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Tan J, Roca X. Informational Suppression to Probe RNA:RNA Interactions in the Context of Ribonucleoproteins: U1 and 5' Splice-Site Base-Pairing. Methods Mol Biol 2016; 1421:243-68. [PMID: 26965270 DOI: 10.1007/978-1-4939-3591-8_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Informational suppression is a method to map specific RNA:RNA interactions by taking advantage of the rules of base complementarity. First, a predicted Watson-Crick base pair is broken by single-nucleotide substitution which disrupts the RNA's structure and/or function. Second, the base pair is restored by mutating the opposing nucleotide, thereby rescuing structure and/or function. This method applies to RNP:RNA interactions such as 5' splice-site (5'ss) base-pairing to the 5' end of U1 small nuclear RNA as part of a small nuclear RNP. Our protocol aims to determine the 5'ss:U1 base-pairing register for natural 5'ss, because for distinct 5'ss sequences the nucleotides on each strand can be aligned differently. This methodology includes cloning of a wild-type splicing minigene and introduction of 5'ss variants by PCR mutagenesis. A U1-expression plasmid is mutated to construct "suppressor U1" snRNAs with restored base-pairing to mutant 5'ss in different registers. Cells are transfected with combinations of minigenes and suppressor U1s, and the splicing patterns are analyzed by reverse transcription and semiquantitative PCR, followed by gel electrophoresis. The identity of suppressor U1s that rescue splicing for specific mutations indicates the register used in that 5'ss. We also provide tips to adapt this protocol to other minigenes or registers.
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Affiliation(s)
- Jiazi Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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52
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Georgomanolis T, Sofiadis K, Papantonis A. Cutting a Long Intron Short: Recursive Splicing and Its Implications. Front Physiol 2016; 7:598. [PMID: 27965595 PMCID: PMC5126111 DOI: 10.3389/fphys.2016.00598] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
Over time eukaryotic genomes have evolved to host genes carrying multiple exons separated by increasingly larger intronic, mostly non-protein-coding, sequences. Initially, little attention was paid to these intronic sequences, as they were considered not to contain regulatory information. However, advances in molecular biology, sequencing, and computational tools uncovered that numerous segments within these genomic elements do contribute to the regulation of gene expression. Introns are differentially removed in a cell type-specific manner to produce a range of alternatively-spliced transcripts, and many span tens to hundreds of kilobases. Recent work in human and fruitfly tissues revealed that long introns are extensively processed cotranscriptionally and in a stepwise manner, before their two flanking exons are spliced together. This process, called "recursive splicing," often involves non-canonical splicing elements positioned deep within introns, and different mechanisms for its deployment have been proposed. Still, the very existence and widespread nature of recursive splicing offers a new regulatory layer in the transcript maturation pathway, which may also have implications in human disease.
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Affiliation(s)
- Theodore Georgomanolis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
| | - Konstantinos Sofiadis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
| | - Argyris Papantonis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
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Yadegari H, Biswas A, Akhter MS, Driesen J, Ivaskevicius V, Marquardt N, Oldenburg J. Intron retention resulting from a silent mutation in the VWF gene that structurally influences the 5' splice site. Blood 2016; 128:2144-2152. [PMID: 27543438 PMCID: PMC5161009 DOI: 10.1182/blood-2016-02-699686] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/08/2016] [Indexed: 12/26/2022] Open
Abstract
Disease-associated silent mutations are considered to affect the accurate pre-messenger RNA (mRNA) splicing either by influencing regulatory elements, leading to exon skipping, or by creating a new cryptic splice site. This study describes a new molecular pathological mechanism by which a silent mutation inhibits splicing and leads to intron retention. We identified a heterozygous silent mutation, c.7464C>T, in exon 44 of the von Willebrand factor (VWF) gene in a family with type 1 von Willebrand disease. In vivo and ex vivo transcript analysis revealed an aberrantly spliced transcript, with intron 44 retained in the mRNA, implying disruption of the first catalytic step of splicing at the 5' splice site (5'ss). The abnormal transcript with the retained intronic region coded a truncated protein that lacked the carboxy-terminal end of the VWF protein. Confocal immunofluorescence characterizations of blood outgrowth endothelial cells derived from the patient confirmed the presence of the truncated protein by demonstrating accumulation of VWF in the endoplasmic reticulum. In silico pre-mRNA secondary and tertiary structure analysis revealed that this substitution, despite its distal position from the 5'ss (85 bp downstream), induces cis alterations in pre-mRNA structure that result in the formation of a stable hairpin at the 5'ss. This hairpin sequesters the 5'ss residues involved in U1 small nuclear RNA interactions, thereby inhibiting excision of the pre-mRNA intronic region. This study is the first to show the allosteric-like/far-reaching effect of an exonic variation on pre-mRNA splicing that is mediated by structural changes in the pre-mRNA.
