1
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Osterhoudt K, Bagno O, Katzman S, Zahler AM. Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage. RNA (NEW YORK, N.Y.) 2024; 30:404-417. [PMID: 38282418 PMCID: PMC10946429 DOI: 10.1261/rna.079888.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
RNA helicases drive necessary rearrangements and ensure fidelity during the pre-mRNA splicing cycle. DEAD-box helicase DDX41 has been linked to human disease and has recently been shown to interact with DEAH-box helicase PRP22 in the spliceosomal C* complex, yet its function in splicing remains unknown. Depletion of DDX41 homolog SACY-1 from somatic cells has been previously shown to lead to changes in alternative 3' splice site (3'ss) usage. Here, we show by transcriptomic analysis of published and novel data sets that SACY-1 perturbation causes a previously unreported pattern in alternative 3' splicing in introns with pairs of 3' splice sites ≤18 nt away from each other. We find that both SACY-1 depletion and the allele sacy-1(G533R) lead to a striking unidirectional increase in the usage of the proximal (upstream) 3'ss. We previously discovered a similar alternative splicing pattern between germline tissue and somatic tissue, in which there is a unidirectional increase in proximal 3'ss usage in the germline for ∼200 events; many of the somatic SACY-1 alternative 3' splicing events overlap with these developmentally regulated events. We generated targeted mutant alleles of the Caenorhabditis elegans homolog of PRP22, mog-5, in the region of MOG-5 that is predicted to interact with SACY-1 based on the human C* structure. These viable alleles, and a mimic of the myelodysplastic syndrome-associated allele DDX41(R525H), all promote the usage of proximal alternative adjacent 3' splice sites. We show that PRP22/MOG-5 and DDX41/SACY-1 have overlapping roles in proofreading the 3'ss.
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Affiliation(s)
- Kenneth Osterhoudt
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Orazio Bagno
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Sol Katzman
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Alan M Zahler
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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2
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Yıldırım B, Vogl C. Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract. J Evol Biol 2023; 36:1295-1312. [PMID: 37564008 PMCID: PMC10946897 DOI: 10.1111/jeb.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 08/12/2023]
Abstract
Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3' splice signal is characterized by over-representation of pyrimidines. If the over-representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, we hypothesize that AG should be the most under-represented dimer. Through the use of DNA-strand asymmetry patterns, we confirm this prediction in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, we quantify the selection strength acting on each motif. Moreover, our inference and simulation method revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3' splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.
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Affiliation(s)
- Burçin Yıldırım
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Claus Vogl
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
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3
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Dybkov O, Preußner M, El Ayoubi L, Feng VY, Harnisch C, Merz K, Leupold P, Yudichev P, Agafonov DE, Will CL, Girard C, Dienemann C, Urlaub H, Kastner B, Heyd F, Lührmann R. Regulation of 3' splice site selection after step 1 of splicing by spliceosomal C* proteins. SCIENCE ADVANCES 2023; 9:eadf1785. [PMID: 36867703 PMCID: PMC9984181 DOI: 10.1126/sciadv.adf1785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3' splice site (3'ss) usage contribute to human disease. We demonstrate by small interfering RNA-mediated knockdowns, followed by RNA sequencing, that many proteins first recruited to human C* spliceosomes, which catalyze step 2 of splicing, regulate alternative splicing, including the selection of alternatively spliced NAGNAG 3'ss. Cryo-electron microscopy and protein cross-linking reveal the molecular architecture of these proteins in C* spliceosomes, providing mechanistic and structural insights into how they influence 3'ss usage. They further elucidate the path of the 3' region of the intron, allowing a structure-based model for how the C* spliceosome potentially scans for the proximal 3'ss. By combining biochemical and structural approaches with genome-wide functional analyses, our studies reveal widespread regulation of alternative 3'ss usage after step 1 of splicing and the likely mechanisms whereby C* proteins influence NAGNAG 3'ss choices.
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Affiliation(s)
- Olexandr Dybkov
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Marco Preußner
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Leyla El Ayoubi
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Vivi-Yun Feng
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Caroline Harnisch
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Kilian Merz
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Paula Leupold
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Peter Yudichev
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Dmitry E. Agafonov
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Cindy L. Will
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Cyrille Girard
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Henning Urlaub
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, Göttingen D-37075, Germany
| | - Berthold Kastner
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Florian Heyd
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Reinhard Lührmann
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
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4
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Regulation of Arp5 expression by alternative splicing coupled to nonsense-mediated RNA decay. Biochem Biophys Res Commun 2023; 657:50-58. [PMID: 36977368 DOI: 10.1016/j.bbrc.2023.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
Actin-related protein 5 (ARP5) inhibits the differentiation of skeletal, smooth, and cardiac muscle tissues, and ARP5 expression increases or decreases according to physiological and pathological changes in the muscle differentiation status. However, the regulatory mechanisms of ARP5 expression are largely unknown. Here, we identified a novel Arp5 mRNA isoform that contains premature termination codons in alternative exon 7b and is thus targeted by nonsense-mediated mRNA decay (NMD). In mouse skeletal muscle cells, switching from the canonical Arp5 isoform, i.e., Arp5(7a), to the NMD-targeted isoform Arp5(7b) occurred during differentiation, suggesting that Arp5 expression is regulated by alternative splicing coupled to NMD (AS-NMD). We developed an original method to accurately quantify the proportion of both Arp5 isoforms and measured higher levels of Arp5(7b) in muscle and brain tissues, where ARP5 is less expressed. The 3' splice site in Arp5 exon 7 has an unusual acceptor sequence that often leads to the skip of the authentic splice site and the use of the cryptic splice site localized 16 bases downstream. When the unusual acceptor sequence was mutated to the usual one, the Arp5(7b) isoform was barely detectable. The expression of several splicing factors involved in 3' splice site recognition was reduced after muscle differentiation. Additionally, knockdown of splicing factors increased the levels of Arp5(7b) and decreased the expression of Arp5(7a). Furthermore, strong positive correlations were found between Arp5 expression and the levels of these splicing factors in human skeletal and cardiac muscle tissues. Thus, Arp5 expression in muscle tissues is most likely regulated by the AS-NMD pathway.
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5
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Lee TA, Han H, Polash A, Cho SK, Lee JW, Ra EA, Lee E, Park A, Kang S, Choi JL, Kim JH, Lee JE, Min KW, Yang SW, Hafner M, Lee I, Yoon JH, Lee S, Park B. The nucleolus is the site for inflammatory RNA decay during infection. Nat Commun 2022; 13:5203. [PMID: 36057640 PMCID: PMC9440930 DOI: 10.1038/s41467-022-32856-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/16/2022] [Indexed: 11/12/2022] Open
Abstract
Inflammatory cytokines are key signaling molecules that can promote an immune response, thus their RNA turnover must be tightly controlled during infection. Most studies investigate the RNA decay pathways in the cytosol or nucleoplasm but never focused on the nucleolus. Although this organelle has well-studied roles in ribosome biogenesis and cellular stress sensing, the mechanism of RNA decay within the nucleolus is not completely understood. Here, we report that the nucleolus is an essential site of inflammatory pre-mRNA instability during infection. RNA-sequencing analysis reveals that not only do inflammatory genes have higher intronic read densities compared with non-inflammatory genes, but their pre-mRNAs are highly enriched in nucleoli during infection. Notably, nucleolin (NCL) acts as a guide factor for recruiting cytosine or uracil (C/U)-rich sequence-containing inflammatory pre-mRNAs and the Rrp6-exosome complex to the nucleolus through a physical interaction, thereby enabling targeted RNA delivery to Rrp6-exosomes and subsequent degradation. Consequently, Ncl depletion causes aberrant hyperinflammation, resulting in a severe lethality in response to LPS. Importantly, the dynamics of NCL post-translational modifications determine its functional activity in phases of LPS. This process represents a nucleolus-dependent pathway for maintaining inflammatory gene expression integrity and immunological homeostasis during infection. The nucleolus is the traditional site for ribosomal RNA biogenesis. Here, the authors find that the nucleolus is a site of inflammatory pre-mRNA turnover and elucidated how immune homeostasis can be maintained by controlling inflammatory gene expression.
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Affiliation(s)
- Taeyun A Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Heonjong Han
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Division of Tumor Immunology, Research Institute, National Cancer Center, Goyang, South Korea
| | - Ahsan Polash
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, MD, USA
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji Won Lee
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung, South Korea
| | - Eun A Ra
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Eunhye Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Areum Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Junhee L Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji Hyun Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji Eun Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea.,Samsung Genome Institute (SGI), Samsung Medical Center, Seoul, South Korea
| | - Kyung-Won Min
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung, South Korea.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, MD, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA.
| | - Sungwook Lee
- Division of Tumor Immunology, Research Institute, National Cancer Center, Goyang, South Korea.
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.
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6
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Hujová P, Souček P, Radová L, Kramárek M, Kováčová T, Freiberger T. Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites. Cell Mol Life Sci 2021; 78:6979-6993. [PMID: 34596691 PMCID: PMC11072513 DOI: 10.1007/s00018-021-03943-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/31/2022]
Abstract
Among alternative splicing events in the human transcriptome, tandem NAGNAG acceptor splice sites represent an appreciable proportion. Both proximal and distal NAG can be used to produce two splicing isoforms differing by three nucleotides. In some cases, the upstream exon can be alternatively spliced as well, which further increases the number of possible transcripts. In this study, we showed that NAG choice in tandem splice site depends considerably not only on the concerned acceptor, but also on the upstream donor splice site sequence. Using an extensive set of experiments with systematically modified two-exonic minigene systems of AFAP1L2 or CSTD gene, we recognized the third and fifth intronic upstream donor splice site position and the tandem acceptor splice site region spanning from -10 to +2, including NAGNAG itself, as the main drivers. In addition, competition between different branch points and their composition were also shown to play a significant role in NAG choice. All these nucleotide effects appeared almost additive, which explained the high variability in proximal versus distal NAG usage.
