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Bauer M, Schöbel CM, Wickenhauser C, Seliger B, Jasinski-Bergner S. Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies. Front Immunol 2024; 15:1386993. [PMID: 38736877 PMCID: PMC11082354 DOI: 10.3389/fimmu.2024.1386993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Alternative splicing (AS) is an important molecular biological mechanism regulated by complex mechanisms involving a plethora of cis and trans-acting elements. Furthermore, AS is tissue specific and altered in various pathologies, including infectious, inflammatory, and neoplastic diseases. Recently developed immuno-oncological therapies include monoclonal antibodies (mAbs) and chimeric antigen receptor (CAR) T cells targeting, among others, immune checkpoint (ICP) molecules. Despite therapeutic successes have been demonstrated, only a limited number of patients showed long-term benefit from these therapies with tumor entity-related differential response rates were observed. Interestingly, splice variants of common immunotherapeutic targets generated by AS are able to completely escape and/or reduce the efficacy of mAb- and/or CAR-based tumor immunotherapies. Therefore, the analyses of splicing patterns of targeted molecules in tumor specimens prior to therapy might help correct stratification, thereby increasing therapy success by antibody panel selection and antibody dosages. In addition, the expression of certain splicing factors has been linked with the patients' outcome, thereby highlighting their putative prognostic potential. Outstanding questions are addressed to translate the findings into clinical application. This review article provides an overview of the role of AS in (tumor) diseases, its molecular mechanisms, clinical relevance, and therapy response.
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Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Chiara-Maria Schöbel
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
- Department of Good Manufacturing Practice (GMP) Development & Advanced Therapy Medicinal Products (ATMP) Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Institute for Medical Immunology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Simon Jasinski-Bergner
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
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2
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Hoppe ER, Udy DB, Bradley RK. Recursive splicing discovery using lariats in total RNA sequencing. Life Sci Alliance 2023; 6:e202201889. [PMID: 37137707 PMCID: PMC10156609 DOI: 10.26508/lsa.202201889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Recursive splicing is a non-canonical splicing mechanism in which an intron is removed in segments via multiple splicing reactions. Relatively few recursive splice sites have been identified with high confidence in human introns, and more comprehensive analyses are needed to better characterize where recursive splicing happens and whether or not it has a regulatory function. In this study, we use an unbiased approach using intron lariats to search for recursive splice sites in constitutive introns and alternative exons in the human transcriptome. We find evidence for recursive splicing in a broader range of intron sizes than previously reported and detail a new location for recursive splicing at the distal ends of cassette exons. In addition, we identify evidence for the conservation of these recursive splice sites among higher vertebrates and the use of these sites to influence alternative exon exclusion. Together, our data demonstrate the prevalence of recursive splicing and its potential influence on gene expression through alternatively spliced isoforms.
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Affiliation(s)
- Emma R Hoppe
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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3
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Ferrández-Peral L, Zhan X, Alvarez-Estape M, Chiva C, Esteller-Cucala P, García-Pérez R, Julià E, Lizano E, Fornas Ò, Sabidó E, Li Q, Marquès-Bonet T, Juan D, Zhang G. Transcriptome innovations in primates revealed by single-molecule long-read sequencing. Genome Res 2022; 32:1448-1462. [PMID: 35840341 PMCID: PMC9435740 DOI: 10.1101/gr.276395.121] [Citation(s) in RCA: 1] [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: 11/16/2021] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
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Affiliation(s)
| | | | | | - Cristina Chiva
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | | | | | - Eva Julià
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Òscar Fornas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen 2200, Denmark
- Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou 310058, China
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4
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Petersen USS, Doktor TK, Andresen BS. Pseudoexon activation in disease by non-splice site deep intronic sequence variation - wild type pseudoexons constitute high-risk sites in the human genome. Hum Mutat 2021; 43:103-127. [PMID: 34837434 DOI: 10.1002/humu.24306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 12/27/2022]
Abstract
Accuracy of pre-messenger RNA (pre-mRNA) splicing is crucial for normal gene expression. Complex regulation supports the spliceosomal distinction between authentic exons and the many seemingly functional splice sites delimiting pseudoexons. Pseudoexons are nonfunctional intronic sequences that can be activated for aberrant inclusion in mRNA, which may cause disease. Pseudoexon activation is very challenging to predict, in particular when activation occurs by sequence variants that alter the splicing regulatory environment without directly affecting splice sites. As pseudoexon inclusion often evades detection due to activation of nonsense-mediated mRNA decay, and because conventional diagnostic procedures miss deep intronic sequence variation, pseudoexon activation is a heavily underreported disease mechanism. Pseudoexon characteristics have mainly been studied based on in silico predicted sequences. Moreover, because recognition of sequence variants that create or strengthen splice sites is possible by comparison with well-established consensus sequences, this type of pseudoexon activation is by far the most frequently reported. Here we review all known human disease-associated pseudoexons that carry functional splice sites and are activated by deep intronic sequence variants located outside splice site sequences. We delineate common characteristics that make this type of wild type pseudoexons distinct high-risk sites in the human genome.