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Affiliation(s)
- Hamideh Yadegari
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Arijit Biswas
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Mohammad Suhail Akhter
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Julia Driesen
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Vytautas Ivaskevicius
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Natascha Marquardt
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
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54
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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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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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Tang SJ, Luo S, Ho JXJ, Ly PT, Goh E, Roca X. Characterization of the Regulation of CD46 RNA Alternative Splicing. J Biol Chem 2016; 291:14311-14323. [PMID: 27226545 DOI: 10.1074/jbc.m115.710350] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Indexed: 11/06/2022] Open
Abstract
Here we present a detailed analysis of the alternative splicing regulation of human CD46, which generates different isoforms with distinct functions. CD46 is a ubiquitous membrane protein that protects host cells from complement and plays other roles in immunity, autophagy, and cell adhesion. CD46 deficiency causes an autoimmune disorder, and this protein is also involved in pathogen infection and cancer. Before this study, the mechanisms of CD46 alternative splicing remained unexplored even though dysregulation of this process has been associated with autoimmune diseases. We proved that the 5' splice sites of CD46 cassette exons 7 and 8 encoding extracellular domains are defined by noncanonical mechanisms of base pairing to U1 small nuclear RNA. Next we characterized the regulation of CD46 cassette exon 13, whose inclusion or skipping generates different cytoplasmic tails with distinct functions. Using splicing minigenes, we identified multiple exonic and intronic splicing enhancers and silencers that regulate exon 13 inclusion via trans-acting splicing factors like PTBP1 and TIAL1. Interestingly, a common splicing activator such as SRSF1 appears to repress CD46 exon 13 inclusion. We also report that expression of CD46 mRNA isoforms is further regulated by non-sense-mediated mRNA decay and transcription speed. Finally, we successfully manipulated CD46 exon 13 inclusion using antisense oligonucleotides, opening up opportunities for functional studies of the isoforms as well as for therapeutics for autoimmune diseases. This study provides insight into CD46 alternative splicing regulation with implications for its function in the immune system and for genetic disease.
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Affiliation(s)
- Sze Jing Tang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shufang Luo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jia Xin Jessie Ho
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Phuong Thao Ly
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Eling Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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57
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Kawaguchi R, Kiryu H. Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. BMC Bioinformatics 2016; 17:203. [PMID: 27153986 PMCID: PMC4858847 DOI: 10.1186/s12859-016-1067-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/29/2016] [Indexed: 02/08/2023] Open
Abstract
Background RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems. Results Our novel software, “ParasoR”, is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions. Conclusions We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a million bases in the human genome. In our analyses, transcribed regions including introns are indicated to be subject to various types of structural constraints that cannot be explained from simple sequence composition biases. ParasoR is freely available at https://github.com/carushi/ParasoR. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1067-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Risa Kawaguchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
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58
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Tan J, Ho JXJ, Zhong Z, Luo S, Chen G, Roca X. Noncanonical registers and base pairs in human 5' splice-site selection. Nucleic Acids Res 2016; 44:3908-21. [PMID: 26969736 PMCID: PMC4856993 DOI: 10.1093/nar/gkw163] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/27/2022] Open
Abstract
Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5' splice sites are mainly recognized by canonical base-pairing to the 5' end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5' splice site/U1 helix contributes to the recognition of certain 5' splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5' splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5' splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences.
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Affiliation(s)
- Jiazi Tan
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Jia Xin Jessie Ho
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zhensheng Zhong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Shufang Luo
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Gang Chen
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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59
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Yamauchi Y, Nobe Y, Izumikawa K, Higo D, Yamagishi Y, Takahashi N, Nakayama H, Isobe T, Taoka M. A mass spectrometry-based method for direct determination of pseudouridine in RNA. Nucleic Acids Res 2015; 44:e59. [PMID: 26673725 PMCID: PMC4824092 DOI: 10.1093/nar/gkv1462] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/27/2015] [Indexed: 02/01/2023] Open
Abstract
Pseudouridine (5-ribosyluracil, Ψ) is the only ‘mass-silent’ nucleoside produced by post-transcriptional RNA modification. We describe here a novel mass spectrometry (MS)-based method for direct determination of Ψ in RNA. The method assigns a Ψ-containing nucleolytic RNA fragment by an accurate measurement of a signature doubly dehydrated nucleoside anion ([C9H7N2O4]1−, m/z 207.04) produced by collision-induced dissociation MS, and it determines the Ψ-containing nucleotide sequence by pseudo-MS3, i.e. in-source fragmentation followed by MS2. By applying this method, we identified all of the known Ψs in the canonical human spliceosomal snRNAs and, unexpectedly, found two previously unknown Ψs in the U5 and U6 snRNAs. Because the method allows direct determination of Ψ in a subpicomole quantity of RNA, it will serve as a useful tool for the structure/function studies of a wide variety of non-coding RNAs.