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Affiliation(s)
- Pavla Hujová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic.
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic.
| | - Lenka Radová
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
| | - Tatiana Kováčová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
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7
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Kadri NK, Mapel XM, Pausch H. The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome. Commun Biol 2021; 4:1206. [PMID: 34675361 PMCID: PMC8531310 DOI: 10.1038/s42003-021-02725-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022] Open
Abstract
The branch point sequence is a cis-acting intronic motif required for mRNA splicing. Despite their functional importance, branch point sequences are not routinely annotated. Here we predict branch point sequences in 179,476 bovine introns and investigate their variability using a catalogue of 29.4 million variants detected in 266 cattle genomes. We localize the bovine branch point within a degenerate heptamer "nnyTrAy". An adenine residue at position 6, that acts as branch point, and a thymine residue at position 4 of the heptamer are more strongly depleted for mutations than coding sequences suggesting extreme purifying selection. We provide evidence that mutations affecting these evolutionarily constrained residues lead to alternative splicing. We confirm evolutionary constraints on branch point sequences using a catalogue of 115 million SNPs established from 3,942 human genomes of the gnomAD database.
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Affiliation(s)
- Naveen Kumar Kadri
- grid.5801.c0000 0001 2156 2780Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Xena Marie Mapel
- grid.5801.c0000 0001 2156 2780Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Hubert Pausch
- grid.5801.c0000 0001 2156 2780Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
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8
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Urabe VK, Stevers M, Ghosh AK, Jurica MS. U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors. PLoS One 2021; 16:e0258551. [PMID: 34648557 PMCID: PMC8516221 DOI: 10.1371/journal.pone.0258551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/29/2021] [Indexed: 11/19/2022] Open
Abstract
U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. We previously found that the first SF3B inhibited-complex is less stable than A-complex and hypothesized that SF3B inhibitors interfere with U2 snRNA secondary structure changes required to form the branch helix. Using RNA chemical modifiers, we probed U2 snRNA structure in A-complex and SF3B inhibited splicing complexes. The reactivity pattern for U2 snRNA in the SF3B inhibited-complex is indistinguishable from that of A-complex, suggesting that they have the same secondary structure conformation, including the branch helix. This observation suggests SF3B inhibited-complex instability does not stem from an alternate RNA conformation and instead points to the inhibitors interfering with protein component interactions that normally stabilize U2 snRNP’s association with an intron. In addition, we probed U2 snRNA in the free U2 snRNP in the presence of SF3B inhibitor and again saw no differences. However, increased protection of nucleotides upstream of Stem I in the absence of SF3A and SF3B proteins suggests a change of secondary structure at the very 5′ end of U2 snRNA. Chemical probing of synthetic U2 snRNA in the absence of proteins results in similar protections and predicts a previously uncharacterized extension of Stem I. Because this stem must be disrupted for SF3A and SF3B proteins to stably join the snRNP, the structure has the potential to influence snRNP assembly and recycling after spliceosome disassembly.
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Affiliation(s)
- Veronica K. Urabe
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
| | - Meredith Stevers
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
| | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Melissa S. Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California, United States of America
- * E-mail:
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9
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Gamboa Lopez A, Allu SR, Mendez P, Chandrashekar Reddy G, Maul-Newby HM, Ghosh AK, Jurica MS. Herboxidiene Features That Mediate Conformation-Dependent SF3B1 Interactions to Inhibit Splicing. ACS Chem Biol 2021; 16:520-528. [PMID: 33617218 DOI: 10.1021/acschembio.0c00965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Small molecules that target the spliceosome SF3B complex are potent inhibitors of cancer cell growth. The compounds affect an early stage of spliceosome assembly when U2 snRNP first engages the branch point sequence of an intron. Employing an inactive herboxidiene analog (iHB) as a competitor, we investigated factors that influence inhibitor interactions with SF3B to interfere with pre-mRNA splicing in vitro. Order-of-addition experiments show that inhibitor interactions are long lasting and affected by both temperature and the presence of ATP. Our data are also consistent with the model that not all SF3B conformations observed in structural studies are conducive to productive inhibitor interactions. Notably, SF3B inhibitors do not impact an ATP-dependent rearrangement in U2 snRNP that exposes the branch binding sequence for base pairing. We also report extended structure-activity relationship analysis of the splicing inhibitor herboxidiene. We identified features of the tetrahydropyran ring that mediate its interactions with SF3B and its ability to interfere with splicing. In the context of recent structures of SF3B bound to inhibitor, our results lead us to extend the model for early spliceosome assembly and inhibitor mechanism. We postulate that interactions between a carboxylic acid substituent of herboxidiene and positively charged SF3B1 side chains in the inhibitor binding channel are needed to maintain inhibitor occupancy while counteracting the SF3B transition to a closed state that is required for stable U2 snRNP interactions with the intron.
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Affiliation(s)
| | - Srinivasa Rao Allu
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Guddeti Chandrashekar Reddy
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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10
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Královičová J, Borovská I, Pengelly R, Lee E, Abaffy P, Šindelka R, Grutzner F, Vořechovský I. Restriction of an intron size en route to endothermy. Nucleic Acids Res 2021; 49:2460-2487. [PMID: 33550394 PMCID: PMC7969005 DOI: 10.1093/nar/gkab046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 11/15/2022] Open
Abstract
Ca2+-insensitive and -sensitive E1 subunits of the 2-oxoglutarate dehydrogenase complex (OGDHC) regulate tissue-specific NADH and ATP supply by mutually exclusive OGDH exons 4a and 4b. Here we show that their splicing is enforced by distant lariat branch points (dBPs) located near the 5' splice site of the intervening intron. dBPs restrict the intron length and prevent transposon insertions, which can introduce or eliminate dBP competitors. The size restriction was imposed by a single dominant dBP in anamniotes that expanded into a conserved constellation of four dBP adenines in amniotes. The amniote clusters exhibit taxon-specific usage of individual dBPs, reflecting accessibility of their extended motifs within a stable RNA hairpin rather than U2 snRNA:dBP base-pairing. The dBP expansion took place in early terrestrial species and was followed by a uridine enrichment of large downstream polypyrimidine tracts in mammals. The dBP-protected megatracts permit reciprocal regulation of exon 4a and 4b by uridine-binding proteins, including TIA-1/TIAR and PUF60, which promote U1 and U2 snRNP recruitment to the 5' splice site and BP, respectively, but do not significantly alter the relative dBP usage. We further show that codons for residues critically contributing to protein binding sites for Ca2+ and other divalent metals confer the exon inclusion order that mirrors the Irving-Williams affinity series, linking the evolution of auxiliary splicing motifs in exons to metallome constraints. Finally, we hypothesize that the dBP-driven selection for Ca2+-dependent ATP provision by E1 facilitated evolution of endothermy by optimizing the aerobic scope in target tissues.
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Affiliation(s)
- Jana Královičová
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Borovská
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben Pengelly
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
| | - Eunice Lee
- School of Biological Sciences, University of Adelaide, Adelaide 5005, SA, Australia
| | - Pavel Abaffy
- Czech Academy of Sciences, Institute of Biotechnology, 25250 Vestec, Czech Republic
| | - Radek Šindelka
- Czech Academy of Sciences, Institute of Biotechnology, 25250 Vestec, Czech Republic
| | - Frank Grutzner
- School of Biological Sciences, University of Adelaide, Adelaide 5005, SA, Australia
| | - Igor Vořechovský
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
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11
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Ling Z, Brockmöller T, Baldwin IT, Xu S. Evolution of Alternative Splicing in Eudicots. FRONTIERS IN PLANT SCIENCE 2019; 10:707. [PMID: 31244865 PMCID: PMC6581728 DOI: 10.3389/fpls.2019.00707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/13/2019] [Indexed: 05/30/2023]
Abstract
Alternative pre-mRNA splicing (AS) is prevalent in plants and is involved in many interactions between plants and environmental stresses. However, the patterns and underlying mechanisms of AS evolution in plants remain unclear. By analyzing the transcriptomes of four eudicot species, we revealed that the divergence of AS is largely due to the gains and losses of AS events among orthologous genes. Furthermore, based on a subset of AS, in which AS can be directly associated with specific transcripts, we found that AS that generates transcripts containing premature termination codons (PTC), are likely more conserved than those that generate non-PTC containing transcripts. This suggests that AS coupled with nonsense-mediated decay (NMD) might play an important role in affecting mRNA levels post-transcriptionally. To understand the mechanisms underlying the divergence of AS, we analyzed the key determinants of AS using a machine learning approach. We found that the presence/absence of alternative splice site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5' donor site and 3' acceptor site among the studied species, suggesting a relatively conserved AS mechanism. The comparative analysis further demonstrated that variations of the identified AS determinants significantly contributed to the AS divergence among closely related species in both Solanaceae and Brassicaceae taxa. Together, these results provide detailed insights into the evolution of AS in plants.
