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Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
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Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
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2
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Rotival M, Quach H, Quintana-Murci L. Defining the genetic and evolutionary architecture of alternative splicing in response to infection. Nat Commun 2019; 10:1671. [PMID: 30975994 PMCID: PMC6459842 DOI: 10.1038/s41467-019-09689-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 03/21/2019] [Indexed: 12/17/2022] Open
Abstract
Host and environmental factors contribute to variation in human immune responses, yet the genetic and evolutionary drivers of alternative splicing in response to infection remain largely uncharacterised. Leveraging 970 RNA-sequencing profiles of resting and stimulated monocytes from 200 individuals of African- and European-descent, we show that immune activation elicits a marked remodelling of the isoform repertoire, while increasing the levels of erroneous splicing. We identify 1,464 loci associated with variation in isoform usage (sQTLs), 9% of them being stimulation-specific, which are enriched in disease-related loci. Furthermore, we detect a longstanding increased plasticity of immune gene splicing, and show that positive selection and Neanderthal introgression have both contributed to diversify the splicing landscape of human populations. Together, these findings suggest that differential isoform usage has been an important substrate of innovation in the long-term evolution of immune responses and a more recent vehicle of population local adaptation. Genetic ancestry might influence immunological response to infection at different regulatory levels. Here, the authors use RNA-Seq to investigate the variability of alternative splicing patterns in resting and stimulated monocytes of African- and European-descent.
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Affiliation(s)
- Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, CNRS UMR2000, 25-28 rue Dr Roux, Paris, 75015, France.
| | - Hélène Quach
- Human Evolutionary Genetics Unit, Institut Pasteur, CNRS UMR2000, 25-28 rue Dr Roux, Paris, 75015, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, CNRS UMR2000, 25-28 rue Dr Roux, Paris, 75015, France.
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3
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Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0474. [PMID: 27994117 DOI: 10.1098/rstb.2015.0474] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Stephen J Bush
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Lu Chen
- West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, People's Republic of China
| | | | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK .,Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
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4
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Zhang XH, Lian XD, Dai ZX, Zheng HY, Chen X, Zheng YT. α3-Deletion Isoform of HLA-A11 Modulates Cytotoxicity of NK Cells: Correlations with HIV-1 Infection of Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:2030-2042. [PMID: 28784847 DOI: 10.4049/jimmunol.1602183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/14/2017] [Indexed: 01/16/2023]
Abstract
Alternative splicing occurs frequently in many genes, especially those involved in immunity. Unfortunately, the functions of many alternatively spliced molecules from immunologically relevant genes remain unknown. Classical HLA-I molecules are expressed on almost all nucleated cells and play a pivotal role in both innate and adaptive immunity. Although splice variants of HLA-I genes have been reported, the details of their functions have not been reported. In the current study, we determined the characteristics, expression, and function of a novel splice variant of HLA-A11 named HLA-A11svE4 HLA-A11svE4 is located on the cell surface without β2-microglobulin (β2m). Additionally, HLA-A11svE4 forms homodimers as well as heterodimers with HLA-A open conformers, instead of combining with β2m. Moreover, HLA-A11svE4 inhibits the activation of NK cells to protect target cells. Compared with β2m and HLA-A11, the heterodimer of HLA-A11svE4 and HLA-A11 protected target cells from lysis by NK cells more effectively. Furthermore, HLA-AsvE4 expression was upregulated by HIV-1 in vivo and by HSV, CMV, and hepatitis B virus in vitro. In addition, our findings indicated that HLA-A11svE4 molecules were functional in activating CD8+ T cells through Ag presentation. Taken together, these results suggested that HLA-A11svE4 can homodimerize and form a novel heterodimeric complex with HLA-A11 open conformers. Furthermore, the data are consistent with HLA-A11svE4 playing a role in the immune escape of HIV-1.
