, which increases the activity of the heterododecameric enzyme. Surprisingly, we can increase enzyme activity from residual levels in not only patient fibroblasts harboring PCCA missense variants but also those harboring PCCB missense variants. This is a potential treatment strategy for propionic acidemia.
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Affiliation(s)
- Ulrika Simone Spangsberg Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ainhoa Martínez-Pizarro
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lourdes Ruiz Desviat
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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2
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Skrdlant L, Lin RJ. Characterization of RNA-Protein Interactions: Lessons from Two RNA-Binding Proteins, SRSF1 and SRSF2. Methods Mol Biol 2016; 1421:1-13. [PMID: 26965252 DOI: 10.1007/978-1-4939-3591-8_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
SR proteins are a class of RNA-binding proteins whose RNA-binding ability is required for both constitutive and alternative splicing. While members of the SR protein family were once thought to have redundant functions, in-depth biochemical analysis of their RNA-binding abilities has revealed distinct binding profiles for each SR protein, that often lead to either synergistic or antagonistic functions. SR protein family members SRSF1 and SRSF2 are two of the most highly studied RNA-binding proteins. Here we examine the various methods used to differentiate SRSF1 and SRSF2 RNA-binding ability. We discuss the benefits and type of information that can be determined using each method.
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Affiliation(s)
- Lindsey Skrdlant
- Irell & Manella Graduate School of Biological Sciences of the City of Hope, Duarte, CA, USA
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Ren-Jang Lin
- Irell & Manella Graduate School of Biological Sciences of the City of Hope, Duarte, CA, USA.
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA, 91010, USA.
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3
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Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities. Proc Natl Acad Sci U S A 2015; 112:E4726-34. [PMID: 26261309 DOI: 10.1073/pnas.1514105112] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Serine/arginine-rich splicing factor 2 (SRSF2) is an RNA-binding protein that plays important roles in splicing of mRNA precursors. SRSF2 mutations are frequently found in patients with myelodysplastic syndromes and certain leukemias, but how these mutations affect SRSF2 function has only begun to be examined. We used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease to introduce the P95H mutation to SRSF2 in K562 leukemia cells, generating an isogenic model so that splicing alterations can be attributed solely to mutant SRSF2. We found that SRSF2 (P95H) misregulates 548 splicing events (<1% of total). Of these events, 374 involved the inclusion of cassette exons, and the inclusion was either increased (206) or decreased (168). We detected a specific motif (UCCA/UG) enriched in the more-included exons and a distinct motif (UGGA/UG) in the more-excluded exons. RNA gel shift assays showed that a mutant SRSF2 derivative bound more tightly than its wild-type counterpart to RNA sites containing UCCAG but bound less tightly to UGGAG sites. Thus in most cases the pattern of exon inclusion or exclusion correlated with stronger or weaker RNA binding, respectively. We further show that the P95H mutation does not affect other functions of SRSF2, i.e., protein-protein interactions with key splicing factors. Our results thus demonstrate that the P95H mutation positively or negatively alters the binding affinity of SRSF2 for cognate RNA sites in target transcripts, leading to misregulation of exon inclusion. Our findings shed light on the mechanism of the disease-associated SRSF2 mutation in splicing regulation and also reveal a group of misspliced mRNA isoforms for potential therapeutic targeting.