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Affiliation(s)
- Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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5
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Cottrell E, Maharaj A, Williams J, Chatterjee S, Cirillo G, Miraglia del Giudice E, Festa A, Palumbo S, Capalbo D, Salerno M, Pignata C, Savage MO, Schilbach K, Bidlingmaier M, Hwa V, Metherell LA, Grandone A, Storr HL. Growth Hormone Receptor (Ghr) 6ω Pseudoexon Activation: A Novel Cause Of Severe Growth Hormone Insensitivity (Ghi). J Clin Endocrinol Metab 2021; 107:dgab550. [PMID: 34318893 PMCID: PMC8684449 DOI: 10.1210/clinem/dgab550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Indexed: 12/15/2022]
Abstract
CONTEXT Severe forms of Growth Hormone Insensitivity (GHI) are characterized by extreme short stature, dysmorphism and metabolic anomalies. OBJECTIVE Identification of the genetic cause of growth failure in 3 'classical' GHI subjects. DESIGN A novel intronic GHR variant was identified, and in vitro splicing assays confirmed aberrant splicing. A 6Ω pseudoexon GHR vector and patient fibroblast analysis assessed the consequences of the novel pseudoexon inclusion and the impact on GHR function. RESULTS We identified a novel homozygous intronic GHR variant (g.5:42700940T>G, c.618 + 836T> G), 44bp downstream of the previously recognized intronic 6Ψ GHR pseudoexon mutation in the index patient. Two siblings also harbored the novel intronic 6Ω pseudoexon GHR variant in compound heterozygosity with the known GHR c.181C>T (R43X) mutation. In vitro splicing analysis confirmed inclusion of a 151bp mutant 6Ω pseudoexon not identified in wild-type constructs. Inclusion of the 6Ω pseudoexon causes a frameshift resulting in a non-functional truncated GHR lacking the transmembrane and intracellular domains. The truncated 6Ω pseudoexon protein demonstrated extracellular accumulation and diminished activation of STAT5B signaling following growth hormone stimulation. CONCLUSION Novel GHR 6Ω pseudoexon inclusion results in loss of GHR function consistent with a severe GHI phenotype. This represents a novel mechanism of Laron syndrome and is the first deep intronic variant identified causing severe postnatal growth failure. The 2 kindreds originate from the same town in Campania, Southern Italy, implying common ancestry. Our findings highlight the importance of studying variation in deep intronic regions as a cause of monogenic disorders.
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Affiliation(s)
- Emily Cottrell
- Centre for Endocrinology, William Harvey Research Institute: Barts and The London School of Medicine and Dentistry William Harvey Research Institute, London EC1M 6BQ, UK
| | - Avinaash Maharaj
- Centre for Endocrinology, William Harvey Research Institute: Barts and The London School of Medicine and Dentistry William Harvey Research Institute, London EC1M 6BQ, UK
| | - Jack Williams
- Centre for Endocrinology, William Harvey Research Institute: Barts and The London School of Medicine and Dentistry William Harvey Research Institute, London EC1M 6BQ, UK
| | - Sumana Chatterjee
- Centre for Endocrinology, William Harvey Research Institute: Barts and The London School of Medicine and Dentistry William Harvey Research Institute, London EC1M 6BQ, UK
| | - Grazia Cirillo
- Studies of Campania Luigi Vanvitelli, Department of Woman, Child, General and Specialized Surgery, Naples 80138, Italy
| | - Emanuele Miraglia del Giudice
- Studies of Campania Luigi Vanvitelli, Department of Woman, Child, General and Specialized Surgery, Naples 80138, Italy
| | - Adalgisa Festa
- Studies of Campania Luigi Vanvitelli, Department of Woman, Child, General and Specialized Surgery, Naples 80138, Italy
| | - Stefania Palumbo
- Studies of Campania Luigi Vanvitelli, Department of Woman, Child, General and Specialized Surgery, Naples 80138, Italy
| | - Donatella Capalbo
- Federico II University Hospital: Azienda Ospedaliera Universitaria Federico II, Naples 80131, Italy
| | - Mariacarolina Salerno
- University of Naples Federico II Department of Translational Medical Sciences: Universita degli Studi di Napoli Federico II Dipartimento di Scienze Mediche Traslazionali, Naples 80138, Italy
| | - Claudio Pignata
- University of Naples Federico II Department of Translational Medical Sciences: Universita degli Studi di Napoli Federico II Dipartimento di Scienze Mediche Traslazionali, Naples 80138, Italy
| | - Martin O Savage
- Centre for Endocrinology, William Harvey Research Institute: Barts and The London School of Medicine and Dentistry William Harvey Research Institute, London EC1M 6BQ, UK
| | | | | | - Vivian Hwa
- Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, USA
| | - Louise A Metherell
- Centre for Endocrinology, William Harvey Research Institute: Barts and The London School of Medicine and Dentistry William Harvey Research Institute, London EC1M 6BQ, UK
| | - Anna Grandone
- Studies of Campania Luigi Vanvitelli, Department of Woman, Child, General and Specialized Surgery, Naples 80138, Italy
| | - Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute: Barts and The London School of Medicine and Dentistry William Harvey Research Institute, London EC1M 6BQ, UK
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6
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Movassat M, Forouzmand E, Reese F, Hertel KJ. Exon size and sequence conservation improves identification of splice-altering nucleotides. RNA (NEW YORK, N.Y.) 2019; 25:1793-1805. [PMID: 31554659 PMCID: PMC6859846 DOI: 10.1261/rna.070987.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Pre-mRNA splicing is regulated through multiple trans-acting splicing factors. These regulators interact with the pre-mRNA at intronic and exonic positions. Given that most exons are protein coding, the evolution of exons must be modulated by a combination of selective coding and splicing pressures. It has previously been demonstrated that selective splicing pressures are more easily deconvoluted when phylogenetic comparisons are made for exons of identical size, suggesting that exon size-filtered sequence alignments may improve identification of nucleotides evolved to mediate efficient exon ligation. To test this hypothesis, an exon size database was created, filtering 76 vertebrate sequence alignments based on exon size conservation. In addition to other genomic parameters, such as splice-site strength, gene position, or flanking intron length, this database permits the identification of exons that are size- and/or sequence-conserved. Highly size-conserved exons are always sequence-conserved. However, sequence conservation does not necessitate exon size conservation. Our analysis identified evolutionarily young exons and demonstrated that length conservation is a strong predictor of alternative splicing. A published data set of approximately 5000 exonic SNPs associated with disease was analyzed to test the hypothesis that exon size-filtered sequence comparisons increase detection of splice-altering nucleotides. Improved splice predictions could be achieved when mutations occur at the third codon position, especially when a mutation decreases exon inclusion efficiency. The results demonstrate that coding pressures dominate nucleotide composition at invariable codon positions and that exon size-filtered sequence alignments permit identification of splice-altering nucleotides at wobble positions.