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Affiliation(s)
- Xi-He Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; and
| | - Xiao-Dong Lian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; and
| | - Zheng-Xi Dai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; and
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
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5
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Skandalis A. Estimation of the minimum mRNA splicing error rate in vertebrates. Mutat Res 2016; 784-785:34-8. [PMID: 26811995 DOI: 10.1016/j.mrfmmm.2016.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 01/06/2016] [Accepted: 01/10/2016] [Indexed: 10/22/2022]
Abstract
The majority of protein coding genes in vertebrates contain several introns that are removed by the mRNA splicing machinery. Errors during splicing can generate aberrant transcripts and degrade the transmission of genetic information thus contributing to genomic instability and disease. However, estimating the error rate of constitutive splicing is complicated by the process of alternative splicing which can generate multiple alternative transcripts per locus and is particularly active in humans. In order to estimate the error frequency of constitutive mRNA splicing and avoid bias by alternative splicing we have characterized the frequency of splice variants at three loci, HPRT, POLB, and TRPV1 in multiple tissues of six vertebrate species. Our analysis revealed that the frequency of splice variants varied widely among loci, tissues, and species. However, the lowest observed frequency is quite constant among loci and approximately 0.1% aberrant transcripts per intron. Arguably this reflects the "irreducible" error rate of splicing, which consists primarily of the combination of replication errors by RNA polymerase II in splice consensus sequences and spliceosome errors in correctly pairing exons.
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Affiliation(s)
- A Skandalis
- Brock University, St. Catharines, Ontario, Canada.
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Thompson B, Martins A, Spurdle A. A review of mismatch repair gene transcripts: issues for interpretation of mRNA splicing assays. Clin Genet 2014; 87:100-8. [DOI: 10.1111/cge.12450] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/17/2014] [Accepted: 06/24/2014] [Indexed: 12/21/2022]
Affiliation(s)
- B.A. Thompson
- Department of Genetics and Computational Biology; QIMR Berghofer Medical Research Institute; Brisbane Australia
- School of Medicine; University of Queensland; Brisbane Australia
| | - A. Martins
- Inserm U1079; University of Rouen, Institute for Research and Innovation in Biomedicine; Rouen France
| | - A.B. Spurdle
- Department of Genetics and Computational Biology; QIMR Berghofer Medical Research Institute; Brisbane Australia
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7
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Wu X, Gaffney B, Hunt AG, Li QQ. Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics 2014; 15:615. [PMID: 25048171 PMCID: PMC4117952 DOI: 10.1186/1471-2164-15-615] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/15/2014] [Indexed: 11/16/2022] Open
Abstract
Background Alternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression. Little is known about how APA sites may evolve in homologous genes in different plant species. To this end, comparative studies of APA sites in different organisms are needed. In this study, a collection of poly(A) sites in Medicago truncatula, a model system for legume plants, has been generated and compared with APA sites in Arabidopsis thaliana. Results The poly(A) tags from a deep-sequencing protocol were mapped to the annotated M. truncatula genome, and the identified poly(A) sites used to update the annotations of 14,203 genes. The results show that 64% of M. truncatula genes possess more than one poly(A) site, comparable to the percentages reported for Arabidopsis and rice. In addition, the poly(A) signals associated with M. truncatula genes were similar to those seen in Arabidopsis and other plants. The 3′-UTR lengths are correlated in pairs of orthologous genes between M. truncatula and Arabidopsis. Very little conservation of intronic poly(A) sites was found between Arabidopsis and M. truncatula, which suggests that such sites are likely to be species-specific in plants. In contrast, there is a greater conservation of CDS-localized poly(A) sites in these two species. A sizeable number of M. truncatula antisense poly(A) sites were found. A high percentage of the associated target genes possess Arabidopsis orthologs that are also associated with antisense sites. This is suggestive of important roles for antisense regulation of these target genes. Conclusions Our results reveal some distinct patterns of sense and antisense poly(A) sites in Arabidopsis and M. truncatula. In so doing, this study lends insight into general evolutionary trends of alternative polyadenylation in plants. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-615) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA.