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Romano M, Buratti E, Romano G, Klima R, Del Bel Belluz L, Stuani C, Baralle F, Feiguin F. Evolutionarily conserved heterogeneous nuclear ribonucleoprotein (hnRNP) A/B proteins functionally interact with human and Drosophila TAR DNA-binding protein 43 (TDP-43). J Biol Chem 2014; 289:7121-7130. [PMID: 24492607 DOI: 10.1074/jbc.m114.548859] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human TDP-43 represents the main component of neuronal inclusions found in patients with neurodegenerative diseases, especially frontotemporal lobar degeneration and amyotrophic lateral sclerosis. In vitro and in vivo studies have shown that the TAR DNA-binding protein 43 (TDP-43) Drosophila ortholog (TBPH) can biochemically and functionally overlap the properties of the human factor. The recent direct implication of the human heterogeneous nuclear ribonucleoproteins (hnRNPs) A2B1 and A1, known TDP-43 partners, in the pathogenesis of multisystem proteinopathy and amyotrophic lateral sclerosis supports the hypothesis that the physical and functional interplay between TDP-43 and hnRNP A/B orthologs might play a crucial role in the pathogenesis of neurodegenerative diseases. To test this hypothesis and further validate the fly system as a useful model to study this type of diseases, we have now characterized human TDP-43 and Drosophila TBPH similarity in terms of protein-protein interaction pathways. In this work we show that TDP-43 and TBPH share the ability to associate in vitro with Hrp38/Hrb98DE/CG9983, the fruit fly ortholog of the human hnRNP A1/A2 factors. Interestingly, the protein regions of TDP-43 and Hrp38 responsible for reciprocal interactions are conserved through evolution. Functionally, experiments in HeLa cells demonstrate that TDP-43 is necessary for the inhibitory activity of Hrp38 on splicing. Finally, Drosophila in vivo studies show that Hrp38 deficiency produces locomotive defects and life span shortening in TDP-43 with and without animals. These results suggest that hnRNP protein levels can play a modulatory role on TDP-43 functions.
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Affiliation(s)
- Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy.
| | - Emanuele Buratti
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Giulia Romano
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Raffaella Klima
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Lisa Del Bel Belluz
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
| | - Cristiana Stuani
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Francisco Baralle
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Fabian Feiguin
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
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Kim T, Kim JO, Oh JG, Hong SE, Kim DH. Pressure-overload cardiac hypertrophy is associated with distinct alternative splicing due to altered expression of splicing factors. Mol Cells 2014; 37:81-7. [PMID: 24552714 PMCID: PMC3907004 DOI: 10.14348/molcells.2014.2337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/18/2013] [Indexed: 01/05/2023] Open
Abstract
Chronic pressure-overload cardiac hypertrophy is associated with an increased risk of morbidity/mortality, largely due to maladaptive remodeling and dilatation that progresses to dilated cardiomyopathy. Alternative splicing is an important biological mechanism that generates proteomic complexity and diversity. The recent development of next-generation RNA sequencing has improved our understanding of the qualitative signatures associated with alternative splicing in various biological conditions. However, the role of alternative splicing in cardiac hypertrophy is yet unknown. The present study employed RNA-Seq and a bioinformatic approach to detect the RNA splicing regulatory elements involved in alternative splicing during pressure-overload cardiac hypertrophy. We found GC-rich exonic motifs that regulate intron retention in 5' UTRs and AT-rich exonic motifs that are involved in exclusion of the AT-rich elements that cause mRNA instability in 3' UTRs. We also identified motifs in the intronic regions involved in exon exclusion and inclusion, which predicted splicing factors that bind to these motifs. We found, through Western blotting, that the expression levels of three splicing factors, ESRP1, PTB and SF2/ASF, were significantly altered during cardiac hypertrophy. Collectively, the present results suggest that chronic pressure-overload hypertrophy is closely associated with distinct alternative splicing due to altered expression of splicing factors.
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Affiliation(s)
- Taeyong Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Jin Ock Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | | | - Seong-Eui Hong
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Do Han Kim
- School of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
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6
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Daubner GM, Cléry A, Jayne S, Stevenin J, Allain FHT. A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well. EMBO J 2011; 31:162-74. [PMID: 22002536 DOI: 10.1038/emboj.2011.367] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/12/2011] [Indexed: 11/09/2022] Open
Abstract
SRSF2 (SC35) is a key player in the regulation of alternative splicing events and binds degenerated RNA sequences with similar affinity in nanomolar range. We have determined the solution structure of the SRSF2 RRM bound to the 5'-UCCAGU-3' and 5'-UGGAGU-3' RNA, both identified as SRSF2 binding sites in the HIV-1 tat exon 2. RNA recognition is achieved through a novel sandwich-like structure with both termini forming a positively charged cavity to accommodate the four central nucleotides. To bind both RNA sequences equally well, SRSF2 forms a nearly identical network of intermolecular interactions by simply flipping the bases of the two consecutive C or G nucleotides into either anti or syn conformation. We validate this unusual mode of RNA recognition functionally by in-vitro and in-vivo splicing assays and propose a 5'-SSNG-3' (S=C/G) high-affinity binding consensus sequence for SRSF2. In conclusion, in addition to describe for the first time the RNA recognition mode of SRSF2, we provide the precise consensus sequence to identify new putative binding sites for this splicing factor.