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Affiliation(s)
- Zhihao Ling
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Ian T. Baldwin
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Shuqing Xu
- Plant Adaptation-in-action Group, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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Jourdy Y, Fretigny M, Nougier C, Négrier C, Bozon D, Vinciguerra C. Splicing analysis of 26 F8 nucleotide variations using a minigene assay. Haemophilia 2019; 25:306-315. [PMID: 30690819 DOI: 10.1111/hae.13687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/05/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Classically, the study of splicing impact of variation located near the splice site is performed by both in silico and mRNA analysis. However, RNA sample was rarely available. OBJECTIVE To characterize a panel of putative haemophilia A splicing variations. MATERIALS AND METHODS Twenty-six F8 variations identified from a cohort of 2075 haemophilia A families were studied using both bioinformatic tools and in vitro minigene assays in HeLa and Huh7 cells. RESULTS An aberrant splicing was demonstrated for 21/26 tested sequence variations. A good correlation between in silico and in vitro analysis was obtained for variations affecting donor splice site (12/14) and for the synonymous variations located inside an exon (6/6). Conversely, no concordant results were observed for the six variations affecting acceptor splice sites. The variations resulted more frequently in exon skipping (n = 13) than in activation of nearby cryptic splice sites (n = 5), in use of a de novo splice site (n = 2) or in insertion of large intronic sequences (n = 1). This study allowed to reclassify 5 synonymous substitutions c.1167A>G (p.Gln389Gln), c.1569G>T (p.Leu523Leu), c.1752G>A (p.Gln584Gln), c.5586G>A (p.Leu1862Leu) and c.6066C>T (p.Gly2022Gly) as splicing variations. The pathological significance of five variations remained unclear (c.222G>A [p.Thr74Thr], c.237C>T [p.Asn79Asn], c.240C>T [p.Ile80Ile], c.2113+5_2113+8del and c.2113+5G>A). DISCUSSION The minigene assay herein gave additional evidences for the clinical significance of 21/26 F8 putative splice site mutations. Such investigation should be performed for each F8 putative splice site variation for which no mRNA sample is available, notably to greatly improve the genetic counselling given to female carriers.
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Affiliation(s)
- Yohann Jourdy
- Service d'Hématologie Biologique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France.,EA 4609 Hémostase et Cancer, Université Claude Bernard Lyon 1, University Lyon, Lyon, France
| | - Mathilde Fretigny
- Service d'Hématologie Biologique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Christophe Nougier
- Service d'Hématologie Biologique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Claude Négrier
- Service d'Hématologie Biologique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France.,EA 4609 Hémostase et Cancer, Université Claude Bernard Lyon 1, University Lyon, Lyon, France
| | - Dominique Bozon
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Christine Vinciguerra
- Service d'Hématologie Biologique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France.,EA 4609 Hémostase et Cancer, Université Claude Bernard Lyon 1, University Lyon, Lyon, France
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Van de Water N, Tan T, Crowley M, Kerr R, Browett P. Novel α-Globin Splice Site Mutation (HBA2: c.96-5C>A) in Combination with Three-Gene Deletion Hb H Disease. Hemoglobin 2018; 42:122-125. [PMID: 30200833 DOI: 10.1080/03630269.2018.1487307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The choice of acceptor splice site during exon-exon splicing by the spliceosome is determined by a variety of factors. We report here a family with a novel acceptor splice site variant within intron 1 of the α-globin gene that provides some in vivo insight into the rules governing RNA splicing in homo sapiens. A 2-year-old female with Hb H disease, was found to have not only three α-globin genes deleted (- -FIL/-α3.7) but also a HBA2: c.96-5C>A variant on her remaining α-globin gene. The HBA2: c.96-5C>A variant was in cis with -α3.7 and mRNA studies indicate that this variant creates a new acceptor splice site which is used in approximately 35.0% of α-globin mRNA transcripts. The reduced levels of normal mRNA transcript predicts a more severe Hb H disease than expected for the three-gene deletion Hb H disease with a phenotype similar to nondeletional Hb H disease. We propose that this variant be called Hb Beach Haven (HBA2: c.96-5C>A).
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Affiliation(s)
- Neil Van de Water
- a Diagnostic Genetics Department , LabPlus, Auckland City Hospital , Auckland , New Zealand
| | - Tina Tan
- a Diagnostic Genetics Department , LabPlus, Auckland City Hospital , Auckland , New Zealand
| | - Megan Crowley
- a Diagnostic Genetics Department , LabPlus, Auckland City Hospital , Auckland , New Zealand
| | - Romy Kerr
- b Genetic Health Service , Auckland City Hospital , New Zealand
| | - Peter Browett
- a Diagnostic Genetics Department , LabPlus, Auckland City Hospital , Auckland , New Zealand.,c Department of Molecular Medicine & Pathology , University of Auckland , Auckland , New Zealand
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Ohno K, Takeda JI, Masuda A. Rules and tools to predict the splicing effects of exonic and intronic mutations. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [DOI: 10.1002/wrna.1451] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Jun-ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
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Original tandem duplication in FXIIIA gene with splicing site modification and four amino acids insertion causes factor XIII deficiency. Blood Coagul Fibrinolysis 2017; 28:237-243. [PMID: 27427785 DOI: 10.1097/mbc.0000000000000587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
: Recessive mutations of F13A gene are reported to be responsible of FXIIIA subunit deficiency (FXIIIA). In all, some intronic nucleotide changes identified in this gene were investigated by in-silico analysis and occasionally supported by experimental data or reported in some cases as a polymorphism. To determine the molecular defects responsible of congenital factor XIII deficiency in Libyan patient, molecular analysis was performed by direct DNA sequencing of the coding regions and splice junctions of the FXIIIA subunit gene (F13A). A splicing minigene assay was used to study the effect of this mutation. Bioinformatics exploration was fulfilled to conceive consequences on protein. A 12-bp duplication straddling the border of intron 9 and exon 10 leads to two 3' acceptor splice sites, resulting in silencing of the downstream wild 3' splice site. It caused an in-frame insertion of 12 nucleotides into mRNA and four amino acids into protein. Bioinformatic analysis predicts that the insertion of four amino acids affects the site 3 of calcium binding site, which disturbs the smooth function of the FXIIIA peptide causing the factor XIII deficiency. This study showed that a small duplication seems to weaken the original 3' splice site and enhance the activation of a new splice site responsible for an alternative splicing. It would be interesting to examine the underlying molecular mechanism involved in this rearrangement.
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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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17
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Vega Y, Delgado E, de la Barrera J, Carrera C, Zaballos Á, Cuesta I, Mariño A, Ocampo A, Miralles C, Pérez-Castro S, Álvarez H, López-Miragaya I, García-Bodas E, Díez-Fuertes F, Thomson MM. Sequence Analysis of In Vivo-Expressed HIV-1 Spliced RNAs Reveals the Usage of New and Unusual Splice Sites by Viruses of Different Subtypes. PLoS One 2016; 11:e0158525. [PMID: 27355361 PMCID: PMC4927154 DOI: 10.1371/journal.pone.0158525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/16/2016] [Indexed: 11/18/2022] Open
Abstract
HIV-1 RNAs are generated through a complex splicing mechanism, resulting in a great diversity of transcripts, which are classified in three major categories: unspliced, singly spliced (SS), and doubly spliced (DS). Knowledge on HIV-1 RNA splicing in vivo and by non-subtype B viruses is scarce. Here we analyze HIV-1 RNA splice site usage in CD4+CD25+ lymphocytes from HIV-1-infected individuals through pyrosequencing. HIV-1 DS and SS RNAs were amplified by RT-PCR in 19 and 12 samples, respectively. 13,108 sequences from HIV-1 spliced RNAs, derived from viruses of five subtypes (A, B, C, F, G), were identified. In four samples, three of non-B subtypes, five 3' splice sites (3'ss) mapping to unreported positions in the HIV-1 genome were identified. Two, designated A4i and A4j, were used in 22% and 25% of rev RNAs in two viruses of subtypes B and A, respectively. Given their close proximity (one or two nucleotides) to A4c and A4d, respectively, they could be viewed as variants of these sites. Three 3'ss, designated A7g, A7h, and A7i, located 20, 32, and 18 nucleotides downstream of A7, respectively, were identified in a subtype C (A7g, A7h) and a subtype G (A7i) viruses, each in around 2% of nef RNAs. The new splice sites or variants of splice sites were associated with the usual sequence features of 3'ss. Usage of unusual 3'ss A4d, A4e, A5a, A7a, and A7b was also detected. A4f, previously identified in two subtype C viruses, was preferentially used by rev RNAs of a subtype C virus. These results highlight the great diversity of in vivo splice site usage by HIV-1 RNAs. The fact that four of five newly identified splice sites or variants of splice sites were detected in non-subtype B viruses allows anticipating an even greater diversity of HIV-1 splice site usage than currently known.
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Affiliation(s)
- Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Jorge de la Barrera
- Bioinformatics Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Ángel Zaballos
- Genomics Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Isabel Cuesta
- Bioinformatics Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Ana Mariño
- Hospital Arquitecto Marcide. Ferrol, A Coruña, Spain
| | - Antonio Ocampo
- Complejo Hospitalario Universitario de Vigo. Vigo, Pontevedra, Spain
| | - Celia Miralles
- Complejo Hospitalario Universitario de Vigo. Vigo, Pontevedra, Spain
| | | | | | | | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathogenesis Unit. Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
- * E-mail:
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18
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Sohail M, Xie J. Diverse regulation of 3' splice site usage. Cell Mol Life Sci 2015; 72:4771-93. [PMID: 26370726 PMCID: PMC11113787 DOI: 10.1007/s00018-015-2037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/12/2015] [Accepted: 09/03/2015] [Indexed: 01/13/2023]
Abstract
The regulation of splice site (SS) usage is important for alternative pre-mRNA splicing and thus proper expression of protein isoforms in cells; its disruption causes diseases. In recent years, an increasing number of novel regulatory elements have been found within or nearby the 3'SS in mammalian genes. The diverse elements recruit a repertoire of trans-acting factors or form secondary structures to regulate 3'SS usage, mostly at the early steps of spliceosome assembly. Their mechanisms of action mainly include: (1) competition between the factors for RNA elements, (2) steric hindrance between the factors, (3) direct interaction between the factors, (4) competition between two splice sites, or (5) local RNA secondary structures or longer range loops, according to the mode of protein/RNA interactions. Beyond the 3'SS, chromatin remodeling/transcription, posttranslational modifications of trans-acting factors and upstream signaling provide further layers of regulation. Evolutionarily, some of the 3'SS elements seem to have emerged in mammalian ancestors. Moreover, other possibilities of regulation such as that by non-coding RNA remain to be explored. It is thus likely that there are more diverse elements/factors and mechanisms that influence the choice of an intron end. The diverse regulation likely contributes to a more complex but refined transcriptome and proteome in mammals.
