1
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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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2
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Ptok J, Müller L, Theiss S, Schaal H. Context matters: Regulation of splice donor usage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194391. [PMID: 31202784 DOI: 10.1016/j.bbagrm.2019.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 11/16/2022]
Abstract
Elaborate research on splicing, starting in the late seventies, evolved from the discovery that 5' splice sites are recognized by their complementarity to U1 snRNA towards the realization that RNA duplex formation cannot be the sole basis for 5'ss selection. Rather, their recognition is highly influenced by a number of context factors including transcript architecture as well as splicing regulatory elements (SREs) in the splice site neighborhood. In particular, proximal binding of splicing regulatory proteins highly influences splicing outcome. The importance of SRE integrity especially becomes evident in the light of human pathogenic mutations where single nucleotide changes in SREs can severely affect the resulting transcripts. Bioinformatics tools nowadays greatly assist in the computational evaluation of 5'ss, their neighborhood and the impact of pathogenic mutations. Although predictions are already quite robust, computational evaluation of the splicing regulatory landscape still faces challenges to increase future reliability. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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3
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Marshall CM, Tartaglio V, Duarte M, Harmon FG. The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing. THE PLANT CELL 2016; 28:2560-2575. [PMID: 27624757 PMCID: PMC5134976 DOI: 10.1105/tpc.16.00223] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/29/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
The circadian clock allows plants to anticipate and respond to daily changes in ambient temperature. Mechanisms establishing the timing of circadian rhythms in Arabidopsis thaliana through temperature entrainment remain unclear. Also incompletely understood is the temperature compensation mechanism that maintains consistent period length within a range of ambient temperatures. A genetic screen for Arabidopsis mutants affecting temperature regulation of the PSEUDO-RESPONSE REGULATOR7 promoter yielded a novel allele of the SICKLE (SIC) gene. This mutant, sic-3, and the existing sic-1 mutant both exhibit low-amplitude or arrhythmic expression of core circadian clock genes under cool ambient temperature cycles, but not under light-dark entrainment. sic mutants also lengthen free running period in a manner consistent with impaired temperature compensation. sic mutant alleles accumulate LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) splice variants, among other alternatively spliced transcripts, which is exacerbated by cool temperatures. The cca1-1 lhy-20 double mutant is epistatic to sic-3, indicating the LHY and CCA1 splice variants are needed for sic-3 circadian clock phenotypes. It is not expected that SIC is directly involved in the circadian clock mechanism; instead, SIC likely contributes to pre-mRNA metabolism, and the splice variants that accumulate in sic mutants likely affect the circadian clock response to cool ambient temperature.
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Affiliation(s)
- Carine M Marshall
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Virginia Tartaglio
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Maritza Duarte
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Frank G Harmon
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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4
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Lin L, Park JW, Ramachandran S, Zhang Y, Tseng YT, Shen S, Waldvogel HJ, Curtis MA, Faull RLM, Troncoso JC, Pletnikova O, Ross CA, Davidson BL, Xing Y. Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease. Hum Mol Genet 2016; 25:3454-3466. [PMID: 27378699 DOI: 10.1093/hmg/ddw187] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/11/2016] [Accepted: 06/14/2016] [Indexed: 12/25/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansion in the gene-encoding Huntingtin (HTT). Transcriptome dysregulation is a major feature of HD pathogenesis, as revealed by a large body of work on gene expression profiling of tissues from human HD patients and mouse models. These studies were primarily focused on transcriptional changes affecting steady-state overall gene expression levels using microarray based approaches. A major missing component, however, has been the study of transcriptome changes at the post-transcriptional level, such as alternative splicing. Alternative splicing is a critical mechanism for expanding regulatory and functional diversity from a limited number of genes, and is particularly complex in the mammalian brain. Here we carried out a deep RNA-seq analysis of the BA4 (Brodmann area 4) motor cortex from seven human HD brains and seven controls to systematically discover aberrant alternative splicing events and characterize potential associated splicing factors in HD. We identified 593 differential alternative splicing events between HD and control brains. Using two expanded panels with a total of 108 BA4 tissues from patients and controls, we identified four splicing factors exhibiting significantly altered expression levels in HD patient brains. Moreover, follow-up molecular analyses of one splicing factor PTBP1 revealed its impact on disease-associated splicing patterns in HD. Collectively, our data provide genomic evidence for widespread splicing dysregulation in HD brains, and suggest the role of aberrant alternative splicing in the pathogenesis of HD.