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Affiliation(s)
- Maliheh Movassat
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Elmira Forouzmand
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Fairlie Reese
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
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7
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Attig J, Ule J. Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA-Binding Proteins: A Hypothesis. Bioessays 2019; 41:e1800132. [DOI: 10.1002/bies.201800132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/14/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Jan Attig
- Dr. J. Attig, Prof. J. Ule; The Francis Crick Institute; 1 Midland Road London NW1 1AT UK
| | - Jernej Ule
- Dr. J. Attig, Prof. J. Ule; The Francis Crick Institute; 1 Midland Road London NW1 1AT UK
- Prof. J. Ule; Department of Molecular Neuroscience; UCL Institute of Neurology; Queen Square London WC1N 3BG UK
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8
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Attig J, Agostini F, Gooding C, Chakrabarti AM, Singh A, Haberman N, Zagalak JA, Emmett W, Smith CWJ, Luscombe NM, Ule J. Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing. Cell 2018; 174:1067-1081.e17. [PMID: 30078707 PMCID: PMC6108849 DOI: 10.1016/j.cell.2018.07.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/23/2018] [Accepted: 07/01/2018] [Indexed: 12/30/2022]
Abstract
Long mammalian introns make it challenging for the RNA processing machinery to identify exons accurately. We find that LINE-derived sequences (LINEs) contribute to this selection by recruiting dozens of RNA-binding proteins (RBPs) to introns. This includes MATR3, which promotes binding of PTBP1 to multivalent binding sites within LINEs. Both RBPs repress splicing and 3' end processing within and around LINEs. Notably, repressive RBPs preferentially bind to evolutionarily young LINEs, which are located far from exons. These RBPs insulate the LINEs and the surrounding intronic regions from RNA processing. Upon evolutionary divergence, changes in RNA motifs within LINEs lead to gradual loss of their insulation. Hence, older LINEs are located closer to exons, are a common source of tissue-specific exons, and increasingly bind to RBPs that enhance RNA processing. Thus, LINEs are hubs for the assembly of repressive RBPs and also contribute to the evolution of new, lineage-specific transcripts in mammals. VIDEO ABSTRACT.
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Affiliation(s)
- Jan Attig
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Federico Agostini
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Aarti Singh
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Comparative Biomedical Sciences, The Royal Veterinary College, Royal College Street, London NW1 0TU, UK
| | - Nejc Haberman
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Julian A Zagalak
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Warren Emmett
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
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9
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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10
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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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11
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Lin L, Jiang P, Park JW, Wang J, Lu ZX, Lam MPY, Ping P, Xing Y. The contribution of Alu exons to the human proteome. Genome Biol 2016; 17:15. [PMID: 26821878 PMCID: PMC4731929 DOI: 10.1186/s13059-016-0876-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/08/2016] [Indexed: 12/19/2022] Open
Abstract
Background Alu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as Alu elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins. Results We adopt a proteotranscriptomics approach to systematically assess the contribution of Alu exons to the human proteome. Using RNA sequencing, ribosome profiling, and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of Alu exons and the presence of Alu exon derived peptides in human proteins. These Alu exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances between humans and closely related primates. In the case of the RNA editing enzyme ADARB1, which contains an Alu exon peptide in its catalytic domain, RNA sequencing analyses of A-to-I editing demonstrate that both the Alu exon skipping and inclusion isoforms encode active enzymes. The Alu exon derived peptide may fine tune the overall editing activity and, in limited cases, the site selectivity of ADARB1 protein products. Conclusions Our data indicate that Alu elements have contributed to the acquisition of novel protein sequences during primate and human evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0876-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lan Lin
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Peng Jiang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53707, USA.
| | - Juw Won Park
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40292, USA. .,KBRIN Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA.
| | - Jinkai Wang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Zhi-Xiang Lu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Maggie P Y Lam
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Peipei Ping
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Department of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Yi Xing
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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12
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Kim YH, Choe SH, Song BS, Park SJ, Kim MJ, Park YH, Yoon SB, Lee Y, Jin YB, Sim BW, Kim JS, Jeong KJ, Kim SU, Lee SR, Park YI, Huh JW, Chang KT. Macaca specific exon creation event generates a novel ZKSCAN5 transcript. Gene 2015; 577:236-43. [PMID: 26657034 DOI: 10.1016/j.gene.2015.11.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 10/20/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
ZKSCAN5 (also known as ZFP95) is a zinc-finger protein belonging to the Krűppel family. ZKSCAN5 contains a SCAN box and a KRAB A domain and is proposed to play a distinct role during spermatogenesis. In humans, alternatively spliced ZKSCAN5 transcripts with different 5'-untranslated regions (UTRs) have been identified. However, investigation of our Macaca UniGene Database revealed novel alternative ZKSCAN5 transcripts that arose due to an exon creation event. Therefore, in this study, we identified the full-length sequences of ZKSCAN5 and its alternative transcripts in Macaca spp. Additionally, we investigated different nonhuman primate sequences to elucidate the molecular mechanism underlying the exon creation event. We analyzed the evolutionary features of the ZKSCAN5 transcripts by reverse transcription polymerase chain reaction (RT-PCR) and genomic PCR, and by sequencing various nonhuman primate DNA and RNA samples. The exon-created transcript was only detected in the Macaca lineage (crab-eating monkey and rhesus monkey). Full-length sequence analysis by rapid amplification of cDNA ends (RACE) identified ten full-length transcripts and four functional isoforms of ZKSCAN5. Protein sequence analyses revealed the presence of two groups of isoforms that arose because of differences in start-codon usage. Together, our results demonstrate that there has been specific selection for a discrete set of ZKSCAN5 variants in the Macaca lineage. Furthermore, study of this locus (and perhaps others) in Macaca spp. might facilitate our understanding of the evolutionary pressures that have shaped the mechanism of exon creation in primates.
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Affiliation(s)
- Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea
| | - Bong-Seok Song
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Myung-Jin Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Young-Ho Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Seung-Bin Yoon
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Bo-Woong Sim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Ji-Su Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea
| | - Kang-Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea
| | - Young-Il Park
- Graduate School Department of Digital Media, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea.
| | - Kyu-Tae Chang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 363-883, Republic of Korea; University of Science & Technology, National Primate Research Center, KRIBB, Cheongju 363-883, Republic of Korea.