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8
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Colombo M, Blok MJ, Whiley P, Santamariña M, Gutiérrez-Enríquez S, Romero A, Garre P, Becker A, Smith LD, De Vecchi G, Brandão RD, Tserpelis D, Brown M, Blanco A, Bonache S, Menéndez M, Houdayer C, Foglia C, Fackenthal JD, Baralle D, Wappenschmidt B, Díaz-Rubio E, Caldés T, Walker L, Díez O, Vega A, Spurdle AB, Radice P, De La Hoya M. Comprehensive annotation of splice junctions supports pervasive alternative splicing at the BRCA1 locus: a report from the ENIGMA consortium. Hum Mol Genet 2014; 23:3666-80. [DOI: 10.1093/hmg/ddu075] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Mara Colombo
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands,
| | - Phillip Whiley
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia,
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia,
| | - Marta Santamariña
- Grupo de Medicina Xenómica-USC, Universidad de Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain,
| | | | - Atocha Romero
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
| | - Pilar Garre
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
| | - Alexandra Becker
- Center of Familial Breast and Ovarian Cancer, University Hospital Cologne, Cologne, Germany,
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,
| | - Lindsay Denise Smith
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK,
| | - Giovanna De Vecchi
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - Rita D. Brandão
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands,
| | - Demis Tserpelis
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands,
| | - Melissa Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia,
| | - Ana Blanco
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain,
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and
- Oncogenetics Group, Vall d'Hebron Research Institute (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain,
| | - Mireia Menéndez
- Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d'Oncologia, Barcelona, Spain,
| | - Claude Houdayer
- Service de Génétique and INSERM U830, Institut Curie and Université Paris Descartes, Sorbonne Paris Cité, Paris, France,
| | - Claudia Foglia
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - James D. Fackenthal
- Department of Medicine, The University of Chicago Medical Center, Chicago, IL, USA,
| | - Diana Baralle
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK,
| | - Barbara Wappenschmidt
- Center of Familial Breast and Ovarian Cancer, University Hospital Cologne, Cologne, Germany,
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,
| | - Eduardo Díaz-Rubio
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
- Servicio de Oncología Médica, Hospital Clínico San Carlos, Madrid, Spain,
| | - Trinidad Caldés
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
| | - Logan Walker
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and
- Oncogenetics Group, Vall d'Hebron Research Institute (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain,
- Oncogenetics Group, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain,
| | - Amanda B. Spurdle
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia,
| | - Paolo Radice
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - Miguel De La Hoya
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
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Spinelli R, Pirola A, Redaelli S, Sharma N, Raman H, Valletta S, Magistroni V, Piazza R, Gambacorti-Passerini C. Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases. Mol Genet Genomic Med 2013; 1:246-59. [PMID: 24498620 PMCID: PMC3865592 DOI: 10.1002/mgg3.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 12/13/2022] Open
Abstract
Point mutations in intronic regions near mRNA splice junctions can affect the splicing process. To identify novel splicing variants from exome sequencing data, we developed a bioinformatics splice-site prediction procedure to analyze next-generation sequencing (NGS) data (SpliceFinder). SpliceFinder integrates two functional annotation tools for NGS, ANNOVAR and MutationTaster and two canonical splice site prediction programs for single mutation analysis, SSPNN and NetGene2. By SpliceFinder, we identified somatic mutations affecting RNA splicing in a colon cancer sample, in eight atypical chronic myeloid leukemia (aCML), and eight CML patients. A novel homozygous splicing mutation was found in APC (NM_000038.4:c.1312+5G>A) and six heterozygous in GNAQ (NM_002072.2:c.735+1C>T), ABCC3 (NM_003786.3:c.1783-1G>A), KLHDC1 (NM_172193.1:c.568-2A>G), HOOK1 (NM_015888.4:c.1662-1G>A), SMAD9 (NM_001127217.2:c.1004-1C>T), and DNAH9 (NM_001372.3:c.10242+5G>A). Integrating whole-exome and RNA sequencing in aCML and CML, we assessed the phenotypic effect of mutations on mRNA splicing for GNAQ, ABCC3, HOOK1. In ABCC3 and HOOK1, RNA-Seq showed the presence of aberrant transcripts with activation of a cryptic splice site or intron retention, validated by the reverse transcription-polymerase chain reaction (RT-PCR) in the case of HOOK1. In GNAQ, RNA-Seq showed 22% of wild-type transcript and 78% of mRNA skipping exon 5, resulting in a 4–6 frameshift fusion confirmed by RT-PCR. The pipeline can be useful to identify intronic variants affecting RNA sequence by complementing conventional exome analysis.