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Affiliation(s)
- Muhammad Sohail
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
- Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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19
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Dillon LAL, Okrah K, Hughitt VK, Suresh R, Li Y, Fernandes MC, Belew AT, Corrada Bravo H, Mosser DM, El-Sayed NM. Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation. Nucleic Acids Res 2015; 43:6799-813. [PMID: 26150419 PMCID: PMC4538839 DOI: 10.1093/nar/gkv656] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Protozoan parasites of the genus Leishmania are the etiological agents of leishmaniasis, a group of diseases with a worldwide incidence of 0.9–1.6 million cases per year. We used RNA-seq to conduct a high-resolution transcriptomic analysis of the global changes in gene expression and RNA processing events that occur as L. major transforms from non-infective procyclic promastigotes to infective metacyclic promastigotes. Careful statistical analysis across multiple biological replicates and the removal of batch effects provided a high quality framework for comprehensively analyzing differential gene expression and transcriptome remodeling in this pathogen as it acquires its infectivity. We also identified precise 5′ and 3′ UTR boundaries for a majority of Leishmania genes and detected widespread alternative trans-splicing and polyadenylation. An investigation of possible correlations between stage-specific preferential trans-splicing or polyadenylation sites and differentially expressed genes revealed a lack of systematic association, establishing that differences in expression levels cannot be attributed to stage-regulated alternative RNA processing. Our findings build on and improve existing expression datasets and provide a substantially more detailed view of L. major biology that will inform the field and potentially provide a stronger basis for drug discovery and vaccine development efforts.
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Affiliation(s)
- Laura A L Dillon
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Kwame Okrah
- Department of Mathematics, University of Maryland, College Park, MD 20742, USA
| | - V Keith Hughitt
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Rahul Suresh
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Yuan Li
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Maria Cecilia Fernandes
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - A Trey Belew
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Hector Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - David M Mosser
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
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20
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Ragle JM, Katzman S, Akers TF, Barberan-Soler S, Zahler AM. Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans. Genome Res 2015; 25:982-94. [PMID: 25922281 PMCID: PMC4484395 DOI: 10.1101/gr.186783.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/27/2015] [Indexed: 12/30/2022]
Abstract
Adjacent alternative 3′ splice sites, those separated by ≤18 nucleotides, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis-elements that define the adjacent sites. Identification of the intron's 3′ end depends upon sequence elements that define the branchpoint, polypyrimidine tract, and terminal AG dinucleotide. Starting with RNA-seq data from germline-enriched and somatic cell-enriched Caenorhabditis elegans samples, we identify hundreds of introns with adjacent alternative 3′ splice sites. We identify 203 events that undergo tissue-specific alternative splicing. For these, the regulation is monodirectional, with somatic cells preferring to splice at the distal 3′ splice site (furthest from the 5′ end of the intron) and germline cells showing a distinct shift toward usage of the adjacent proximal 3′ splice site (closer to the 5′ end of the intron). Splicing patterns in somatic cells follow C. elegans consensus rules of 3′ splice site definition; a short stretch of pyrimidines preceding an AG dinucleotide. Splicing in germline cells occurs at proximal 3′ splice sites that lack a preceding polypyrimidine tract, and in three instances the germline-specific site lacks the AG dinucleotide. We provide evidence that use of germline-specific proximal 3′ splice sites is conserved across Caenorhabditis species. We propose that there are differences between germline and somatic cells in the way that the basal splicing machinery functions to determine the intron terminus.
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Affiliation(s)
- James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Sol Katzman
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Taylor F Akers
- Department of Molecular, Cell, and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Sergio Barberan-Soler
- Gene Regulation, Stem Cells, and Cancer Program, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Alan M Zahler
- Department of Molecular, Cell, and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
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E6^E7, a novel splice isoform protein of human papillomavirus 16, stabilizes viral E6 and E7 oncoproteins via HSP90 and GRP78. mBio 2015; 6:e02068-14. [PMID: 25691589 PMCID: PMC4337564 DOI: 10.1128/mbio.02068-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcripts of human papillomavirus 16 (HPV16) E6 and E7 oncogenes undergo alternative RNA splicing to produce multiple splice isoforms. However, the importance of these splice isoforms is poorly understood. Here we report a critical role of E6^E7, a novel isoform containing the 41 N-terminal amino acid (aa) residues of E6 and the 38 C-terminal aa residues of E7, in the regulation of E6 and E7 stability. Through mass spectrometric analysis, we identified that HSP90 and GRP78, which are frequently upregulated in cervical cancer tissues, are two E6^E7-interacting proteins responsible for the stability and function of E6^E7, E6, and E7. Although GRP78 and HSP90 do not bind each other, GRP78, but not HSP90, interacts with E6 and E7. E6^E7 protein, in addition to self-binding, interacts with E6 and E7 in the presence of GRP78 and HSP90, leading to the stabilization of E6 and E7 by prolonging the half-life of each protein. Knocking down E6^E7 expression in HPV16-positive CaSki cells by a splice junction-specific small interfering RNA (siRNA) destabilizes E6 and E7 and prevents cell growth. The same is true for the cells with a GRP78 knockdown or in the presence of an HSP90 inhibitor. Moreover, mapping and alignment analyses for splicing elements in 36 alpha-HPVs (α-HPVs) suggest the possible expression of E6^E7 mostly by other oncogenic or possibly oncogenic α-HPVs (HPV18, -30, -31, -39, -42, -45, -56, -59, -70, and -73). HPV18 E6^E7 is detectable in HPV18-positive HeLa cells and HPV18-infected raft tissues. All together, our data indicate that viral E6^E7 and cellular GRP78 or HSP90 might be novel targets for cervical cancer therapy. HPV16 is the most prevalent HPV genotype, being responsible for 60% of invasive cervical cancer cases worldwide. What makes HPV16 so potent in the development of cervical cancer remains a mystery. We discovered in this study that, besides producing two well-known oncoproteins, E6 and E7, seen in other high-risk HPVs, HPV16 produces E6^E7, a novel splice isoform of E6 and E7. E6^E7, in addition to self-interacting, binds cellular chaperone proteins, HSP90 and GRP78, and viral E6 and E7 to increase the steady-state levels and half-lives of viral oncoproteins, leading to cell proliferation. The splicing cis elements in the regulation of HPV16 E6^E7 production are highly conserved in 11 oncogenic or possibly oncogenic HPVs, and we confirmed the production of HPV18 E6^E7 in HPV18-infected cells. This study provides new insight into the mechanism of splicing, the interplay between different products of the polycistronic viral message, and the role of the host chaperones as they function.
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Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Genome-wide discovery of human splicing branchpoints. Genome Res 2015; 25:290-303. [PMID: 25561518 PMCID: PMC4315302 DOI: 10.1101/gr.182899.114] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During the splicing reaction, the 5′ intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3′ splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron–exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.
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Affiliation(s)
- Tim R Mercer
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Michael B Clark
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Stacey B Andersen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marion E Brunck
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; Illumina, Inc., San Diego, California 92122, USA; School of Medicine and Health Services, Department of Integrated Systems Biology and Department of Pediatrics, George Washington University, Washington DC 20037, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia;
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Kergourlay V, Raï G, Blandin G, Salgado D, Béroud C, Lévy N, Krahn M, Bartoli M. Identification of Splicing Defects Caused by Mutations in the Dysferlin Gene. Hum Mutat 2014; 35:1532-41. [DOI: 10.1002/humu.22710] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/03/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Virginie Kergourlay
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - Ghadi Raï
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - Gaëlle Blandin
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - David Salgado
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - Christophe Béroud
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
| | - Nicolas Lévy
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
| | - Martin Krahn
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
| | - Marc Bartoli
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
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24
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Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell 2014; 54:698-710. [PMID: 24837679 PMCID: PMC4077618 DOI: 10.1016/j.molcel.2014.04.022] [Citation(s) in RCA: 309] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 04/15/2014] [Accepted: 04/18/2014] [Indexed: 01/23/2023]
Abstract
RNA-based regulation and CRISPR/Cas transcription factors (CRISPR-TFs) have the potential to be integrated for the tunable modulation of gene networks. A major limitation of this methodology is that guide RNAs (gRNAs) for CRISPR-TFs can only be expressed from RNA polymerase III promoters in human cells, limiting their use for conditional gene regulation. We present new strategies that enable expression of functional gRNAs from RNA polymerase II promoters and multiplexed production of proteins and gRNAs from a single transcript in human cells. We use multiple RNA regulatory strategies, including RNA-triple-helix structures, introns, microRNAs, and ribozymes, with Cas9-based CRISPR-TFs and Cas6/Csy4-based RNA processing. Using these tools, we efficiently modulate endogenous promoters and implement tunable synthetic circuits, including multistage cascades and RNA-dependent networks that can be rewired with Csy4 to achieve complex behaviors. This toolkit can be used for programming scalable gene circuits and perturbing endogenous networks for biology, therapeutic, and synthetic biology applications.
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Affiliation(s)
- Lior Nissim
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Samuel D Perli
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Alexandra Fridkin
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pablo Perez-Pinera
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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25
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Panunzi LG, Agüero F. A genome-wide analysis of genetic diversity in Trypanosoma cruzi intergenic regions. PLoS Negl Trop Dis 2014; 8:e2839. [PMID: 24784238 PMCID: PMC4006747 DOI: 10.1371/journal.pntd.0002839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 03/20/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi is the causal agent of Chagas Disease. Recently, the genomes of representative strains from two major evolutionary lineages were sequenced, allowing the construction of a detailed genetic diversity map for this important parasite. However this map is focused on coding regions of the genome, leaving a vast space of regulatory regions uncharacterized in terms of their evolutionary conservation and/or divergence. METHODOLOGY Using data from the hybrid CL Brener and Sylvio X10 genomes (from the TcVI and TcI Discrete Typing Units, respectively), we identified intergenic regions that share a common evolutionary ancestry, and are present in both CL Brener haplotypes (TcII-like and TcIII-like) and in the TcI genome; as well as intergenic regions that were conserved in only two of the three genomes/haplotypes analyzed. The genetic diversity in these regions was characterized in terms of the accumulation of indels and nucleotide changes. PRINCIPAL FINDINGS Based on this analysis we have identified i) a core of highly conserved intergenic regions, which remained essentially unchanged in independently evolving lineages; ii) intergenic regions that show high diversity in spite of still retaining their corresponding upstream and downstream coding sequences; iii) a number of defined sequence motifs that are shared by a number of unrelated intergenic regions. A fraction of indels explains the diversification of some intergenic regions by the expansion/contraction of microsatellite-like repeats.