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13
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Park SJ, Kim YH, Lee SR, Choe SH, Kim MJ, Kim SU, Kim JS, Sim BW, Song BS, Jeong KJ, Jin YB, Lee Y, Park YH, Park YI, Huh JW, Chang KT. Gain of a New Exon by a Lineage-Specific Alu Element-Integration Event in the BCS1L Gene during Primate Evolution. Mol Cells 2015; 38:950-8. [PMID: 26537194 PMCID: PMC4673409 DOI: 10.14348/molcells.2015.0121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 11/27/2022] Open
Abstract
BCS1L gene encodes mitochondrial protein and is a member of conserved AAA protein family. This gene is involved in the incorporation of Rieske FeS and Qcr10p into complex III of respiratory chain. In our previous study, AluYRa2-derived alternative transcript in rhesus monkey genome was identified. However, this transcript has not been reported in human genome. In present study, we conducted evolutionary analysis of AluYRa2-exonized transcript with various primate genomic DNAs and cDNAs from humans, rhesus monkeys, and crab-eating monkeys. Remarkably, our results show that AluYRa2 element has only been integrated into genomes of Macaca species. This Macaca lineage-specific integration of AluYRa2 element led to exonization event in the first intron region of BCS1L gene by producing a conserved 3' splice site. Intriguingly, in rhesus and crab-eating monkeys, more diverse transcript variants by alternative splicing (AS) events, including exon skipping and different 5' splice sites from humans, were identified. Alignment of amino acid sequences revealed that AluYRa2-exonized transcript has short N-terminal peptides. Therefore, AS events play a major role in the generation of various transcripts and proteins during primate evolution. In particular, lineage-specific integration of Alu elements and species-specific Alu-derived exonization events could be important sources of gene diversification in primates.
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Affiliation(s)
- Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Myung-Jin Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Ji-Su Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Bo-Woong Sim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Bong-Seok Song
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Kang-Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Yeung-Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Youngjeon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Young-Ho Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Young Il Park
- Graduate School Department of Digital Media, Ewha Womans University, Seoul 120-750,
Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
| | - Kyu-Tae Chang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883,
Korea
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14
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Wang J, Lu ZX, Tokheim CJ, Miller SE, Xing Y. Species-specific exon loss in human transcriptomes. Mol Biol Evol 2014; 32:481-94. [PMID: 25398629 DOI: 10.1093/molbev/msu317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Changes in exon-intron structures and splicing patterns represent an important mechanism for the evolution of gene functions and species-specific regulatory networks. Although exon creation is widespread during primate and human evolution and has been studied extensively, much less is known about the scope and potential impact of human-specific exon loss events. Historically, transcriptome data and exon annotations are significantly biased toward humans over nonhuman primates. This ascertainment bias makes it challenging to discover human-specific exon loss events. We carried out a transcriptome-wide search of human-specific exon loss events, by taking advantage of RNA sequencing (RNA-seq) as a powerful and unbiased tool for exon discovery and annotation. Using RNA-seq data of humans, chimpanzees, and other primates, we reconstructed and compared transcript structures across the primate phylogeny. We discovered 33 candidate human-specific exon loss events, among which six exons passed stringent experimental filters for the complete loss of splicing activities in diverse human tissues. These events may result from human-specific deletion of genomic DNA, or small-scale sequence changes that inactivated splicing signals. The impact of human-specific exon loss events is predominantly regulatory. Three of the six events occurred in the 5' untranslated region (5'-UTR) and affected cis-regulatory elements of mRNA translation. In SLC7A6, a gene encoding an amino acid transporter, luciferase reporter assays suggested that both a human-specific exon loss event and an independent human-specific single nucleotide substitution in the 5'-UTR increased mRNA translational efficiency. Our study provides novel insights into the molecular mechanisms and evolutionary consequences of exon loss during human evolution.
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Affiliation(s)
- Jinkai Wang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
| | - Zhi-xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
| | - Collin J Tokheim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
| | | | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
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15
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Plass M, Eyras E. Approaches to link RNA secondary structures with splicing regulation. Methods Mol Biol 2014; 1126:341-56. [PMID: 24549676 DOI: 10.1007/978-1-62703-980-2_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitating or hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This chapter describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3' splice site (3'ss).
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Affiliation(s)
- Mireya Plass
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
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16
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Zhou K, Kuo A, Grigoriev IV. Reverse transcriptase and intron number evolution. Stem Cell Investig 2014; 1:17. [PMID: 27358863 DOI: 10.3978/j.issn.2306-9759.2014.08.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/04/2014] [Indexed: 11/14/2022]
Abstract
BACKGROUND Introns are universal in eukaryotic genomes and play important roles in transcriptional regulation, mRNA export to the cytoplasm, nonsense-mediated decay as both a regulatory and a splicing quality control mechanism, R-loop avoidance, alternative splicing, chromatin structure, and evolution by exon-shuffling. METHODS Sixteen complete fungal genomes were used 13 of which were sequenced and annotated by JGI. Ustilago maydis, Cryptococcus neoformans, and Coprinus cinereus (also named Coprinopsis cinerea) were from the Broad Institute. Gene models from JGI-annotated genomes were taken from the GeneCatalog track that contained the best representative gene models. Varying fractions of the GeneCatalog were manually curated by external users. For clarity, we used the JGI unique database identifier. RESULTS The last common ancestor of eukaryotes (LECA) has an estimated 6.4 coding exons per gene (EPG) and evolved into the diverse eukaryotic life forms, which is recapitulated by the development of a stem cell. We found a parallel between the simulated reverse transcriptase (RT)-mediated intron loss and the comparative analysis of 16 fungal genomes that spanned a wide range of intron density. Although footprints of RT (RTF) were dynamic, relative intron location (RIL) to the 5'-end of mRNA faithfully traced RT-mediated intron loss and revealed 7.7 EPG for LECA. The mode of exon length distribution was conserved in simulated intron loss, which was exemplified by the shared mode of 75 nt between fungal and Chlamydomonas genomes. The dominant ancient exon length was corroborated by the average exon length of the most intron-rich genes in fungal genomes and consistent with ancient protein modules being ~25 aa. Combined with the conservation of a protein length of 400 aa, the earliest ancestor of eukaryotes could have 16 EPG. During earlier evolution, Ascomycota's ancestor had significantly more 3'-biased RT-mediated intron loss that was followed by dramatic RTF loss. There was a down trend of EPG from more conserved to less conserved genes. Moreover, species-specific genes have higher exon-densities, shorter exons, and longer introns when compared to genes conserved at the phylum level. However, intron length in species-specific genes became shorter than that of genes conserved in all species after genomes experiencing drastic intron loss. The estimated EPG from the most frequent exon length is more than double that from the RIL method. CONCLUSIONS This implies significant intron loss during the very early period of eukaryotic evolution. De novo gene-birth contributes to shorter exons, longer introns, and higher exon-density in species-specific genes relative to conserved genes.