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Affiliation(s)
- Roberta Spinelli
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Alessandra Pirola
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Sara Redaelli
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Nitesh Sharma
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Hima Raman
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Simona Valletta
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Vera Magistroni
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Rocco Piazza
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Carlo Gambacorti-Passerini
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy ; Hematology and Clinical Research Unit, San Gerardo Hospital Monza, Italy
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10
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Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol 2013; 14:R70. [PMID: 23815980 PMCID: PMC4053754 DOI: 10.1186/gb-2013-14-7-r70] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 07/01/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering the relative abundances of different transcripts from the same gene. RESULTS Here we show that, in a given condition, most protein coding genes have one major transcript expressed at significantly higher level than others, that in human tissues the major transcripts contribute almost 85 percent to the total mRNA from protein coding loci, and that often the same major transcript is expressed in many tissues. We detect a high degree of overlap between the set of major transcripts and a recently published set of alternatively spliced transcripts that are predicted to be translated utilizing proteomic data. Thus, we hypothesize that although some minor transcripts may play a functional role, the major ones are likely to be the main contributors to the proteome. However, we still detect a non-negligible fraction of protein coding genes for which the major transcript does not code a protein. CONCLUSIONS Overall, our findings suggest that the transcriptome from protein coding loci is dominated by one transcript per gene and that not all the transcripts that contribute to transcriptome diversity are equally likely to contribute to protein diversity. This observation can help to prioritize candidate targets in proteomics research and to predict the functional impact of the detected changes in variation studies.
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11
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Abstract
PURPOSE OF REVIEW With the advent of whole-transcriptome sequencing, or RNA-seq, we now know that alternative splicing is a generalized phenomenon, with nearly all multiexonic genes subject to alternative splicing. In this review, we highlight recent studies examining alternative splicing as a modulator of cellular cholesterol homeostasis and as an underlying mechanism of dyslipidemia. RECENT FINDINGS A number of key genes involved in cholesterol metabolism are known to undergo functionally relevant alternative splicing. Recently, we have identified coordinated changes in alternative splicing in multiple genes in response to alterations in cellular sterol content. We and others have implicated several splicing factors as regulators of lipid metabolism. Furthermore, a number of cis-acting human gene variants that modulate alternative splicing have been implicated in a variety of human metabolic diseases. SUMMARY Alternative splicing is of importance in various types of genetically influenced dyslipidemias and in the regulation of cellular cholesterol metabolism.
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Affiliation(s)
- Marisa W Medina
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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12
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Hon CC, Weber C, Sismeiro O, Proux C, Koutero M, Deloger M, Das S, Agrahari M, Dillies MA, Jagla B, Coppee JY, Bhattacharya A, Guillen N. Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica. Nucleic Acids Res 2012; 41:1936-52. [PMID: 23258700 PMCID: PMC3561952 DOI: 10.1093/nar/gks1271] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alternative usage of splicing and polyadenylation sites in Entamoeba histolytica using RNA-Seq. First, we identified a large number of rarely spliced alternative junctions and then showed that the occurrence of these alternative splicing events is correlated with splicing site sequence, occurrence of constitutive splicing events and messenger RNA abundance. Our results implied the majority of these alternative splicing events are likely to be stochastic error of splicing machineries, and we estimated the corresponding error rates. Second, we observed extensive microheterogeneity of polyadenylation cleavage sites, and the extent of such microheterogeneity is correlated with the occurrence of constitutive cleavage events, suggesting most of such microheterogeneity is likely to be stochastic. Overall, we only observed a small fraction of alternative splicing and polyadenylation isoforms that are unlikely to be solely stochastic, implying the functional relevance of alternative splicing and polyadenylation in E. histolytica is limited. Lastly, we revised the gene models and annotated their 3′UTR in AmoebaDB, providing valuable resources to the community.
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Affiliation(s)
- Chung-Chau Hon
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie cellulaire et infection, F-75015 Paris, France, INSERM U786, F-75015 Paris, France.