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Affiliation(s)
- Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Keiichi Izumikawa
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Daisuke Higo
- Thermo Fisher Scientific, 3-9 Moriya-cho, Kanagawa-ku, Yokohama-shi, Kanagawa 221-0022, Japan
| | - Yoko Yamagishi
- Thermo Fisher Scientific, 3-9 Moriya-cho, Kanagawa-ku, Yokohama-shi, Kanagawa 221-0022, Japan
| | - Nobuhiro Takahashi
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Hiroshi Nakayama
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
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60
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Papasaikas P, Valcárcel J. The Spliceosome: The Ultimate RNA Chaperone and Sculptor. Trends Biochem Sci 2015; 41:33-45. [PMID: 26682498 DOI: 10.1016/j.tibs.2015.11.003] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
The spliceosome, one of the most complex machineries of eukaryotic cells, removes intronic sequences from primary transcripts to generate functional messenger and long noncoding RNAs (lncRNA). Genetic, biochemical, and structural data reveal that the spliceosome is an RNA-based enzyme. Striking mechanistic and structural similarities strongly argue that pre-mRNA introns originated from self-catalytic group II ribozymes. However, in the spliceosome, protein components organize and activate the catalytic-site RNAs, and recognize and pair together splice sites at intron boundaries. The spliceosome is a dynamic, reversible, and flexible machine that chaperones small nuclear (sn) RNAs and a variety of pre-mRNA sequences into conformations that enable intron removal. This malleability likely contributes to the regulation of alternative splicing, a prevalent process contributing to cell differentiation, homeostasis, and disease.
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Affiliation(s)
- Panagiotis Papasaikas
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu-Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu-Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain.
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61
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Becerra S, Andrés-León E, Prieto-Sánchez S, Hernández-Munain C, Suñé C. Prp40 and early events in splice site definition. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:17-32. [PMID: 26494226 DOI: 10.1002/wrna.1312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/18/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022]
Abstract
The alternative splicing (AS) of precursor messenger RNA (pre-mRNA) is a tightly regulated process through which introns are removed to leave the resulting exons in the mRNA appropriately aligned and ligated. The AS of pre-mRNA is a key mechanism for increasing the complexity of proteins encoded in the genome. In humans, more than 90% of genes undergo AS, underscoring the importance of this process in RNA biogenesis. As such, AS misregulation underlies multiple human diseases. The splicing reaction is catalyzed by the spliceosome, a highly dynamic complex that assembles at or near the intron/exon boundaries and undergoes sequential conformational and compositional changes during splicing. The initial recognition of splice sites defines the exons that are going to be removed, which is a critical step in the highly regulated splicing process. Although the available lines of evidence are increasing, the molecular mechanisms governing AS, including the initial interactions occurring at intron/exon boundaries, and the factors that modulate these critical connections by functioning as a scaffold for active-site RNAs or proteins, remain poorly understood. In this review, we summarize the major hallmarks of the initial steps in the splicing process and the role of auxiliary factors that contribute to the assembly of the spliceosomal complex. We also discuss the role of the essential yeast Prp40 protein and its mammalian homologs in the specificity of this pre-mRNA processing event. In addition, we provide the first exhaustive phylogenetic analysis of the molecular evolution of Prp40 family members. WIREs RNA 2016, 7:17-32. doi: 10.1002/wrna.1312 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soraya Becerra
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
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62
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RNA-Binding Proteins: Splicing Factors and Disease. Biomolecules 2015; 5:893-909. [PMID: 25985083 PMCID: PMC4496701 DOI: 10.3390/biom5020893] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/22/2015] [Accepted: 04/29/2015] [Indexed: 12/12/2022] Open
Abstract
Pre-mRNA splicing is mediated by interactions of the Core Spliceosome and an array of accessory RNA binding proteins with cis-sequence elements. Splicing is a major regulatory component in higher eukaryotes. Disruptions in splicing are a major contributor to human disease. One in three hereditary disease alleles are believed to cause aberrant splicing. Hereditary disease alleles can alter splicing by disrupting a splicing element, creating a toxic RNA, or affecting splicing factors. One of the challenges of medical genetics is identifying causal variants from the thousands of possibilities discovered in a clinical sequencing experiment. Here we review the basic biochemistry of splicing, the mechanisms of splicing mutations, the methods for identifying splicing mutants, and the potential of therapeutic interventions.