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Affiliation(s)
- Kemin Zhou
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Igor V Grigoriev
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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17
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Novel kinin B₁ receptor splice variant and 5'UTR regulatory elements are responsible for cell specific B₁ receptor expression. PLoS One 2014; 9:e87175. [PMID: 24475248 PMCID: PMC3903636 DOI: 10.1371/journal.pone.0087175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/20/2013] [Indexed: 12/04/2022] Open
Abstract
The kinin B1 receptor (B1R) is rapidly upregulated after tissue trauma or inflammation and is involved in cancer and inflammatory diseases such as asthma. However, the role of the: promoter; a postulated alternative promoter; and spliced variants in airway epithelial and other lung cells are poorly understood. We identified, in various lung cell lines and leucocytes, a novel, naturally occurring splice variant (SV) of human B1R gene with a shorter 5′untranslated region. This novel SV is ≈35% less stable than the wild-type (WT) transcript in lung adenocarcinoma cells (H2126), but does not influence translation efficiency. Cell-specific differences in splice variant expression were observed post des[Arg10]-kallidin stimulation with delayed upregulation of SV compared to WT suggesting potentially different regulatory responses to inflammation. Although an alternative promoter was not identified in our cell-lines, several cell-specific regulatory elements within the postulated alternative promoter region (negative response element (NRE) −1020 to −766 bp in H2126; positive response element (PRE) −766 to −410 bp in 16HBE; −410 to +1 region acts as a PRE in H2126 and NRE in 16HBE cells) were found. These findings reveal complex regulation of B1R receptor expression in pulmonary cells which may allow future therapeutic manipulation in chronic pulmonary inflammation and cancer.
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18
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Schad E, Kalmar L, Tompa P. Exon-phase symmetry and intrinsic structural disorder promote modular evolution in the human genome. Nucleic Acids Res 2013; 41:4409-22. [PMID: 23460204 PMCID: PMC3632108 DOI: 10.1093/nar/gkt110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A key signature of module exchange in the genome is phase symmetry of exons, suggestive of exon shuffling events that occurred without disrupting translation reading frame. At the protein level, intrinsic structural disorder may be another key element because disordered regions often serve as functional elements that can be effectively integrated into a protein structure. Therefore, we asked whether exon-phase symmetry in the human genome and structural disorder in the human proteome are connected, signalling such evolutionary mechanisms in the assembly of multi-exon genes. We found an elevated level of structural disorder of regions encoded by symmetric exons and a preferred symmetry of exons encoding for mostly disordered regions (>70% predicted disorder). Alternatively spliced symmetric exons tend to correspond to the most disordered regions. The genes of mostly disordered proteins (>70% predicted disorder) tend to be assembled from symmetric exons, which often arise by internal tandem duplications. Preponderance of certain types of short motifs (e.g. SH3-binding motif) and domains (e.g. high-mobility group domains) suggests that certain disordered modules have been particularly effective in exon-shuffling events. Our observations suggest that structural disorder has facilitated modular assembly of complex genes in evolution of the human genome.
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Affiliation(s)
- Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1113, Hungary
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19
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Mandal AK, Pandey R, Jha V, Mukerji M. Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. Nucleic Acids Res 2013; 41:2121-37. [PMID: 23303787 PMCID: PMC3575813 DOI: 10.1093/nar/gks1457] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 12/13/2012] [Accepted: 12/13/2012] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs from transposable elements of human genome are gaining prominence in modulating transcriptome dynamics. Alu elements, as exonized, edited and antisense components within same transcripts could create novel regulatory switches in response to different transcriptional cues. We provide the first evidence for co-occurrences of these events at transcriptome-wide scale through integrative analysis of data sets across diverse experimental platforms and tissues. This involved the following: (i) positional anchoring of Alu exonization events in the UTRs and CDS of 4663 transcript isoforms from RefSeq mRNAs and (ii) mapping on to them A→I editing events inferred from ∼7 million ESTs from dbEST and antisense transcripts identified from virtual serial analysis of gene expression tags represented in Cancer Genome Anatomy Project next-generation sequencing data sets across 20 tissues. We observed significant enrichment of these events in the 3'UTR as well as positional preference within the embedded Alus. More than 300 genes had co-occurrence of all these events at the exon level and were significantly enriched in apoptosis and lysosomal processes. Further, we demonstrate functional evidence of such dynamic interactions between Alu-mediated events in a time series data from Integrated Personal Omics Profiling during recovery from a viral infection. Such 'single transcript-multiple fate' opportunity facilitated by Alu elements may modulate transcriptional response, especially during stress.
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Affiliation(s)
- Amit K. Mandal
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Rajesh Pandey
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Vineet Jha
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Mitali Mukerji
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
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20
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Kim DS, Hahn Y. Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence. BMC Bioinformatics 2012; 13:299. [PMID: 23148531 PMCID: PMC3538075 DOI: 10.1186/1471-2105-13-299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 11/09/2012] [Indexed: 11/16/2022] Open
Abstract
Background Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence. Results We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors) in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of SMOX gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways. Conclusions Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution.