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Affiliation(s)
- Leonardo G. Panunzi
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
- * E-mail: ;
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26
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Anokhina M, Bessonov S, Miao Z, Westhof E, Hartmuth K, Lührmann R. RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core. EMBO J 2013; 32:2804-18. [PMID: 24002212 DOI: 10.1038/emboj.2013.198] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 07/24/2013] [Indexed: 11/09/2022] Open
Abstract
Although U snRNAs play essential roles in splicing, little is known about the 3D arrangement of U2, U6, and U5 snRNAs and the pre-mRNA in active spliceosomes. To elucidate their relative spatial organization and dynamic rearrangement, we examined the RNA structure of affinity-purified, human spliceosomes before and after catalytic step 1 by chemical RNA structure probing. We found a stable 3-way junction of the U2/U6 snRNA duplex in active spliceosomes that persists minimally through step 1. Moreover, the formation of alternating, mutually exclusive, U2 snRNA conformations, as observed in yeast, was not detected in different assembly stages of human spliceosomal complexes (that is, B, B(act), or C complexes). Psoralen crosslinking revealed an interaction during/after step 1 between internal loop 1 of the U5 snRNA, and intron nucleotides immediately downstream of the branchpoint. Using the experimentally derived structural constraints, we generated a model of the RNA network of the step 1 spliceosome, based on the crystal structure of a group II intron through homology modelling. The model is topologically consistent with current genetic, biochemical, and structural data.
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Affiliation(s)
- Maria Anokhina
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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27
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Huang CC, Kuo TM, Yeh CT, Hu CP, Chen YL, Tsai YL, Chen ML, Chou YC, Chang C. One single nucleotide difference alters the differential expression of spliced RNAs between HBV genotypes A and D. Virus Res 2013; 174:18-26. [PMID: 23501362 DOI: 10.1016/j.virusres.2013.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/08/2013] [Accepted: 02/08/2013] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is generally classified into eight genotypes (A to H) based on genomic sequence divergence. The sequence variation among the different HBV genotypes suggests that the spliced RNAs should be different from genotype to genotype. However, the cis-acting element involved in the modulation of the distinct expression profiles of spliced HBV RNAs remains unidentified. Moreover, the biological role of splicing in the life cycle of HBV is not yet understood. In this study, spliced RNAs generated from genotypes A and D were carefully characterized in transfected HepG2 cells. The species and frequency of the spliced RNAs were dramatically different in the two genotypes. Of note, a population of multiply spliced RNAs with intron 2067-2350 excision was identified in HBV genotype A-transfected HepG2 cells, but not in genotype D transfected HepG2 cells. Further, we found a single nucleotide difference (2335) located within the polypyrimidine tract of the splice acceptor site 2350 between the two genotypes, and a single base substitution at 2335 was able to convert the splicing pattern of genotype D (or genotype A) to that of genotype A (or genotype D). These findings suggest that different unique splice sites may be preferentially used in different HBV genotypes resulting in distinct populations of spliced RNAs. The possible significance of the distinct spliced RNAs generated from the different HBV genotypes in HBV infection is discussed.
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Affiliation(s)
- Chien-Chiao Huang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.
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28
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Ajiro M, Jia R, Zhang L, Liu X, Zheng ZM. Intron definition and a branch site adenosine at nt 385 control RNA splicing of HPV16 E6*I and E7 expression. PLoS One 2012; 7:e46412. [PMID: 23056301 PMCID: PMC3464268 DOI: 10.1371/journal.pone.0046412] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
HPV16 E6 and E7, two viral oncogenes, are expressed from a single bicistronic pre-mRNA. In this report, we provide the evidence that the bicistronic pre-mRNA intron 1 contains three 5' splice sites (5' ss) and three 3' splice sites (3' ss) normally used in HPV16(+) cervical cancer and its derived cell lines. The choice of two novel alternative 5' ss (nt 221 5' ss and nt 191 5' ss) produces two novel isoforms of E6E7 mRNAs (E6*V and E6*VI). The nt 226 5' ss and nt 409 3' ss is preferentially selected over the other splice sites crossing over the intron to excise a minimal length of the intron in RNA splicing. We identified AACAAAC as the preferred branch point sequence (BPS) and an adenosine at nt 385 (underlined) in the BPS as a branch site to dictate the selection of the nt 409 3' ss for E6*I splicing and E7 expression. Introduction of point mutations into the mapped BPS led to reduced U2 binding to the BPS and thereby inhibition of the second step of E6E7 splicing at the nt 409 3' ss. Importantly, the E6E7 bicistronic RNA with a mutant BPS and inefficient splicing makes little or no E7 and the resulted E6 with mutations of (91)QYNK(94) to (91)PSFW(94) displays attenuate activity on p53 degradation. Together, our data provide structural basis of the E6E7 intron 1 for better understanding of how viral E6 and E7 expression is regulated by alternative RNA splicing. This study elucidates for the first time a mapped branch point in HPV16 genome involved in viral oncogene expression.
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Affiliation(s)
- Masahiko Ajiro
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Rong Jia
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Lifang Zhang
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Xuefeng Liu
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
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29
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Taggart AJ, DeSimone AM, Shih JS, Filloux ME, Fairbrother WG. Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo. Nat Struct Mol Biol 2012; 19:719-21. [PMID: 22705790 DOI: 10.1038/nsmb.2327] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/17/2012] [Indexed: 01/07/2023]
Abstract
We present the first large-scale identification of lariats-the transient branched introns that are released as a byproduct of pre-mRNA splicing. The locations of the branchpoints in these introns provide insight into the early steps of splicing. From this data set, we have developed a comprehensive model of 3' splice-site selection, identified new mechanisms of alternative splicing and mapped the distribution of splicing factors around branchpoints.
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Affiliation(s)
- Allison J Taggart
- Laboratory of Molecular Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
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30
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Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol 2012; 10:e1001229. [PMID: 22235189 PMCID: PMC3250501 DOI: 10.1371/journal.pbio.1001229] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 11/18/2011] [Indexed: 11/19/2022] Open
Abstract
Thousands of human genes contain introns ending in NAGNAG (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms that differ by inclusion/exclusion of three bases. However, few models exist for how such splicing might be regulated, and some studies have concluded that NAGNAG splicing is purely stochastic and nonfunctional. Here, we used deep RNA-Seq data from 16 human and eight mouse tissues to analyze the regulation and evolution of NAGNAG splicing. Using both biological and technical replicates to estimate false discovery rates, we estimate that at least 25% of alternatively spliced NAGNAGs undergo tissue-specific regulation in mammals, and alternative splicing of strongly tissue-specific NAGNAGs was 10 times as likely to be conserved between species as was splicing of non-tissue-specific events, implying selective maintenance. Preferential use of the distal NAG was associated with distinct sequence features, including a more distal location of the branch point and presence of a pyrimidine immediately before the first NAG, and alteration of these features in a splicing reporter shifted splicing away from the distal site. Strikingly, alignments of orthologous exons revealed a ∼15-fold increase in the frequency of three base pair gaps at 3' splice sites relative to nearby exon positions in both mammals and in Drosophila. Alternative splicing of NAGNAGs in human was associated with dramatically increased frequency of exon length changes at orthologous exon boundaries in rodents, and a model involving point mutations that create, destroy, or alter NAGNAGs can explain both the increased frequency and biased codon composition of gained/lost sequence observed at the beginnings of exons. This study shows that NAGNAG alternative splicing generates widespread differences between the proteomes of mammalian tissues, and suggests that the evolutionary trajectories of mammalian proteins are strongly biased by the locations and phases of the introns that interrupt coding sequences.
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31
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Horowitz DS. The mechanism of the second step of pre-mRNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:331-50. [PMID: 22012849 DOI: 10.1002/wrna.112] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The molecular mechanisms of the second step of pre-mRNA splicing in yeast and higher eukaryotes are reviewed. The important elements in the pre-mRNA, the participating proteins, and the proposed secondary structures and roles of the snRNAs are described. The sequence of events in the second step is presented, focusing on the actions of the proteins in setting up and facilitating the second reaction. Mechanisms for avoiding errors in splicing are discussed.
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Affiliation(s)
- David S Horowitz
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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32
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Wang F, Fang Q, Yu N, Zhao D, Zhang Y, Wang J, Wang Q, Zhou X, Cao X, Fan X. Association between genetic polymorphism of the angiotensin-converting enzyme and diabetic nephropathy: a meta-analysis comprising 26,580 subjects. J Renin Angiotensin Aldosterone Syst 2011; 13:161-74. [PMID: 21810896 DOI: 10.1177/1470320311417655] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Introduction: The effect of angiotensin-converting enzyme ( ACE) insertion/deletion (I/D) polymorphism on risk of diabetic nephropathy (DN) is still conflicting. The present meta-analysis was performed to evaluate the overall risk of this polymorphism associated with DN in different groups. Materials and methods: A predefined search was performed on 14,108 DN cases and 12,472 controls from 63 published studies by searching electronic databases and reference lists of relevant articles. Results: In this meta-analysis, we found a significant association between the ACE I/D polymorphism and the risk of DN for all genetic models (ID versus II: odds ratio [OR] = 1.12, 95% confidence interval [CI] 1.02–1.24; DD versus II: OR = 1.27, 95% CI 1.13–1.44; allele contrast: OR = 1.15, 95% CI 1.08–1.23; dominant model: OR = 1.18, 95% CI 1.07–1.31; and recessive model: OR = 1.18, 95% CI 1.08–1.30, respectively). In stratified analysis by ethnicity and DM type, we further found that the Asian group with type 2 diabetes mellitus (T2DM) showed a significant association for all genetic models (ID versus II: OR = 1.25, 95% CI 1.07–1.47; DD versus II: OR = 1.57, 95% CI 1.24–1.98; allele contrast: OR = 1.30, 95% CI 1.15–1.46; dominant model: OR = 1.37, 95% CI 1.10–1.69; and recessive model: OR = 1.34, 95% CI 1.15–1.56, respectively). Conclusions: Our study suggested that the ACE I/D polymorphism may contribute to DN development, especially in the Asian group with T2DM.