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63
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Zhong Z, Soh LH, Lim MH, Chen G. A U⋅U Pair-to-U⋅C Pair Mutation-Induced RNA Native Structure Destabilisation and Stretching-Force-Induced RNA Misfolding. Chempluschem 2015; 80:1267-1278. [PMID: 31973291 DOI: 10.1002/cplu.201500144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/21/2015] [Indexed: 12/21/2022]
Abstract
Little is known about how a non-Watson-Crick pair affects the RNA folding dynamics. We studied the effects of a U⋅U-to-U⋅C pair mutation on the folding of a hairpin in human telomerase RNA. The ensemble thermal melting of the hairpins shows an on-pathway intermediate with the disruption of the internal loop structure containing the U⋅U/U⋅C pairs. By using optical tweezers, we applied a stretching force on the terminal ends of the hairpins to probe directly the non-nearest-neighbour effects upon the mutations. The single U⋅U to U⋅C mutations are observed to 1) lower the mechanical unfolding force by approximately 1 picoNewton (pN) per mutation without affecting the unfolding reaction transition-state position (thus suggesting that removing a single hydrogen bond affects the structural dynamics at least two base pairs away), 2) result in more frequent misfolding into a small hairpin at approximately 10 pN and 3) shift the folding reaction transition-state position towards the native hairpin structure and slightly increase the mechanical folding kinetics (thus suggesting that untrapping from the misfolded state is not the rate-limiting step).
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Affiliation(s)
- Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
| | - Lai Huat Soh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
| | - Ming Hui Lim
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
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64
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Kelly S, Georgomanolis T, Zirkel A, Diermeier S, O'Reilly D, Murphy S, Längst G, Cook PR, Papantonis A. Splicing of many human genes involves sites embedded within introns. Nucleic Acids Res 2015; 43:4721-32. [PMID: 25897131 PMCID: PMC4482092 DOI: 10.1093/nar/gkv386] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 04/12/2015] [Indexed: 02/03/2023] Open
Abstract
The conventional model for splicing involves excision of each intron in one piece; we demonstrate this inaccurately describes splicing in many human genes. First, after switching on transcription of SAMD4A, a gene with a 134 kb-long first intron, splicing joins the 3′ end of exon 1 to successive points within intron 1 well before the acceptor site at exon 2 is made. Second, genome-wide analysis shows that >60% of active genes yield products generated by such intermediate intron splicing. These products are present at ∼15% the levels of primary transcripts, are encoded by conserved sequences similar to those found at canonical acceptors, and marked by distinctive structural and epigenetic features. Finally, using targeted genome editing, we demonstrate that inhibiting the formation of these splicing intermediates affects efficient exon–exon splicing. These findings greatly expand the functional and regulatory complexity of the human transcriptome.
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Affiliation(s)
- Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | | | - Anne Zirkel
- Centre for Molecular Medicine, University of Cologne, Cologne D-50931, Germany
| | - Sarah Diermeier
- Institut für Biochemie III, University of Regensburg, Regensburg D-93053, Germany
| | - Dawn O'Reilly
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Gernot Längst
- Institut für Biochemie III, University of Regensburg, Regensburg D-93053, Germany
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Argyris Papantonis
- Centre for Molecular Medicine, University of Cologne, Cologne D-50931, Germany
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65
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Morrison A, Chekaluk Y, Bacares R, Ladanyi M, Zhang L. BAP1 missense mutation c.2054 A>T (p.E685V) completely disrupts normal splicing through creation of a novel 5' splice site in a human mesothelioma cell line. PLoS One 2015; 10:e0119224. [PMID: 25830670 PMCID: PMC4382119 DOI: 10.1371/journal.pone.0119224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 01/12/2015] [Indexed: 12/11/2022] Open
Abstract
BAP1 is a tumor suppressor gene that is lost or deleted in diverse cancers, including uveal mela¬noma, malignant pleural mesothelioma (MPM), clear cell renal carcinoma, and cholangiocarcinoma. Recently, BAP1 germline mutations have been reported in families with combinations of these same cancers. A particular challenge for mutation screening is the classification of non-truncating BAP1 sequence variants because it is not known whether these subtle changes can affect the protein function sufficiently to predispose to cancer development. Here we report mRNA splicing analysis on a homozygous substitution mutation, BAP1 c. 2054 A&T (p.Glu685Val), identified in an MPM cell line derived from a mesothelioma patient. The mutation occurred at the 3rd nucleotide from the 3' end of exon 16. RT-PCR, cloning and subsequent sequencing revealed several aberrant splicing products not observed in the controls: 1) a 4 bp deletion at the end of exon 16 in all clones derived from the major splicing product. The BAP1 c. 2054 A&T mutation introduced a new 5' splice site (GU), which resulted in the deletion of 4 base pairs and presumably protein truncation; 2) a variety of alternative splicing products that led to retention of different introns: introns 14-16; introns 15-16; intron 14 and intron 16; 3) partial intron 14 and 15 retentions caused by activation of alternative 3' splice acceptor sites (AG) in the introns. Taken together, we were unable to detect any correctly spliced mRNA transcripts in this cell line. These results suggest that aberrant splicing caused by this mutation is quite efficient as it completely abolishes normal splicing through creation of a novel 5' splice site and activation of cryptic splice sites. These data support the conclusion that BAP1 c.2054 A&T (p.E685V) variant is a pathogenic mutation and contributes to MPM through disruption of normal splicing.