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Affiliation(s)
- Lan Lin
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Shyam Ramachandran
- The Raymond G Perelman Center for Cellular and Molecular Therapy, The Children's Hospital of Philadelphia, PA, USA
| | - Yida Zhang
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Yu-Ting Tseng
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Shihao Shen
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Henry J Waldvogel
- Department of Anatomy and Medical Imaging and Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Maurice A Curtis
- Department of Anatomy and Medical Imaging and Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging and Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christopher A Ross
- Division of Neurobiology; Departments of Psychiatry, Neurology Neuroscience, and Pharmacology; and Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Beverly L Davidson
- The Raymond G Perelman Center for Cellular and Molecular Therapy, The Children's Hospital of Philadelphia, PA, USA .,The Department of Pathology & Laboratory Medicine, The University of Pennsylvania, PA 19104, USA
| | - Yi Xing
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
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5
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Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Res 2015; 43:10612-22. [PMID: 26578562 PMCID: PMC4678817 DOI: 10.1093/nar/gkv1099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/09/2015] [Indexed: 01/27/2023] Open
Abstract
RNA-seq has become a popular technology for studying genetic variation of pre-mRNA alternative splicing. Commonly used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across splice junctions. Consequently, genomic variants that create novel splice site dinucleotides may produce splice junction RNA-seq reads that cannot be mapped to the reference genome. We developed and evaluated an approach to identify ‘hidden’ splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Computational analysis and experimental validation indicate that this approach identifies personal specific splice junctions at a low false positive rate. Applying this approach to an RNA-seq data set of 75 individuals, we identified 506 personal specific splice junctions, among which 437 were novel splice junctions not documented in current human transcript annotations. 94 splice junctions had splice site SNPs associated with GWAS signals of human traits and diseases. These involve genes whose splicing variations have been implicated in diseases (such as OAS1), as well as novel associations between alternative splicing and diseases (such as ICA1). Collectively, our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.
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Affiliation(s)
- Shayna Stein
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhi-Xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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6
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Wu X, Hurst LD. Determinants of the Usage of Splice-Associated cis-Motifs Predict the Distribution of Human Pathogenic SNPs. Mol Biol Evol 2015; 33:518-29. [PMID: 26545919 PMCID: PMC4866546 DOI: 10.1093/molbev/msv251] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 10/25/2015] [Indexed: 12/11/2022] Open
Abstract
Where in genes do pathogenic mutations tend to occur and does this provide clues as to the possible underlying mechanisms by which single nucleotide polymorphisms (SNPs) cause disease? As splice-disrupting mutations tend to occur predominantly at exon ends, known also to be hot spots of cis-exonic splice control elements, we examine the relationship between the relative density of such exonic cis-motifs and pathogenic SNPs. In particular, we focus on the intragene distribution of exonic splicing enhancers (ESE) and the covariance between them and disease-associated SNPs. In addition to showing that disease-causing genes tend to be genes with a high intron density, consistent with missplicing, five factors established as trends in ESE usage, are considered: relative position in exons, relative position in genes, flanking intron size, splice sites usage, and phase. We find that more than 76% of pathogenic SNPs are within 3–69 bp of exon ends where ESEs generally reside, this being 13% more than expected. Overall from enrichment of pathogenic SNPs at exon ends, we estimate that approximately 20–45% of SNPs affect splicing. Importantly, we find that within genes pathogenic SNPs tend to occur in splicing-relevant regions with low ESE density: they are found to occur preferentially in the terminal half of genes, in exons flanked by short introns and at the ends of phase (0,0) exons with 3′ non-“AGgt” splice site. We suggest the concept of the “fragile” exon, one home to pathogenic SNPs owing to its vulnerability to splice disruption owing to low ESE density.