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13
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Rhein C, Tripal P, Seebahn A, Konrad A, Kramer M, Nagel C, Kemper J, Bode J, Mühle C, Gulbins E, Reichel M, Becker CM, Kornhuber J. Functional implications of novel human acid sphingomyelinase splice variants. PLoS One 2012; 7:e35467. [PMID: 22558155 PMCID: PMC3338701 DOI: 10.1371/journal.pone.0035467] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 03/16/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acid sphingomyelinase (ASM) hydrolyses sphingomyelin and generates the lipid messenger ceramide, which mediates a variety of stress-related cellular processes. The pathological effects of dysregulated ASM activity are evident in several human diseases and indicate an important functional role for ASM regulation. We investigated alternative splicing as a possible mechanism for regulating cellular ASM activity. METHODOLOGY/PRINCIPAL FINDINGS We identified three novel ASM splice variants in human cells, termed ASM-5, -6 and -7, which lack portions of the catalytic- and/or carboxy-terminal domains in comparison to full-length ASM-1. Differential expression patterns in primary blood cells indicated that ASM splicing might be subject to regulatory processes. The newly identified ASM splice variants were catalytically inactive in biochemical in vitro assays, but they decreased the relative cellular ceramide content in overexpression studies and exerted a dominant-negative effect on ASM activity in physiological cell models. CONCLUSIONS/SIGNIFICANCE These findings indicate that alternative splicing of ASM is of functional significance for the cellular stress response, possibly representing a mechanism for maintaining constant levels of cellular ASM enzyme activity.
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Affiliation(s)
- Cosima Rhein
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Philipp Tripal
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Angela Seebahn
- Institute of Biochemistry, Emil-Fischer-Centre, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Alice Konrad
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Marcel Kramer
- Leibniz Institute for Age Research – Fritz Lipmann Institute and Center for Sepsis Control and Care at Jena University Hospital, Jena, Germany
| | - Christine Nagel
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Jonas Kemper
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Jens Bode
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Christiane Mühle
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Erich Gulbins
- Department of Molecular Biology, University of Duisburg-Essen, Essen, Germany
| | - Martin Reichel
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Cord-Michael Becker
- Institute of Biochemistry, Emil-Fischer-Centre, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University Hospital, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
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14
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Frankish A, Mudge JM, Thomas M, Harrow J. The importance of identifying alternative splicing in vertebrate genome annotation. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2012; 2012:bas014. [PMID: 22434846 PMCID: PMC3308168 DOI: 10.1093/database/bas014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
While alternative splicing (AS) can potentially expand the functional repertoire of vertebrate genomes, relatively few AS transcripts have been experimentally characterized. We describe our detailed manual annotation of vertebrate genomes, which is generating a publicly available geneset rich in AS. In order to achieve this we have adopted a highly sensitive approach to annotating gene models supported by correctly mapped, canonically spliced transcriptional evidence combined with a highly cautious approach to adding unsupported extensions to models and making decisions on their functional potential. We use information about the predicted functional potential and structural properties of every AS transcript annotated at a protein-coding or non-coding locus to place them into one of eleven subclasses. We describe the incorporation of new sequencing and proteomics technologies into our annotation pipelines, which are used to identify and validate AS. Combining all data sources has led to the production of a rich geneset containing an average of 6.3 AS transcripts for every human multi-exon protein-coding gene. The datasets produced have proved very useful in providing context to studies investigating the functional potential of genes and the effect of variation may have on gene structure and function. Database URL:http://www.ensembl.org/index.html, http://vega.sanger.ac.uk/index.html
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Affiliation(s)
- Adam Frankish
- Human and Vertebrate Analysis and Annotation Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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15
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Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J. The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol 2011; 28:2949-59. [PMID: 21551269 PMCID: PMC3176834 DOI: 10.1093/molbev/msr127] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution.
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Affiliation(s)
- Jonathan M Mudge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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16
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Cheong CY, Lufkin T. Alternative splicing in self-renewal of embryonic stem cells. Stem Cells Int 2011; 2011:560261. [PMID: 21776282 PMCID: PMC3137993 DOI: 10.4061/2011/560261] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/07/2011] [Indexed: 12/31/2022] Open
Abstract
Much of embryonic stem cell biology has focused on transcriptional expression and regulation of genes that could mediate its unique potential in self-renewal or pluripotency. In alignment with our present understanding on the genetic, protein, and epigenetic factors that may direct cell fate, we present a short overview of the often overlooked contribution of alternative splice variants to regulatory diversity. Progressing beyond the limitations of a fixed genomic sequence, alternative splicing offers an additional layer of complexity to produce protein variants that may differ in function and localization that can direct embryonic stem cells to specific differentiation pathways. In light of the number of variants that can be produced at key ES cell genes alone, it is challenging to consider how much more multifaceted transcriptional regulation truly is, and if this can be captured more fully in future works.