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Affiliation(s)
- Arianne Morrison
- School of Medicine, Wake Forest University, Winston Salem, North Carolina, United States of America
| | - Yvonne Chekaluk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ruben Bacares
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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66
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Sharma S, Wongpalee SP, Vashisht A, Wohlschlegel JA, Black DL. Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly. Genes Dev 2015; 28:2518-31. [PMID: 25403181 PMCID: PMC4233244 DOI: 10.1101/gad.248625.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Sharma et al. report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice, and a component of the U2 snRNP complex, which assembles across the intron at the 3′ splice site. U1-SL4 interacts with the SF3A1 protein of the U2 snRNP, and this interaction occurs within prespliceosomal complexes assembled on the pre-mRNA. The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Interactions that bring the two splice sites together during spliceosome assembly must occur with a high degree of specificity and fidelity to allow expression of functional mRNAs and make particular alternative splicing choices. Here, we report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice site, and a component of the U2 small nuclear ribonucleoprotein particle (snRNP) complex, which assembles across the intron at the 3′ splice site. Using a U1 snRNP complementation assay, we found that SL4 is essential for splicing in vivo. The addition of free U1-SL4 to a splicing reaction in vitro inhibits splicing and blocks complex assembly prior to formation of the prespliceosomal A complex, indicating a requirement for a SL4 contact in spliceosome assembly. To characterize the interactions of this RNA structure, we used a combination of stable isotope labeling by amino acids in cell culture (SILAC), biotin/Neutravidin affinity pull-down, and mass spectrometry. We show that U1-SL4 interacts with the SF3A1 protein of the U2 snRNP. We found that this interaction between the U1 snRNA and SF3A1 occurs within prespliceosomal complexes assembled on the pre-mRNA. Thus, SL4 of the U1 snRNA is important for splicing, and its interaction with SF3A1 mediates contact between the 5′ and 3′ splice site complexes within the assembling spliceosome.
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Affiliation(s)
- Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA; Department of Microbiology, Immunology, and Molecular Genetics
| | | | | | | | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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67
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Dal Mas A, Rogalska M, Bussani E, Pagani F. Improvement of SMN2 pre-mRNA processing mediated by exon-specific U1 small nuclear RNA. Am J Hum Genet 2015; 96:93-103. [PMID: 25557785 PMCID: PMC4289686 DOI: 10.1016/j.ajhg.2014.12.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022] Open
Abstract
Exon-specific U1 snRNAs (ExSpe U1s) are modified U1 snRNAs that interact with intronic sequences downstream of the 5′ splice site (ss) by complementarity. This process restores exon skipping caused by different types of mutation. We have investigated the molecular mechanism and activity of these molecules in spinal muscular atrophy (SMA), a genetic neuromuscular disease where a silent exonic transition on the survival motor neuron 2 (SMN2) leads to exon 7 (E7) skipping. By using different cellular models, we show that a single chromosome-integrated copy of ExSpe U1 induced a significant correction of endogenous SMN2 E7 splicing and resulted in the restoration of the corresponding SMN protein levels. Interestingly, the analysis of pre-mRNA transcript abundance and decay showed that ExSpe U1s promote E7 inclusion and stabilizes the SMN pre-mRNA intermediate. This selective effect on pre-mRNA stability resulted in higher levels of SMN mRNAs in comparison with those after treatment with an antisense oligonucleotide (AON) that targets corresponding intronic sequences. In mice harboring the SMN2 transgene, AAV-mediated delivery of ExSpe U1 increased E7 inclusion in brain, heart, liver, kidney, and skeletal muscle. The positive effect of ExSpe U1s on SMN pre-mRNA processing highlights their therapeutic potential in SMA and in other pathologies caused by exon-skipping mutations.