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Affiliation(s)
- Dong Seon Kim
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Korea
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21
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Yao S, Ireland SJ, Bee A, Beesley C, Forootan SS, Dodson A, Dickinson T, Gerard P, Lian LY, Risk JM, Smith P, Malki MI, Ke Y, Cooper CS, Gosden C, Foster CS. Splice variant PRKC-ζ(-PrC) is a novel biomarker of human prostate cancer. Br J Cancer 2012; 107:388-99. [PMID: 22644296 PMCID: PMC3394965 DOI: 10.1038/bjc.2012.162] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/24/2012] [Accepted: 03/25/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Previously, using gene-knockdown techniques together with genome expression array analysis, we showed the gene protein Kinase C (PKC)-zeta (PRKCZ) to mediate the malignant phenotype of human prostate cancer. However, according to NCBI, the gene has undergone several major iterations. Therefore, to understand the relationship between its structure and biological activities, we have analysed its expressed sequence in prostate cancer cell lines and tissues. METHODS Transcriptome-walking and targeted PCR were used to sequence the mRNA transcribed from PRKCZ. Hydropathy analysis was employed to analyse the hypothetical protein sequence subsequently translated and to identify an appropriate epitope to generate a specific monoclonal antibody. RESULTS A novel sequence was identified within the 3'-terminal domain of human PRKCZ that, in prostate cancer cell lines and tissues, is expressed during transcription and thereafter translated into protein (designated PKC-ζ(-PrC)) independent of conventional PKC-ζ(-a). The monoclonal antibody detected expression of this 96 kD protein only within malignant prostatic epithelium. INTERPRETATION Transcription and translation of this gene sequence, including previous intronic sequences, generates a novel specific biomarker of human prostate cancer. The presence of catalytic domains characteristic of classic PKC-β and atypical PKC-ι within PKC-ζ(-PrC) provides a potential mechanism for this PRKCZ variant to modulate the malignant prostatic phenotype out-with normal cell-regulatory control.
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Affiliation(s)
- S Yao
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - S J Ireland
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - A Bee
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C Beesley
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - S S Forootan
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - A Dodson
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - T Dickinson
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - P Gerard
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - L-Y Lian
- School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - J M Risk
- School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - P Smith
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - M I Malki
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - Y Ke
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C S Cooper
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - C Gosden
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C S Foster
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
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Abstract
New neurons are continuously generated in the subgranular zone of the adult hippocampus and, once sufficiently mature, are thought to integrate into hippocampal memory circuits. However, whether they play an essential role in subsequent memory expression is not known. Previous studies have shown that suppression of adult neurogenesis often (but not always) impairs subsequent hippocampus-dependent learning (i.e., produces anterograde effects). A major challenge for these studies is that these new neurons represent only a small subpopulation of all dentate granule cells, and so there is large potential for either partial or complete compensation by granule cells generated earlier on during development. A potentially more powerful approach to investigate this question would be to ablate adult-generated neurons after they have already become part of a memory trace (i.e., retrograde effects). Here we developed a diphtheria toxin-based strategy in mice that allowed us to selectively ablate a population of predominantly mature, adult-generated neurons either before or after learning, without affecting ongoing neurogenesis. Removal of these neurons before learning did not prevent the formation of new contextual fear or water maze memories. In contrast, removal of an equivalent population after learning degraded existing contextual fear and water maze memories, without affecting nonhippocampal memory. Ablation of these adult-generated neurons even 1 month after learning produced equivalent memory degradation in the water maze. These retrograde effects suggest that adult-generated neurons form a critical and enduring component of hippocampal memory traces.
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Ha HS, Chung WK, Ahn K, Bae JH, Park SJ, Moon JW, Nam KH, Han K, Cho HG, Kim HS. Development of GEBRET: a web-based analysis tool for retroelements in primate genomes. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0103-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res 2011; 22:35-50. [PMID: 21974994 DOI: 10.1101/gr.119834.110] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Exon-intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon-intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3' and 5' splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery.
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Corvelo A, Hallegger M, Smith CWJ, Eyras E. Genome-wide association between branch point properties and alternative splicing. PLoS Comput Biol 2010; 6:e1001016. [PMID: 21124863 PMCID: PMC2991248 DOI: 10.1371/journal.pcbi.1001016] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 10/27/2010] [Indexed: 11/18/2022] Open
Abstract
The branch point (BP) is one of the three obligatory signals required for pre-mRNA splicing. In mammals, the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task of modeling it in silico, and therefore of predicting the location of natural BPs. Consequently, BPs have been disregarded in a considerable fraction of the genome-wide studies on the regulation of splicing in mammals. We present a new computational approach for mammalian BP prediction. Using sequence conservation and positional bias we obtained a set of motifs with good agreement with U2 snRNA binding stability. Using a Support Vector Machine algorithm, we created a model complemented with polypyrimidine tract features, which considerably improves the prediction accuracy over previously published methods. Applying our algorithm to human introns, we show that BP position is highly dependent on the presence of AG dinucleotides in the 3' end of introns, with distance to the 3' splice site and BP strength strongly correlating with alternative splicing. Furthermore, experimental BP mapping for five exons preceded by long AG-dinucleotide exclusion zones revealed that, for a given intron, more than one BP can be chosen throughout the course of splicing. Finally, the comparison between exons of different evolutionary ages and pseudo exons suggests a key role of the BP in the pathway of exon creation in human. Our computational and experimental analyses suggest that BP recognition is more flexible than previously assumed, and it appears highly dependent on the presence of downstream polypyrimidine tracts. The reported association between BP features and the splicing outcome suggests that this, so far disregarded but yet crucial, element buries information that can complement current acceptor site models.
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Affiliation(s)
- André Corvelo
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
- Graduate Program in Areas of Basic and Applied Biology, Universidade do Porto, Porto, Portugal
| | - Martina Hallegger
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Eduardo Eyras
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- * E-mail:
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26
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Paquet Y, Anderson A. Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features. Nucleic Acids Res 2010; 38:4907-16. [PMID: 20392819 PMCID: PMC2926601 DOI: 10.1093/nar/gkq234] [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] [Indexed: 12/02/2022] Open
Abstract
Transposable elements derived from the 7SL RNA gene, such as Alu elements in primates, have had remarkable success in several mammalian lineages. The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene. Using thoroughly documented loci, we report that DNaseI-hypersensitive sites can be singled out in large genomic sequences by an assessment of sequence composition similarities with the 7SL RNA gene. We apply a root word frequency approach to illustrate a distinctive relationship between the sequence of the 7SL RNA gene and several classes of functional genomic features that are not presumed to be of transposable origin. Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5′-untranslated regions of long interspersed repetitive elements. In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions. The latter being the most notoriously difficult to detect, this approach may be useful for finding genomic segments that have regulatory functions and that may have escaped detection by existing methods.