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Affiliation(s)
- Gerrit M Daubner
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
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7
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Kolb SJ, Sutton S, Schoenberg DR. RNA processing defects associated with diseases of the motor neuron. Muscle Nerve 2010; 41:5-17. [PMID: 19697368 DOI: 10.1002/mus.21428] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rapid progress in the discovery of motor neuron disease genes in amyotrophic lateral sclerosis, the spinal muscular atrophies, hereditary motor neuropathies, and lethal congenital contracture syndromes is providing new perspectives and insights into the molecular pathogenesis of the motor neuron. Motor neuron disease genes are often expressed throughout the body with essential functions in all cells. A survey of these functions indicates that motor neurons are uniquely sensitive to perturbations in RNA processing pathways dependent on the interaction of specific RNAs with specific RNA-binding proteins, which presumably result in aberrant formation and function of ribonucleoprotein complexes. This review provides a summary of currently recognized RNA processing defects linked to human motor neuron diseases.
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Affiliation(s)
- Stephen J Kolb
- Department of Neurology, Ohio State University Medical Center, Hamilton Hall, Room 337B, 1645 Neil Avenue, Columbus, Ohio 43210-1228, USA
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8
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Buratti E, Baralle FE. The molecular links between TDP-43 dysfunction and neurodegeneration. ADVANCES IN GENETICS 2009; 66:1-34. [PMID: 19737636 DOI: 10.1016/s0065-2660(09)66001-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TDP-43 nuclear protein is involved in several major neurodegenerative diseases that include frontotemporal lobar degeneration with ubiquitin (FTLD-U) bodies and amyotrophic lateral sclerosis (ALS). As a consequence, the role played by this protein in both normal and diseased cellular metabolism has come under very close scrutiny. In the neuronal tissues of affected individuals TDP-43 undergoes aberrant localization to the cytoplasm to form insoluble aggregates. Furthermore, it is subject to degradation, ubiquitination, and phosphorylation. Understanding the pathways that lead to these changes will be crucial to define the functional role played by this protein in disease. Several recent biochemical and molecular studies have provided new information regarding the potential physiological consequences of these modifications. Moreover, the discovery of TDP-43 mutations associated with disease in a limited number of cases and the data from existing animal models have strengthened the proposed links between this protein and disease. In this review we will discuss the available data regarding the biochemical and functional changes that transform the wild-type endogenous TDP-43 in its pathological form. Furthermore, we will concentrate on examining the potential pathological mechanisms mediated by TDP-43 in different gain- versus loss-of-function scenarios. In the near future, this knowledge will hopefully increase our knowledge on disease progression and development. Moreover, it will allow the design of innovative therapeutic strategies for these pathologies based on the specific molecular defects causing the disease.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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9
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Ayala YM, Zago P, D'Ambrogio A, Xu YF, Petrucelli L, Buratti E, Baralle FE. Structural determinants of the cellular localization and shuttling of TDP-43. J Cell Sci 2008; 121:3778-85. [PMID: 18957508 DOI: 10.1242/jcs.038950] [Citation(s) in RCA: 437] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TDP-43 (also known as TARDBP) regulates different processes of gene expression, including transcription and splicing, through RNA and DNA binding. Moreover, recent reports have shown that the protein interacts with the 3'UTRs of specific mRNAs. The aberrant cellular distribution and aggregation of TDP-43 were recently reported in neurodegenerative diseases, namely frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). A detailed description of the determinants for cellular localization has yet to emerge, including information on how the known functions of TDP-43 and cellular targeting affect each other. We provide the first experimental evidence that TDP-43 continuously shuttles between nucleus and cytoplasm in a transcription-dependent manner. Furthermore, we investigate the role of the functional TDP-43 domains in determining cellular targeting through a combination of immunofluorescence and biochemical fractionation methods. Our analyses indicate that the C-terminus is essential for solubility and cellular localization, because its deletion results in the formation of large nuclear and cytoplasmic aggregates. Disruption of the RNA-recognition domain required for RNA and DNA binding, however, alters nuclear distribution by decreasing TDP-43 presence in the nucleoplasm. Our findings suggest that TDP-43 solubility and localization are particularly sensitive to disruptions that extend beyond the newly found nuclear localization signal and depend on a combination of factors that are closely connected to the functional properties of this protein.