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Affiliation(s)
- Furu Wang
- JiangSu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Qiaoqiao Fang
- Department of Respiratory Medicine, Nanjing Children’s Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Ningle Yu
- JiangSu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Deyu Zhao
- Department of Respiratory Medicine, Nanjing Children’s Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yimei Zhang
- JiangSu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Jin Wang
- JiangSu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Quan Wang
- Department of Respiratory Medicine, Nanjing Children’s Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xianfeng Zhou
- JiangSu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Xingjiang Cao
- JiangSu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Xiangyong Fan
- JiangSu Provincial Center for Disease Prevention and Control, Nanjing, China
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Le Guédard-Méreuze S, Vaché C, Baux D, Faugère V, Larrieu L, Abadie C, Janecke A, Claustres M, Roux AF, Tuffery-Giraud S. Ex vivo splicing assays of mutations at noncanonical positions of splice sites in USHER genes. Hum Mutat 2010; 31:347-55. [PMID: 20052763 DOI: 10.1002/humu.21193] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular diagnosis in Usher syndrome type 1 and 2 patients led to the identification of 21 sequence variations located in noncanonical positions of splice sites in MYO7A, CDH23, USH1C, and USH2A genes. To establish experimentally the splicing pattern of these substitutions, whose impact on splicing is not always predictable by available softwares, ex vivo splicing assays were performed. The branch-point mapping strategy was also used to investigate further a putative branch-point mutation in USH2A intron 43. Aberrant splicing was demonstrated for 16 of the 21 (76.2%) tested sequence variations. The mutations resulted more frequently in activation of a nearby cryptic splice site or use of a de novo splice site than exon skipping (37.5%). This study allowed the reclassification as splicing mutations of one silent (c.7872G>A (p.Glu2624Glu) in CDH23) and four missense mutations (c.2993G>A (p.Arg998Lys) in USH2A, c.592G>A (p.Ala198Thr), c.3503G>C [p.Arg1168Pro], c.5944G>A (p.Gly1982Arg) in MYO7A), whereas it provided clues about a role in structure/function in four other cases: c.802G>A (p.Gly268Arg), c.653T>A (p.Val218Glu) (USH2A), and c.397C>T (p.His133Tyr), c.3502C>T (p.Arg1168Trp) (MYO7A). Our data provide insights into the contribution of splicing mutations in Usher genes and illustrate the need to define accurately their splicing outcome for diagnostic purposes.
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34
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Guyon-Debast A, Lécureuil A, Bonhomme S, Guerche P, Gallois JL. A SNP associated with alternative splicing of RPT5b causes unequal redundancy between RPT5a and RPT5b among Arabidopsis thaliana natural variation. BMC PLANT BIOLOGY 2010; 10:158. [PMID: 20682047 PMCID: PMC3017782 DOI: 10.1186/1471-2229-10-158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 08/03/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND The proteasome subunit RPT5, which is essential for gametophyte development, is encoded by two genes in Arabidopsis thaliana; RPT5a and RPT5b. We showed previously that RPT5a and RPT5b are fully redundant in the Columbia (Col-0) accession, whereas in the Wassilewskia accession (Ws-4), RPT5b does not complement the effect of a strong rpt5a mutation in the male gametophyte, and only partially complements rpt5a mutation in the sporophyte. RPT5bCol-0 and RPT5bWs-4 differ by only two SNPs, one located in the promoter and the other in the seventh intron of the gene. RESULTS By exploiting natural variation at RPT5b we determined that the SNP located in RPT5b intron seven, rather than the promoter SNP, is the sole basis of this lack of redundancy. In Ws-4 this SNP is predicted to create a new splicing branchpoint sequence that induces a partial mis-splicing of the pre-mRNA, leading to the introduction of a Premature Termination Codon. We characterized 5 accessions carrying this A-to-T substitution in intron seven and observed a complete correlation between this SNP and both a 10 to 20% level of the RPT5b pre-mRNA mis-splicing and the lack of ability to complement an rpt5a mutant phenotype. CONCLUSION The accession-dependent unequal redundancy between RPT5a and RPT5b genes illustrates an example of evolutionary drifting between duplicated genes through alternative splicing.
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Affiliation(s)
- Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France, F-78000 Versailles, France
| | - Alain Lécureuil
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France, F-78000 Versailles, France
| | - Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France, F-78000 Versailles, France
| | - Philippe Guerche
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France, F-78000 Versailles, France
| | - Jean-Luc Gallois
- Institut National de la Recherche Agronomique-UR1052 Station de Génétique et d'Amélioration des Fruits et Légumes, Domaine Saint Maurice, BP94, F84143, Montfavet, France
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35
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Tsai KW, Chan WC, Hsu CN, Lin WC. Sequence features involved in the mechanism of 3' splice junction wobbling. BMC Mol Biol 2010; 11:34. [PMID: 20459675 PMCID: PMC2875228 DOI: 10.1186/1471-2199-11-34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 05/07/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative splicing is an important mechanism mediating the diversified functions of genes in multicellular organisms, and such event occurs in around 40-60% of human genes. Recently, a new splice-junction wobbling mechanism was proposed that subtle modifications exist in mRNA maturation by alternatively choosing at 5'- GTNGT and 3'- NAGNAG, which created single amino acid insertion and deletion isoforms. RESULTS By browsing the Alternative Splicing Database information, we observed that most 3' alternative splice site choices occur within six nucleotides of the dominant splice site and the incidence significantly decreases further away from the dominant acceptor site. Although a lower frequency of alternative splicing occurs within the intronic region (alternative splicing at the proximal AG) than in the exonic region (alternative splicing at the distal AG), alternative AG sites located within the intronic region show stronger potential as the acceptor. These observations revealed that the choice of 3' splice sites during 3' splicing junction wobbling could depend on the distance between the duplicated AG and the branch point site (BPS). Further mutagenesis experiments demonstrated that the distance of AG-to-AG and BPS-to-AG can greatly influence 3' splice site selection. Knocking down a known alternative splicing regulator, hSlu7, failed to affect wobble splicing choices. CONCLUSION Our results implied that nucleotide distance between proximal and distal AG sites has an important regulatory function. In this study, we showed that occurrence of 3' wobble splicing occurs in a distance-dependent manner and that most of this wobble splicing is probably caused by steric hindrance from a factor bound at the neighboring tandem motif sequence.
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Affiliation(s)
- Kuo-Wang Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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36
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Hallegger M, Sobala A, Smith CWJ. Four exons of the serotonin receptor 4 gene are associated with multiple distant branch points. RNA (NEW YORK, N.Y.) 2010; 16:839-51. [PMID: 20197377 PMCID: PMC2844630 DOI: 10.1261/rna.2013110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Splicing of vertebrate introns involves recognition of three consensus elements at the 3' end. The branch point (BP) and polypyrimidine tract (PPT) are usually located within 40 nucleotides (nt) of the 3' splice site (3' ss), AG, but can be much more distant. A characteristic of the region between distant BPs (dBPs) and the 3' ss is the absence of intervening AG dinucleotides, leading to its designation as the "AG exclusion zone" (AGEZ). The human HTR4 gene, which encodes serotonin receptor 4 and has been associated with schizophrenia, bipolar disease, and gastrointestinal disorders, has four exons with extensive AGEZs. We have mapped the BPs for HTR4 exons 3, 4, 5, and g generated by in vitro splicing, and validated them by mutagenesis in exon-trapping vectors. All exons used dBPs up to 273 nt upstream of the exon. Strikingly, exons 4 and 5 used combinations of both distant and conventionally located BPs, suggesting that successful splicing of these exons can occur by distinct pathways. Our results emphasize the importance for single nucleotide polymorphism resequencing projects to take account of potential dBPs, as the extended AGEZs are vulnerable to mutations that could affect splicing itself or regulation of alternative splicing.
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Affiliation(s)
- Martina Hallegger
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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37
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Warf MB, Berglund JA. Role of RNA structure in regulating pre-mRNA splicing. Trends Biochem Sci 2009; 35:169-78. [PMID: 19959365 DOI: 10.1016/j.tibs.2009.10.004] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 10/16/2009] [Accepted: 10/19/2009] [Indexed: 01/06/2023]
Abstract
Pre-mRNA splicing involves removing non-coding introns from RNA transcripts. It is carried out by the spliceosome, along with other auxiliary factors. In general, research in splicing has focused on the sequences within the pre-mRNA, without considering the structures that these sequences might form. We propose that the role of RNA structure deserves more consideration when thinking about splicing mechanisms. RNA structures can inhibit or aid binding of spliceosomal components to the pre-mRNA, or can increase splicing efficiency by bringing important sequences into close proximity. Recent reports have identified proteins and small molecules that can regulate splicing by modulating RNA structures, thereby expanding our knowledge of the mechanisms used to regulate splicing.