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68
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Kondo Y, Oubridge C, van Roon AMM, Nagai K. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition. eLife 2015; 4. [PMID: 25555158 PMCID: PMC4383343 DOI: 10.7554/elife.04986] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 12/12/2022] Open
Abstract
U1 snRNP binds to the 5′ exon-intron junction of pre-mRNA and thus plays a
crucial role at an early stage of pre-mRNA splicing. We present two crystal
structures of engineered U1 sub-structures, which together reveal at atomic
resolution an almost complete network of protein–protein and RNA-protein
interactions within U1 snRNP, and show how the 5′ splice site of pre-mRNA is
recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between
pre-mRNA and the 5′-end of U1 snRNA. The binding of the RNA duplex is
stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA
backbone around the splice junction but U1-C makes no base-specific contacts with
pre-mRNA. The structure, together with RNA binding assays, shows that the selection
of 5′-splice site nucleotides by U1 snRNP is achieved predominantly through
basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched
5′-splice sites. DOI:http://dx.doi.org/10.7554/eLife.04986.001 Genes are made up of long stretches of DNA. The regions of a gene that code for
proteins (known as exons) are interrupted by stretches of non-coding DNA called
introns. To produce proteins from a gene, the DNA is ‘transcribed’ to
form pre-mRNA molecules, from which the introns must be removed in a process called
splicing. The remaining exons are then joined together to form a mature mRNA molecule
that contains the instructions to build a protein. Errors in the splicing process can
lead to numerous diseases, such as cancer. A molecular machine known as a spliceosome is responsible for splicing the pre-mRNA
molecules. This consists of five different complexes called small nuclear
ribonucleoprotein particles (snRNPs), which are in turn made up from numerous
proteins and RNA molecules. The spliceosome assembles anew every time it splices, and
an early step in this assembly process involves the interaction of an snRNP called U1
with the start of an intron in the pre-mRNA. This interaction then stimulates the
assembly of the rest of the spliceosome. In 2009, researchers reported the structure
of the U1 snRNP, but the structure did not contain enough detail to reveal how the
snRNP recognizes the start of an intron. Kondo, Oubridge et al., including some of the researchers involved in the 2009 work,
now present the crystal structure of the human version of the U1 snRNP in more
detail. High-quality crystal structures of the complete U1 snRNP molecule could not
be obtained because the arrangement of the RNA molecules in the snRNP prevented a
regular crystal from forming. Kondo, Oubridge et al. instead engineered two
subcomponents of U1 snRNP that each crystallized well, and determined their
structures. This revealed that the interactions between the various parts of the U1
snRNP form a complex network. A protein present in the U1 snRNP, known as U1-C, had previously been reported to be
able to recognize introns on its own—without requiring the complete U1 snRNP.
Kondo, Oubridge et al. reveal that this is not the case and that U1-C does not read
the intron RNA sequence directly. Instead, U1 snRNP is able to find the start of the
intron because the U1 RNA can stably bind to this site. The U1-C protein can however
adjust the strength of this binding to ensure that the spliceosome can operate with a
variety of intron start sequences (or signals). DOI:http://dx.doi.org/10.7554/eLife.04986.002
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Affiliation(s)
- Yasushi Kondo
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chris Oubridge
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Anne-Marie M van Roon
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Kiyoshi Nagai
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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69
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Soemedi R, Vega H, Belmont JM, Ramachandran S, Fairbrother WG. Genetic variation and RNA binding proteins: tools and techniques to detect functional polymorphisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:227-66. [PMID: 25201108 DOI: 10.1007/978-1-4939-1221-6_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
At its most fundamental level the goal of genetics is to connect genotype to phenotype. This question is asked at a basic level evaluating the role of genes and pathways in genetic model organism. Increasingly, this question is being asked in the clinic. Genomes of individuals and populations are being sequenced and compared. The challenge often comes at the stage of analysis. The variant positions are analyzed with the hope of understanding human disease. However after a genome or exome has been sequenced, the researcher is often deluged with hundreds of potentially relevant variations. Traditionally, amino-acid changing mutations were considered the tractable class of disease-causing mutations; however, mutations that disrupt noncoding elements are the subject of growing interest. These noncoding changes are a major avenue of disease (e.g., one in three hereditary disease alleles are predicted to affect splicing). Here, we review some current practices of medical genetics, the basic theory behind biochemical binding and functional assays, and then explore technical advances in how variations that alter RNA protein recognition events are detected and studied. These advances are advances in scale-high-throughput implementations of traditional biochemical assays that are feasible to perform in any molecular biology laboratory. This chapter utilizes a case study approach to illustrate some methods for analyzing polymorphisms. The first characterizes a functional intronic SNP that deletes a high affinity PTB site using traditional low-throughput biochemical and functional assays. From here we demonstrate the utility of high-throughput splicing and spliceosome assembly assays for screening large sets of SNPs and disease alleles for allelic differences in gene expression. Finally we perform three pilot drug screens with small molecules (G418, tetracycline, and valproic acid) that illustrate how compounds that rescue specific instances of differential pre-mRNA processing can be discovered.