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Affiliation(s)
- Yanick Paquet
- Centre de recherche en cancérologie de l’Université Laval, L’Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec G1R 2J6 and Département de biologie, Université Laval, Québec G1K 7P4, Canada
| | - Alan Anderson
- Centre de recherche en cancérologie de l’Université Laval, L’Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec G1R 2J6 and Département de biologie, Université Laval, Québec G1K 7P4, Canada
- *To whom correspondence should be addressed. Tel: + 418 691 5281; Fax: +418 691 5439;
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Sela N, Mersch B, Hotz-Wagenblatt A, Ast G. Characteristics of transposable element exonization within human and mouse. PLoS One 2010; 5:e10907. [PMID: 20532223 PMCID: PMC2879366 DOI: 10.1371/journal.pone.0010907] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 05/06/2010] [Indexed: 12/16/2022] Open
Abstract
Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs) revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.
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Affiliation(s)
- Noa Sela
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Britta Mersch
- Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail: (GA); (AHW)
| | - Gil Ast
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (GA); (AHW)
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28
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Shimada MK, Hayakawa Y, Takeda JI, Gojobori T, Imanishi T. A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing. BMC Evol Biol 2010; 10:122. [PMID: 20433709 PMCID: PMC2882926 DOI: 10.1186/1471-2148-10-122] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 04/30/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) is a key molecular process that endows biological functions with diversity and complexity. Generally, functional redundancy leads to the generation of new functions through relaxation of selective pressure in evolution, as exemplified by duplicated genes. It is also known that alternatively spliced exons (ASEs) are subject to relaxed selective pressure. Within consensus sequences at the splice junctions, the most conserved sites are dinucleotides at both ends of introns (splice dinucleotides). However, a small number of single nucleotide polymorphisms (SNPs) occur at splice dinucleotides. An intriguing question relating to the evolution of AS diversity is whether mutations at splice dinucleotides are maintained as polymorphisms and produce diversity in splice patterns within the human population. We therefore surveyed validated SNPs in the database dbSNP located at splice dinucleotides of all human genes that are defined by the H-Invitational Database. RESULTS We found 212 validated SNPs at splice dinucleotides (sdSNPs); these were confirmed to be consistent with the GT-AG rule at either allele. Moreover, 53 of them were observed to neighbor ASEs (AE dinucleotides). No significant differences were observed between sdSNPs at AE dinucleotides and those at constitutive exons (CE dinucleotides) in SNP properties including average heterozygosity, SNP density, ratio of predicted alleles consistent with the GT-AG rule, and scores of splice sites formed with the predicted allele. We also found that the proportion of non-conserved exons was higher for exons with sdSNPs than for other exons. CONCLUSIONS sdSNPs are found at CE dinucleotides in addition to those at AE dinucleotides, suggesting two possibilities. First, sdSNPs at CE dinucleotides may be robust against sdSNPs because of unknown mechanisms. Second, similar to sdSNPs at AE dinucleotides, those at CE dinucleotides cause differences in AS patterns because of the arbitrariness in the classification of exons into alternative and constitutive type that varies according to the dataset. Taking into account the absence of differences in sdSNP properties between those at AE and CE dinucleotides, the increased proportion of non-conserved exons found in exons flanked by sdSNPs suggests the hypothesis that sdSNPs are maintained at the splice dinucleotides of newly generated exons at which negative selection pressure is relaxed.
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Affiliation(s)
- Makoto K Shimada
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-45 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Yosuke Hayakawa
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-45 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Hitachi Software Engineering Co., Ltd., 1-1-43 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jun-ichi Takeda
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-45 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Takashi Gojobori
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Tadashi Imanishi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
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Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010; 11:345-55. [DOI: 10.1038/nrg2776] [Citation(s) in RCA: 756] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Unique functions of repetitive transcriptomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 285:115-88. [PMID: 21035099 DOI: 10.1016/b978-0-12-381047-2.00003-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Repetitive sequences occupy a huge fraction of essentially every eukaryotic genome. Repetitive sequences cover more than 50% of mammalian genomic DNAs, whereas gene exons and protein-coding sequences occupy only ~3% and 1%, respectively. Numerous genomic repeats include genes themselves. They generally encode "selfish" proteins necessary for the proliferation of transposable elements (TEs) in the host genome. The major part of evolutionary "older" TEs accumulated mutations over time and fails to encode functional proteins. However, repeats have important functions also on the RNA level. Repetitive transcripts may serve as multifunctional RNAs by participating in the antisense regulation of gene activity and by competing with the host-encoded transcripts for cellular factors. In addition, genomic repeats include regulatory sequences like promoters, enhancers, splice sites, polyadenylation signals, and insulators, which actively reshape cellular transcriptomes. TE expression is tightly controlled by the host cells, and some mechanisms of this regulation were recently decoded. Finally, capacity of TEs to proliferate in the host genome led to the development of multiple biotechnological applications.
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31
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Levy A, Schwartz S, Ast G. Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements. Nucleic Acids Res 2009; 38:1515-30. [PMID: 20008508 PMCID: PMC2836564 DOI: 10.1093/nar/gkp1134] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Throughout evolution, eukaryotic genomes have been invaded by transposable elements (TEs). Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion. We analyzed hundreds of thousands nested TEs in the human genome, i.e. insertions of TEs into existing ones. We first discovered that most TEs insert within specific ‘hotspots’ along the targeted TE. In particular, retrotransposed Alu elements contain a non-canonical single nucleotide hotspot for insertion of other Alu sequences. We next devised a method for identification of integration sequence motifs of inserted TEs that are conserved within the targeted TEs. This method revealed novel sequences motifs characterizing insertions of various important TE families: Alu, hAT, ERV1 and MaLR. Finally, we performed a global assessment to determine the extent to which young TEs tend to nest within older transposed elements and identified a 4-fold higher tendency of TEs to insert into existing TEs than to insert within non-TE intergenic regions. Our analysis demonstrates that TEs are highly biased to insert within certain TEs, in specific orientations and within specific targeted TE positions. TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition.
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Affiliation(s)
- Asaf Levy
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Ramat Aviv 69978, Israel
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32
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Gogvadze E, Buzdin A. Retroelements and their impact on genome evolution and functioning. Cell Mol Life Sci 2009; 66:3727-42. [PMID: 19649766 PMCID: PMC11115525 DOI: 10.1007/s00018-009-0107-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/11/2009] [Accepted: 07/14/2009] [Indexed: 12/31/2022]
Abstract
Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.
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Affiliation(s)
- Elena Gogvadze
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya st, 117997 Moscow, Russia.