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Affiliation(s)
- M Bryan Warf
- Institute of Molecular Biology, and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
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38
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Masuda A, Shen XM, Ito M, Matsuura T, Engel AG, Ohno K. hnRNP H enhances skipping of a nonfunctional exon P3A in CHRNA1 and a mutation disrupting its binding causes congenital myasthenic syndrome. Hum Mol Genet 2008; 17:4022-35. [PMID: 18806275 PMCID: PMC2638575 DOI: 10.1093/hmg/ddn305] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 09/01/2008] [Accepted: 09/17/2008] [Indexed: 12/28/2022] Open
Abstract
In humans and great apes, CHRNA1 encoding the muscle nicotinic acetylcholine receptor alpha subunit carries an inframe exon P3A, the inclusion of which yields a nonfunctional alpha subunit. In muscle, the P3A(-) and P3A(+) transcripts are generated in a 1:1 ratio but the functional significance and regulation of the alternative splicing remain elusive. An intronic mutation (IVS3-8G>A), identified in a patient with congenital myasthenic syndrome, disrupts an intronic splicing silencer (ISS) and results in exclusive inclusion of the downstream P3A exon. We found that the ISS-binding splicing trans-factor was heterogeneous nuclear ribonucleoprotein (hnRNP) H and the mutation attenuated the affinity of hnRNP for the ISS approximately 100-fold. We next showed that direct placement of hnRNP H to the 3' end of intron 3 silences, and siRNA-mediated downregulation of hnRNP H enhances recognition of exon P3A. Analysis of the human genome suggested that the hnRNPH-binding UGGG motif is overrepresented close to the 3' ends of introns. Pursuing this clue, we showed that alternative exons of GRIP1, FAS, VPS13C and NRCAM are downregulated by hnRNP H. Our findings imply that the presence of the hnRNP H-binding motif close to the 3' end of an intron is an essential but underestimated splicing regulator of the downstream exon.
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Affiliation(s)
- Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Xin-Ming Shen
- Department of Neurology, Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tohru Matsuura
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Andrew G. Engel
- Department of Neurology, Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Neurology, Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN, USA
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39
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Abstract
Intron sequences in nuclear pre-mRNAs are excised with either the major U2 snRNA-dependent spliceosomal pathway or the minor U12 snRNA-dependent spliceosomal pathway that exist in most eukaryotic organisms. While the predominant dinucleotides bordering each of these types of introns and the catalytic mechanism used in their excision are conserved in plants and animals, several features aiding in the recognition of plant introns are distinct from those in animals and yeast. Along with their short length, high AU content and high variation in their 5' and 3' splice sites and branchpoint consensus sequences are the most prominent characteristics of plant introns. Detailed surveys of site-directed mutant introns tested in vivo and chemically induced and naturally mutant introns analyzed in planta emphasize the effects of changing individual nucleotides in these splice site consensus sequences and highlight a number of noncanonical dinucleotides that are functional in plant systems.
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Affiliation(s)
- M A Schuler
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA.
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40
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Gooding C, Smith CWJ. Tropomyosin exons as models for alternative splicing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 644:27-42. [PMID: 19209811 DOI: 10.1007/978-0-387-85766-4_3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Three of the four mammalian tropomyosin (Tm) genes are alternatively spliced, most commonly by mutually exclusive selection from pairs of internal or 3' end exons. Alternative splicing events in the TPM1, 2 and 3 genes have been analysed experimentally in various levels ofdetail. In particular, mutually exclusive exon pairs in the betaTm (TPM2) and alphaTm (TPM1) genes are among the most intensively studied models for striated and smooth muscle specific alternative splicing, respectively. Analysis of these model systems has provided important insights into general mechanisms and strategies of splicing regulation.
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Affiliation(s)
- Clare Gooding
- Department of Biochemistry, University of Cambridge, CB2 1GA, UK
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41
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Koren E, Lev-Maor G, Ast G. The emergence of alternative 3' and 5' splice site exons from constitutive exons. PLoS Comput Biol 2007; 3:e95. [PMID: 17530917 PMCID: PMC1876488 DOI: 10.1371/journal.pcbi.0030095] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 04/10/2007] [Indexed: 11/19/2022] Open
Abstract
Alternative 3' and 5' splice site (ss) events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases. However, only few of the characteristics that distinguish these events from alternative cassette exons are known currently. In this study, we compared the characteristics of constitutive exons, alternative cassette exons, and alternative 3'ss and 5'ss exons. The results revealed that alternative 3'ss and 5'ss exons are an intermediate state between constitutive and alternative cassette exons, where the constitutive side resembles constitutive exons, and the alternative side resembles alternative cassette exons. The results also show that alternative 3'ss and 5'ss exons exhibit low levels of symmetry (frame-preserving), similar to constitutive exons, whereas the sequence between the two alternative splice sites shows high symmetry levels, similar to alternative cassette exons. In addition, flanking intronic conservation analysis revealed that exons whose alternative splice sites are at least nine nucleotides apart show a high conservation level, indicating intronic participation in the regulation of their splicing, whereas exons whose alternative splice sites are fewer than nine nucleotides apart show a low conservation level. Further examination of these exons, spanning seven vertebrate species, suggests an evolutionary model in which the alternative state is a derivative of an ancestral constitutive exon, where a mutation inside the exon or along the flanking intron resulted in the creation of a new splice site that competes with the original one, leading to alternative splice site selection. This model was validated experimentally on four exons, showing that they indeed originated from constitutive exons that acquired a new competing splice site during evolution.
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Affiliation(s)
- Eli Koren
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gil Ast
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * To whom correspondence should be addressed. E-mail:
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42
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Tsai KW, Tarn WY, Lin WC. Wobble splicing reveals the role of the branch point sequence-to-NAGNAG region in 3' tandem splice site selection. Mol Cell Biol 2007; 27:5835-48. [PMID: 17562859 PMCID: PMC1952111 DOI: 10.1128/mcb.00363-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alternative splicing involving the 3' tandem splice site NAGNAG sequence may play a role in the structure-function diversity of proteins. However, how 3' tandem splice site utilization is determined is not well understood. We previously demonstrated that 3' NAGNAG-based wobble splicing occurs mostly in a tissue- and developmental stage-independent manner. Bioinformatic analysis reveals that the nucleotide preceding the AG dinucleotide may influence 3' splice site utilization; this is also supported by an in vivo splicing assay. Moreover, we found that the intron sequence plays an important role in 3' splice site selection for NAGNAG wobble splicing. Mutations of the region between the branch site and the NAGNAG 3' splice site, indeed, affected the ratio of the distal/proximal AG selection. Finally, we found that single nucleotide polymorphisms around the NAGNAG motif could affect the splice site choice, which may lead to a change in mRNA patterns and influence protein function. We conclude that the NAGNAG motif and its upstream region to the branch point sequence are required for 3' tandem splice site selection.
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Affiliation(s)
- Kuo-Wang Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China
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43
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Buvoli M, Buvoli A, Leinwand LA. Interplay between exonic splicing enhancers, mRNA processing, and mRNA surveillance in the dystrophic Mdx mouse. PLoS One 2007; 2:e427. [PMID: 17487273 PMCID: PMC1855434 DOI: 10.1371/journal.pone.0000427] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 04/15/2007] [Indexed: 02/05/2023] Open
Abstract
Background Pre-mRNA splicing, the removal of introns from RNA, takes place within the spliceosome, a macromolecular complex composed of five small nuclear RNAs and a large number of associated proteins. Spliceosome assembly is modulated by the 5′ and 3′ splice site consensus sequences situated at the ends of each intron, as well as by exonic and intronic splicing enhancers/silencers recognized by SR and hnRNP proteins. Nonsense mutations introducing a premature termination codon (PTC) often result in the activation of cellular quality control systems that reduce mRNA levels or alter the mRNA splicing pattern. The mdx mouse, a commonly used genetic model for Duchenne muscular dystrophy (DMD), lacks dystrophin by virtue of a premature termination codon (PTC) in exon 23 that also severely reduces the level of dystrophin mRNA. However, the effect of the mutation on dystrophin RNA processing has not yet been described. Methodology/Principal Finding Using combinations of different biochemical and cellular assays, we found that the mdx mutation partially disrupts a multisite exonic splicing enhancer (ESE) that is recognized by a 40 kDa SR protein. In spite of the presence of an inefficient intron 22 3′ splice site containing the rare GAG triplet, the mdx mutation does not activate nonsense-associated altered splicing (NAS), but induces exclusively nonsense-mediated mRNA decay (NMD). Functional binding sites for SR proteins were also identified in exon 22 and 24, and in vitro experiments show that SR proteins can mediate direct association between exon 22, 23, and 24. Conclusions/Significance Our findings highlight the complex crosstalk between trans-acting factors, cis-elements and the RNA surveillance machinery occurring during dystrophin mRNA processing. Moreover, they suggest that dystrophin exon–exon interactions could play an important role in preventing mdx exon 23 skipping, as well as in facilitating the pairing of committed splice sites.
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Affiliation(s)
- Massimo Buvoli
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado, United States of America
| | - Ada Buvoli
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado, United States of America
| | - Leslie A. Leinwand
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado, United States of America
- * To whom correspondence should be addressed. E-mail:
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44
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Matlin AJ, Moore MJ. Spliceosome assembly and composition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:14-35. [PMID: 18380338 DOI: 10.1007/978-0-387-77374-2_2] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cells control alternative splicing by modulating assembly of the pre-mRNA splicing machinery at competing splice sites. Therefore, a working knowledge of spliceosome assembly is essential for understanding how alternative splice site choices are achieved. In this chapter, we review spliceosome assembly with particular emphasis on the known steps and factors subject to regulation during alternative splice site selection in mammalian cells. We also review recent advances regarding similarities and differences between the in vivo and in vitro assembly pathways, as well as proofreading mechanisms contributing to the fidelity of splice site selection.