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Affiliation(s)
- Rachel Soemedi
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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70
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Matos L, Canals I, Dridi L, Choi Y, Prata MJ, Jordan P, Desviat LR, Pérez B, Pshezhetsky AV, Grinberg D, Alves S, Vilageliu L. Therapeutic strategies based on modified U1 snRNAs and chaperones for Sanfilippo C splicing mutations. Orphanet J Rare Dis 2014; 9:180. [PMID: 25491247 PMCID: PMC4279800 DOI: 10.1186/s13023-014-0180-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutations affecting RNA splicing represent more than 20% of the mutant alleles in Sanfilippo syndrome type C, a rare lysosomal storage disorder that causes severe neurodegeneration. Many of these mutations are localized in the conserved donor or acceptor splice sites, while few are found in the nearby nucleotides. METHODS In this study we tested several therapeutic approaches specifically designed for different splicing mutations depending on how the mutations affect mRNA processing. For three mutations that affect the donor site (c.234 + 1G > A, c.633 + 1G > A and c.1542 + 4dupA), different modified U1 snRNAs recognizing the mutated donor sites, have been developed in an attempt to rescue the normal splicing process. For another mutation that affects an acceptor splice site (c.372-2A > G) and gives rise to a protein lacking four amino acids, a competitive inhibitor of the HGSNAT protein, glucosamine, was tested as a pharmacological chaperone to correct the aberrant folding and to restore the normal trafficking of the protein to the lysosome. RESULTS Partial correction of c.234 + 1G > A mutation was achieved with a modified U1 snRNA that completely matches the splice donor site suggesting that these molecules may have a therapeutic potential for some splicing mutations. Furthermore, the importance of the splice site sequence context is highlighted as a key factor in the success of this type of therapy. Additionally, glucosamine treatment resulted in an increase in the enzymatic activity, indicating a partial recovery of the correct folding. CONCLUSIONS We have assayed two therapeutic strategies for different splicing mutations with promising results for the future applications.
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Affiliation(s)
- Liliana Matos
- Department of Human Genetics, Research and Development Unit, INSA, Porto, Portugal. .,Department of Biology, Faculty of Sciences, Porto, Portugal.
| | - Isaac Canals
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Larbi Dridi
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada.
| | - Yoo Choi
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada.
| | - Maria João Prata
- Department of Biology, Faculty of Sciences, Porto, Portugal. .,IPATIMUP, Porto, Portugal.
| | - Peter Jordan
- Department of Human Genetics, Research and Development Unit, INSA, Lisbon, Portugal.
| | - Lourdes R Desviat
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Belén Pérez
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Alexey V Pshezhetsky
- Department of Medical Genetics, Sainte-Justine University Hospital Centre, University of Montreal, Montreal, Canada. .,Department of Anatomy and Cell Biology, Faculty of Medicine, McGill University, Montreal, Canada.
| | - Daniel Grinberg
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Sandra Alves
- Department of Human Genetics, Research and Development Unit, INSA, Porto, Portugal.
| | - Lluïsa Vilageliu
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain. .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
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71
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Gandolfi B, Daniel RJ, O'Brien DP, Guo LT, Youngs MD, Leach SB, Jones BR, Shelton GD, Lyons LA. A novel mutation in CLCN1 associated with feline myotonia congenita. PLoS One 2014; 9:e109926. [PMID: 25356766 PMCID: PMC4214686 DOI: 10.1371/journal.pone.0109926] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/05/2014] [Indexed: 12/30/2022] Open
Abstract
Myotonia congenita (MC) is a skeletal muscle channelopathy characterized by inability of the muscle to relax following voluntary contraction. Worldwide population prevalence in humans is 1∶100,000. Studies in mice, dogs, humans and goats confirmed myotonia associated with functional defects in chloride channels and mutations in a skeletal muscle chloride channel (CLCN1). CLCN1 encodes for the most abundant chloride channel in the skeletal muscle cell membrane. Five random bred cats from Winnipeg, Canada with MC were examined. All cats had a protruding tongue, limited range of jaw motion and drooling with prominent neck and proximal limb musculature. All cats had blepharospasm upon palpebral reflex testing and a short-strided gait. Electromyograms demonstrated myotonic discharges at a mean frequency of 300 Hz resembling the sound of a ‘swarm of bees’. Muscle histopathology showed hypertrophy of all fiber types. Direct sequencing of CLCN1 revealed a mutation disrupting a donor splice site downstream of exon 16 in only the affected cats. In vitro translation of the mutated protein predicted a premature truncation and partial lack of the highly conserved CBS1 (cystathionine β-synthase) domain critical for ion transport activity and one dimerization domain pivotal in channel formation. Genetic screening of the Winnipeg random bred population of the cats' origin identified carriers of the mutation. A genetic test for population screening is now available and carrier cats from the feral population can be identified.