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33
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Zhang Z, Zhou L, Wang P, Liu Y, Chen X, Hu L, Kong X. Divergence of exonic splicing elements after gene duplication and the impact on gene structures. Genome Biol 2009; 10:R120. [PMID: 19883501 PMCID: PMC3091315 DOI: 10.1186/gb-2009-10-11-r120] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/28/2009] [Accepted: 11/02/2009] [Indexed: 12/18/2022] Open
Abstract
An analysis of human exonic splicing elements in duplicated genes reveals their important role in the generation of new gene structures. Background The origin of new genes and their contribution to functional novelty has been the subject of considerable interest. There has been much progress in understanding the mechanisms by which new genes originate. Here we examine a novel way that new gene structures could originate, namely through the evolution of new alternative splicing isoforms after gene duplication. Results We studied the divergence of exonic splicing enhancers and silencers after gene duplication and the contributions of such divergence to the generation of new splicing isoforms. We found that exonic splicing enhancers and exonic splicing silencers diverge especially fast shortly after gene duplication. About 10% and 5% of paralogous exons undergo significantly asymmetric evolution of exonic splicing enhancers and silencers, respectively. When compared to pre-duplication ancestors, we found that there is a significant overall loss of exonic splicing enhancers and the magnitude increases with duplication age. Detailed examination reveals net gains and losses of exonic splicing enhancers and silencers in different copies and paralog clusters after gene duplication. Furthermore, we found that exonic splicing enhancer and silencer changes are mainly caused by synonymous mutations, though nonsynonymous changes also contribute. Finally, we found that exonic splicing enhancer and silencer divergence results in exon splicing state transitions (from constitutive to alternative or vice versa), and that the proportion of paralogous exon pairs with different splicing states also increases over time, consistent with previous predictions. Conclusions Our results suggest that exonic splicing enhancer and silencer changes after gene duplication have important roles in alternative splicing divergence and that these changes contribute to the generation of new gene structures.
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Affiliation(s)
- Zhenguo Zhang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) and Shanghai Jiao Tong University School of Medicine (SJTUSM), 225 South Chong Qing Road, Shanghai 200025, PR China.
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Vorechovsky I. Transposable elements in disease-associated cryptic exons. Hum Genet 2009; 127:135-54. [PMID: 19823873 DOI: 10.1007/s00439-009-0752-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/27/2009] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon-intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.
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Affiliation(s)
- Igor Vorechovsky
- Division of Human Genetics, University of Southampton School of Medicine, MP808, Tremona Road, Southampton SO16 6YD, UK.
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35
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Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, Ast G. Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol 2009; 5:e1000300. [PMID: 19266014 PMCID: PMC2639721 DOI: 10.1371/journal.pcbi.1000300] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 01/23/2009] [Indexed: 12/12/2022] Open
Abstract
Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this study, we analyzed Alu exonization events, aiming to understand the requirements for correct selection of exons. Comparison of exonizing Alus to their non-exonizing counterparts is informative because Alus in these two groups have retained high sequence similarity but are perceived differently by the splicing machinery. We identified and characterized numerous features used by the splicing machinery to discriminate between Alu exons and their non-exonizing counterparts. Of these, the most novel is secondary structure: Alu exons in general and their 5′ splice sites (5′ss) in particular are characterized by decreased stability of local secondary structures with respect to their non-exonizing counterparts. We detected numerous further differences between Alu exons and their non-exonizing counterparts, among others in terms of exon–intron architecture and strength of splicing signals, enhancers, and silencers. Support vector machine analysis revealed that these features allow a high level of discrimination (AUC = 0.91) between exonizing and non-exonizing Alus. Moreover, the computationally derived probabilities of exonization significantly correlated with the biological inclusion level of the Alu exons, and the model could also be extended to general datasets of constitutive and alternative exons. This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing. A typical human gene consists of 9 exons around 150 nucleotides in length, separated by introns that are ∼3,000 nucleotides long. The challenge of the splicing machinery is to precisely identify and ligate the exons, while removing the introns. We aimed to understand how the splicing machinery meets this momentous challenge, based on Alu exonization events. Alus are transposable elements, of which approximately one million copies exist in the human genome, a large portion of which within introns. Throughout evolution, some intronic Alus accumulated mutations and became recognized by the splicing machinery as exons, a process termed exonization. Such Alus remain highly similar to their non-exonizing counterparts but are perceived as different by the splicing machinery. By comparing exonizing Alus to their non-exonizing counterparts, we were able to identify numerous features in which they differ and which presumably lead to the recognition only of the former by the splicing machinery. Our findings reveal insights regarding the role of local RNA secondary structures, exon–intron architecture constraints, and splicing regulatory signals. We integrated these features in a computational model, which was able to successfully mimic the function of the splicing machinery and discriminate between true Alu exons and their intronic counterparts, highlighting the functional importance of these features.
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Affiliation(s)
- Schraga Schwartz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
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Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM. Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol 2008; 26:603-12. [PMID: 19064677 DOI: 10.1093/molbev/msn281] [Citation(s) in RCA: 182] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genomes contain a large number of genes that do not have recognizable homologues in other species and that are likely to be involved in important species-specific adaptive processes. The origin of many such "orphan" genes remains unknown. Here we present the first systematic study of the characteristics and mechanisms of formation of primate-specific orphan genes. We determine that codon usage values for most orphan genes fall within the bulk of the codon usage distribution of bona fide human proteins, supporting their current protein-coding annotation. We also show that primate orphan genes display distinctive features in relation to genes of wider phylogenetic distribution: higher tissue specificity, more rapid evolution, and shorter peptide size. We estimate that around 24% are highly divergent members of mammalian protein families. Interestingly, around 53% of the orphan genes contain sequences derived from transposable elements (TEs) and are mostly located in primate-specific genomic regions. This indicates frequent recruitment of TEs as part of novel genes. Finally, we also obtain evidence that a small fraction of primate orphan genes, around 5.5%, might have originated de novo from mammalian noncoding genomic regions.
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Affiliation(s)
- Macarena Toll-Riera
- Evolutionary Genomics Group, Biomedical Informatics Research Programme, Fundació Institut Municipal d'Investigació Mèdica, Barcelona, Spain
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