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Affiliation(s)
- Youhna M Ayala
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
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10
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Buratti E, Brindisi A, Giombi M, Tisminetzky S, Ayala YM, Baralle FE. TDP-43 Binds Heterogeneous Nuclear Ribonucleoprotein A/B through Its C-terminal Tail. J Biol Chem 2005; 280:37572-84. [PMID: 16157593 DOI: 10.1074/jbc.m505557200] [Citation(s) in RCA: 367] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
TDP-43 is a highly conserved nuclear factor of yet unknown function that binds to ug-repeated sequences and is responsible for cystic fibrosis transmembrane conductance regulator exon 9 splicing inhibition. We have analyzed TDP-43 interactions with other splicing factors and identified the critical regions for the protein/protein recognition events that determine this biological function. We show here that the C-terminal region of TDP-43 is capable of binding directly to several proteins of the heterogeneous nuclear ribonucleoprotein (hnRNP) family with well known splicing inhibitory activity, in particular, hnRNP A2/B1 and hnRNP A1. Mutational analysis showed that TDP-43 proteins lacking the C-terminal region could not inhibit splicing probably because they were unable to form the hnRNP-rich complex involved in splicing inhibition. Finally, through splicing complex analysis, we show that splicing inhibition mediated by TDP-43 occurs at the earliest stages of spliceosomal assembly.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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11
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Mercado PA, Ayala YM, Romano M, Buratti E, Baralle FE. Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene. Nucleic Acids Res 2005; 33:6000-10. [PMID: 16254078 PMCID: PMC1270946 DOI: 10.1093/nar/gki897] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 09/19/2005] [Accepted: 09/27/2005] [Indexed: 01/11/2023] Open
Abstract
Exon 3 of the human apolipoprotein A-II (apoA-II) gene is efficiently included in the mRNA although its acceptor site is significantly weak because of a peculiar (GU)16 tract instead of a canonical polypyrimidine tract within the intron 2/exon 3 junction. Our previous studies demonstrated that the SR proteins ASF/SF2 and SC35 bind specifically an exonic splicing enhancer (ESE) within exon 3 and promote exon 3 splicing. In the present study, we show that the ESE is necessary only in the proper context. In addition, we have characterized two novel sequences in the flanking introns that modulate apoA-II exon 3 splicing. There is a G-rich element in intron 2 that interacts with hnRNPH1 and inhibits exon 3 splicing. The second is a purine rich region in intron 3 that binds SRp40 and SRp55 and promotes exon 3 inclusion in mRNA. We have also found that the (GU) repeats in the apoA-II context bind the splicing factor TDP-43 and interfere with exon 3 definition. Significantly, blocking of TDP-43 expression by small interfering RNA overrides the need for all the other cis-acting elements making exon 3 inclusion constitutive even in the presence of disrupted exonic and intronic enhancers. Altogether, our results suggest that exonic and intronic enhancers have evolved to balance the negative effects of the two silencers located in intron 2 and hence rescue the constitutive exon 3 inclusion in apoA-II mRNA.
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Affiliation(s)
- Pablo Arrisi Mercado
- International Centre for Genetic Engineering and BiotechnologyPadriciano 99, I-34012 Trieste, Italy
| | - Youhna M. Ayala
- International Centre for Genetic Engineering and BiotechnologyPadriciano 99, I-34012 Trieste, Italy
| | - Maurizio Romano
- International Centre for Genetic Engineering and BiotechnologyPadriciano 99, I-34012 Trieste, Italy
- Department of Physiology and Pathology, University of TriesteVia A. Fleming 22, 34127 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and BiotechnologyPadriciano 99, I-34012 Trieste, Italy
| | - Francisco E. Baralle
- International Centre for Genetic Engineering and BiotechnologyPadriciano 99, I-34012 Trieste, Italy
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Lei H, Vorechovsky I. Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression. Mol Cell Biol 2005; 25:6912-20. [PMID: 16055705 PMCID: PMC1190243 DOI: 10.1128/mcb.25.16.6912-6920.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3' splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.
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Affiliation(s)
- Haixin Lei
- University of Southampton School of Medicine, Division of Human Genetics, Duthie Building, UK
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