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Affiliation(s)
- Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
- * E-mail:
| | - Rob J. Daniel
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
| | - Dennis P. O'Brien
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
| | - Ling T. Guo
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | | | - Stacey B. Leach
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
| | - Boyd R. Jones
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - G. Diane Shelton
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
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72
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Guiro J, O'Reilly D. Insights into the U1 small nuclear ribonucleoprotein complex superfamily. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:79-92. [DOI: 10.1002/wrna.1257] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/17/2014] [Accepted: 07/14/2014] [Indexed: 12/12/2022]
Affiliation(s)
- J Guiro
- Institute of Biosciences; University of Sao Paulo; Sao Paulo Brazil
| | - D O'Reilly
- Sir William Dunn School of Pathology; Oxford United Kingdom
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73
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Roca X, Krainer AR, Eperon IC. Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev 2013; 27:129-44. [PMID: 23348838 DOI: 10.1101/gad.209759.112] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Splice site selection is fundamental to pre-mRNA splicing and the expansion of genomic coding potential. 5' Splice sites (5'ss) are the critical elements at the 5' end of introns and are extremely diverse, as thousands of different sequences act as bona fide 5'ss in the human transcriptome. Most 5'ss are recognized by base-pairing with the 5' end of the U1 small nuclear RNA (snRNA). Here we review the history of research on 5'ss selection, highlighting the difficulties of establishing how base-pairing strength determines splicing outcomes. We also discuss recent work demonstrating that U1 snRNA:5'ss helices can accommodate noncanonical registers such as bulged duplexes. In addition, we describe the mechanisms by which other snRNAs, regulatory proteins, splicing enhancers, and the relative positions of alternative 5'ss contribute to selection. Moreover, we discuss mechanisms by which the recognition of numerous candidate 5'ss might lead to selection of a single 5'ss and propose that protein complexes propagate along the exon, thereby changing its physical behavior so as to affect 5'ss selection.
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Affiliation(s)
- Xavier Roca
- School of Biological Sciences, Division of Molecular Genetics and Cell Biology, Nanyang Technological University, Singapore.
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74
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Abstract
Several bacterial fermentation products and their synthetic derivatives display antitumour activities and bind tightly to components of the spliceosome, which is the complex molecular machinery involved in the removal of introns from mRNA precursors in eukaryotic cells. The drugs alter gene expression, including alternative splicing, of genes that are important for cancer progression. A flurry of recent reports has revealed that genes encoding splicing factors, including the drug target splicing factor 3B subunit 1 (SF3B1), are among the most highly mutated in various haematological malignancies such as chronic lymphocytic leukaemia and myelodysplastic syndromes. These observations highlight the role of splicing factors in cancer and suggest that an understanding of the molecular effects of drugs targeting these proteins could open new perspectives for studies of the spliceosome and its role in cancer progression, and for the development of novel antitumour therapies.
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75
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Pérez-Valle J, Vilardell J. Intronic features that determine the selection of the 3' splice site. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:707-17. [PMID: 22807288 DOI: 10.1002/wrna.1131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Most eukaryotic primary transcripts include segments, or introns, that will be accurately removed during RNA biogenesis. This process, known as pre-messenger RNA splicing, is catalyzed by the spliceosome, accurately selecting a set of intronic marks from others apparently equivalent. This identification is critical, as incorrectly spliced RNAs can be toxic for the organism. One of these marks, the dinucleotide AG, signals the intronic 3' end, or 3' splice site (ss). In this review we will focus on those intronic features that have an impact on 3' ss selection. These include the location and type of neighboring sequences, and their distance to the 3' end. We will see that their interplay is needed to select the right intronic end, and that this can be modulated by additional intronic elements that contribute to alternative splicing, whereby diverse RNAs can be generated from identical precursors. This complexity, still poorly understood, is fundamental for the accuracy of gene expression. In addition, a clear knowledge of 3' ss selection is needed to fully decipher the coding potential of genomes.
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Affiliation(s)
- Jorge Pérez-Valle
- Department of Molecular Genòmics, Institute of Molecular Biology of Barcelona (IBMB), Barcelona, Spain
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