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Affiliation(s)
- Arianne J Matlin
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
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45
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Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genomics 2006; 7:311. [PMID: 17156453 PMCID: PMC1713244 DOI: 10.1186/1471-2164-7-311] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 12/08/2006] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The signals that determine the specificity and efficiency of splicing are multiple and complex, and are not fully understood. Among other factors, the relative contributions of different mechanisms appear to depend on intron size inasmuch as long introns might hinder the activity of the spliceosome through interference with the proper positioning of the intron-exon junctions. Indeed, it has been shown that the information content of splice sites positively correlates with intron length in the nematode, Drosophila, and fungi. We explored the connections between the length of vertebrate introns, the strength of splice sites, exonic splicing signals, and evolution of flanking exons. RESULTS A compensatory relationship is shown to exist between different types of signals, namely, the splice sites and the exonic splicing enhancers (ESEs). In the range of relatively short introns (approximately, < 1.5 kilobases in length), the enhancement of the splicing signals for longer introns was manifest in the increased concentration of ESEs. In contrast, for longer introns, this effect was not detectable, and instead, an increase in the strength of the donor and acceptor splice sites was observed. Conceivably, accumulation of A-rich ESE motifs beyond a certain limit is incompatible with functional constraints operating at the level of protein sequence evolution, which leads to compensation in the form of evolution of the splice sites themselves toward greater strength. In addition, however, a correlation between sequence conservation in the exon ends and intron length, particularly, in synonymous positions, was observed throughout the entire length range of introns. Thus, splicing signals other than the currently defined ESEs, i.e., potential new classes of ESEs, might exist in exon sequences, particularly, those that flank long introns. CONCLUSION Several weak but statistically significant correlations were observed between vertebrate intron length, splice site strength, and potential exonic splicing signals. Taken together, these findings attest to a compensatory relationship between splice sites and exonic splicing signals, depending on intron length.
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46
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Saulière J, Sureau A, Expert-Bezançon A, Marie J. The polypyrimidine tract binding protein (PTB) represses splicing of exon 6B from the beta-tropomyosin pre-mRNA by directly interfering with the binding of the U2AF65 subunit. Mol Cell Biol 2006; 26:8755-69. [PMID: 16982681 PMCID: PMC1636812 DOI: 10.1128/mcb.00893-06] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 06/27/2006] [Accepted: 09/06/2006] [Indexed: 11/20/2022] Open
Abstract
Splicing of exon 6B from the beta-tropomyosin pre-mRNA is repressed in nonmuscle cells and myoblasts by a complex array of intronic elements surrounding the exon. In this study, we analyzed the proteins that mediate splicing repression of exon 6B through binding to the upstream element. We identified the polypyrimidine tract binding protein (PTB) as a component of complexes isolated from myoblasts that assemble onto the branch point region and the pyrimidine tract. In vitro splicing assays and PTB knockdown experiments by RNA interference demonstrated that PTB acts as a repressor of splicing of exon 6B. Using psoralen experiments, we showed that PTB acts at an early stage of spliceosome assembly by preventing the binding of U2 snRNA on the branch point. Using UV cross-linking and immunoprecipitation experiments with site-specific labeled RNA in PTB-depleted nuclear extracts, we found that the decrease in PTB was correlated with an increase in U2AF65. In addition, competition experiments showed that PTB is able to displace the binding of U2AF65 on the polypyrimidine tract. Our results strongly support a model whereby PTB competes with U2AF65 for binding to the polypyrimidine tract.
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Affiliation(s)
- Jérôme Saulière
- Centre de Génétique Moléculaire, UPR2167, CNRS, 1 avenue de la Terrasse, 91198 Gif sur Yvette, France
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47
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Vorechovský I. Aberrant 3' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 2006; 34:4630-41. [PMID: 16963498 PMCID: PMC1636351 DOI: 10.1093/nar/gkl535] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The frequency distribution of mutation-induced aberrant 3' splice sites (3'ss) in exons and introns is more complex than for 5' splice sites, largely owing to sequence constraints upstream of intron/exon boundaries. As a result, prediction of their localization remains a challenging task. Here, nucleotide sequences of previously reported 218 aberrant 3'ss activated by disease-causing mutations in 131 human genes were compared with their authentic counterparts using currently available splice site prediction tools. Each tested algorithm distinguished authentic 3'ss from cryptic sites more effectively than from de novo sites. The best discrimination between aberrant and authentic 3'ss was achieved by the maximum entropy model. Almost one half of aberrant 3'ss was activated by AG-creating mutations and approximately 95% of the newly created AGs were selected in vivo. The overall nucleotide structure upstream of aberrant 3'ss was characterized by higher purine content than for authentic sites, particularly in position -3, that may be compensated by more stringent requirements for positive and negative nucleotide signatures centred around position -11. A newly developed online database of aberrant 3'ss will facilitate identification of splicing mutations in a gene or phenotype of interest and future optimization of splice site prediction tools.
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Affiliation(s)
- Igor Vorechovský
- University of Southampton School of Medicine, Division of Human Genetics, Mailpoint 808, Southampton SO16 6YD, UK
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48
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Yamanegi K, Tang S, Zheng ZM. Kaposi's sarcoma-associated herpesvirus K8beta is derived from a spliced intermediate of K8 pre-mRNA and antagonizes K8alpha (K-bZIP) to induce p21 and p53 and blocks K8alpha-CDK2 interaction. J Virol 2006; 79:14207-21. [PMID: 16254356 PMCID: PMC1280184 DOI: 10.1128/jvi.79.22.14207-14221.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a lymphotropic DNA tumor virus that induces Kaposi's sarcoma and AIDS-related primary effusion lymphoma. KSHV open reading frame 50 and K8 genes in early viral lytic infection express, respectively, a tricistronic and a bicistronic pre-mRNA, which undergo alternative splicing to create two major spliced mRNA isoforms, alpha and beta, by inclusion (beta) or exclusion (alpha) of an intron at nucleotides 75563 to 75645. This intron contains some suboptimal features, which cause the intron 5' splice site (ss) to interact weakly with U1 snRNA and the 3' ss to bind a U2 auxiliary factor, U2AF, with low affinity. Optimization of this intron in K8 (K8 intron 2) promoted the interaction of the 5' ss with U1 and the 3' ss with U2AF, resulting in a substantial increase in intron splicing. Splicing of K8 intron 2 has also been shown to be stimulated by the splicing of a downstream intron. This was confirmed by the insertion of a human beta-globin intron into the K8beta exon 3-exon 4 splice junction, which promoted splicing of K8beta intron 2 and conversion of the K8beta mRNA to the K8alpha mRNA that encodes a K-bZIP protein. Intron 2 contains a premature termination codon, yet the K8beta mRNA is insensitive to nonsense-mediated mRNA decay, suggesting that the truncated K8beta protein may have a biological function. Indeed, although the truncated K8beta protein is missing only a C-terminal leucine zipper domain from the K-bZIP, its expression antagonizes the ability of the K-bZIP to induce p53 and p21 and blocks K-bZIP-CDK2 interaction through interfering K8alpha mRNA production.
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Affiliation(s)
- Koji Yamanegi
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1868, USA
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49
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Gooding C, Clark F, Wollerton MC, Grellscheid SN, Groom H, Smith CWJ. A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones. Genome Biol 2006; 7:R1. [PMID: 16507133 PMCID: PMC1431707 DOI: 10.1186/gb-2006-7-1-r1] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 09/21/2005] [Accepted: 11/28/2005] [Indexed: 01/19/2023] Open
Abstract
Exons with predicted branch points were identified from a large dataset of human exons and the importance of these branch points for splicing was verified. Background The three consensus elements at the 3' end of human introns - the branch point sequence, the polypyrimidine tract, and the 3' splice site AG dinucleotide - are usually closely spaced within the final 40 nucleotides of the intron. However, the branch point sequence and polypyrimidine tract of a few known alternatively spliced exons lie up to 400 nucleotides upstream of the 3' splice site. The extended regions between the distant branch points (dBPs) and their 3' splice site are marked by the absence of other AG dinucleotides. In many cases alternative splicing regulatory elements are located within this region. Results We have applied a simple algorithm, based on AG dinucleotide exclusion zones (AGEZ), to a large data set of verified human exons. We found a substantial number of exons with large AGEZs, which represent candidate dBP exons. We verified the importance of the predicted dBPs for splicing of some of these exons. This group of exons exhibits a higher than average prevalence of observed alternative splicing, and many of the exons are in genes with some human disease association. Conclusion The group of identified probable dBP exons are interesting first because they are likely to be alternatively spliced. Second, they are expected to be vulnerable to mutations within the entire extended AGEZ. Disruption of splicing of such exons, for example by mutations that lead to insertion of a new AG dinucleotide between the dBP and 3' splice site, could be readily understood even though the causative mutation might be remote from the conventional locations of splice site sequences.
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Affiliation(s)
- Clare Gooding
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Francis Clark
- Advanced Computational Modelling Centre, and ARC Centre for Bioinformatics, University of Queensland, Australia
| | - Matthew C Wollerton
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Harriet Groom
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Christopher WJ Smith
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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50
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Abstract
Alternative splicing (AS) constitutes a major mechanism creating protein diversity in humans. Previous bioinformatics studies based on expressed sequence tag and mRNA data have identified many AS events that are conserved between humans and mice. Of these events, ∼25% are related to alternative choices of 3′ and 5′ splice sites. Surprisingly, half of all these events involve 3′ splice sites that are exactly 3 nt apart. These tandem 3′ splice sites result from the presence of the NAGNAG motif at the acceptor splice site, recently reported to be widely spread in the human genome. Although the NAGNAG motif is common in human genes, only a small subset of sites with this motif is confirmed to be involved in AS. We examined the NAGNAG motifs and observed specific features such as high sequence conservation of the motif, high conservation of ∼30 bp at the intronic regions flanking the 3′ splice site and overabundance of cis-regulatory elements, which are characteristic of alternatively spliced tandem acceptor sites and can distinguish them from the constitutive sites in which the proximal NAG splice site is selected. Our findings imply that AS at tandem splice sites and constitutive splicing of the distal NAG are highly regulated.
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Affiliation(s)
| | - Yael Mandel-Gutfreund
- To whom correspondence should be addressed. Tel: +972 4 8293958; Fax: +972 4 8225153;
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