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Affiliation(s)
- Clara Y Cheong
- Stem Cell & Developmental Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
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17
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Constant splice-isoform ratios in human lymphoblastoid cells support the concept of a splico-stat. Genetics 2011; 187:761-70. [PMID: 21220357 DOI: 10.1534/genetics.110.125096] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Splicing generates mature transcripts from genes in pieces in eukaryotic cells. Overwhelming evidence has accumulated that alternative routes in splicing are possible for most human and mammalian genes, thereby allowing formation of different transcripts from one gene. No function has been assigned to the majority of identified alternative splice forms, and it has been assumed that they compose inert or tolerated waste from aberrant or noisy splicing. Here we demonstrate that five human transcription units (WT1, NOD2, GNAS, RABL2A, RABL2B) have constant splice-isoform ratios in genetically diverse lymphoblastoid cell lines independent of the type of alternative splicing (exon skipping, alternative donor/acceptor, tandem splice sites) and gene expression level. Even splice events that create premature stop codons and potentially trigger nonsense-mediated mRNA decay are found at constant fractions. The analyzed alternative splicing events were qualitatively but not quantitatively conserved in corresponding chimpanzee cell lines. Additionally, subtle splicing at tandem acceptor splice sites (GNAS, RABL2A/B) was highly constrained and strongly depends on the upstream donor sequence content. These results also demonstrate that unusual and unproductive splice variants are produced in a regulated manner.
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18
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Hanna CB, Yao S, Patta MC, Jensen JT, Wu X. Expression of insulin-like 3 (INSL3) and differential splicing of its receptor in the ovary of rhesus macaques. Reprod Biol Endocrinol 2010; 8:150. [PMID: 21138583 PMCID: PMC3008693 DOI: 10.1186/1477-7827-8-150] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/07/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although insulin-like 3 (INSL3) has been identified in the gonad of both sexes in many species, there are only limited reports on the distribution of INSL3 and its receptor, relaxin/insulin-like family peptide receptor 2 (RXFP2), in the primate ovary. Since the hormone-receptor pair is believed to play a role in female reproduction, investigating the transcription of INSL3/RXFP2 genes and the spatiotemporal expression of INSL3 in the nonhuman primate may shed light on the functional aspects of the system in humans. METHODS Database mining, molecular and immunological methods were applied. RESULTS One single INSL3 transcript and three novel splice variant transcripts of RXFP2 were identified in the ovary of rhesus macaques. While the full-length RXFP2 transcript is barely detectable in granulosa cells during the periovulatory period, INSL3 transcript and protein are highly abundant in theca cells surrounding antral follicles. Moreover, the INSL3 level in follicular fluid is 3-4 times higher than that in female serum which remains low throughout the menstrual cycle. CONCLUSIONS The presence of INSL3 and its receptor in the ovary implies a potential role of the ligand-receptor pair in female reproduction in nonhuman primates. However, the existence of multiple splice variants of RXFP2 indicates a very complex nature of the hormone-receptor system.
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Affiliation(s)
- Carol B Hanna
- Division of Reproductive Sciences, Oregon National Primate Research Center, Oregon Health & Science University, West Campus, Beaverton, OR 97006, USA
| | - Shan Yao
- Division of Reproductive Sciences, Oregon National Primate Research Center, Oregon Health & Science University, West Campus, Beaverton, OR 97006, USA
| | - Maristela C Patta
- Division of Reproductive Sciences, Oregon National Primate Research Center, Oregon Health & Science University, West Campus, Beaverton, OR 97006, USA
| | - Jeffrey T Jensen
- Division of Reproductive Sciences, Oregon National Primate Research Center, Oregon Health & Science University, West Campus, Beaverton, OR 97006, USA
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xuemei Wu
- Division of Reproductive Sciences, Oregon National Primate Research Center, Oregon Health & Science University, West Campus, Beaverton, OR 97006, USA
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