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Affiliation(s)
- XianMing Wu
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
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7
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Single-Nucleotide Polymorphisms and Haplotypes of Intercellular Adhesion Molecule-1 in Uterine Cervical Carcinogenesis in Taiwanese Women. Reprod Sci 2015; 23:401-8. [DOI: 10.1177/1933719115604731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Perriaud L, Marcel V, Sagne C, Favaudon V, Guédin A, De Rache A, Guetta C, Hamon F, Teulade-Fichou MP, Hainaut P, Mergny JL, Hall J. Impact of G-quadruplex structures and intronic polymorphisms rs17878362 and rs1642785 on basal and ionizing radiation-induced expression of alternative p53 transcripts. Carcinogenesis 2014; 35:2706-15. [PMID: 25269805 DOI: 10.1093/carcin/bgu206] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex (G4) structures in intron 3 of the p53 pre-mRNA modulate intron 2 splicing, altering the balance between the fully spliced p53 transcript (FSp53, encoding full-length p53) and an incompletely spliced transcript retaining intron 2 (p53I2 encoding the N-terminally truncated Δ40p53 isoform). The nucleotides forming G4s overlap the polymorphism rs17878362 (A1 wild-type allele, A2 16-base pair insertion) which is in linkage disequilibrium with rs1642785 in intron 2 (c.74+38 G>C). Biophysical and biochemical analyses show rs17878362 A2 alleles form similar G4 structures as A1 alleles although their position is shifted with respect to the intron 2 splice acceptor site. In addition basal FSp53 and p53I2 levels showed allele specific differences in both p53-null cells transfected with reporter constructs or lymphoblastoid cell lines. The highest FSp53 and p53I2 levels were associated with combined rs1642785-GG/rs17878362-A1A1 alleles, whereas the presence of rs1642785-C with either rs17878362 allele was associated with lower p53 pre-mRNA, total TP53, FSp53 and p53I2 levels, due to the lower stability of transcripts containing rs1642785-C. Treatment of lymphoblastoid cell with the G4 binding ligands 360A or PhenDC3 or with ionizing radiation increased FSp53 levels only in cells with rs17878362 A1 alleles, suggesting that under this G4 configuration full splicing is favoured. These results demonstrate the complex effects of intronic TP53 polymorphisms on G4 formation and identify a new role for rs1642785 on mRNA splicing and stability, and thus on the differential expression of isoform-specific transcripts of the TP53 gene.
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Affiliation(s)
- Laury Perriaud
- Institut Curie, Centre de Recherche and Inserm, U612, Bât. 110-112, Centre Universitaire, Orsay F-91405, France
| | - Virginie Marcel
- Institut Curie, Centre de Recherche and Inserm, U612, Bât. 110-112, Centre Universitaire, Orsay F-91405, France
| | - Charlotte Sagne
- Institut Curie, Centre de Recherche and Inserm, U612, Bât. 110-112, Centre Universitaire, Orsay F-91405, France
| | - Vincent Favaudon
- Institut Curie, Centre de Recherche and Inserm, U612, Bât. 110-112, Centre Universitaire, Orsay F-91405, France
| | - Aurore Guédin
- Inserm U869, Institut Européen de Chimie et Biologie, Pessac F-33607, France, Univ. Bordeaux, ARNA Laboratory, Bordeaux F-33000, France
| | - Aurore De Rache
- Inserm U869, Institut Européen de Chimie et Biologie, Pessac F-33607, France, Univ. Bordeaux, ARNA Laboratory, Bordeaux F-33000, France
| | - Corinne Guetta
- Institut Curie, Centre de Recherche and CNRS, UMR176, Bât. 110-112, Centre Universitaire, Orsay F-91405, France
| | - Florian Hamon
- Institut Curie, Centre de Recherche and CNRS, UMR176, Bât. 110-112, Centre Universitaire, Orsay F-91405, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, Centre de Recherche and CNRS, UMR176, Bât. 110-112, Centre Universitaire, Orsay F-91405, France
| | - Pierre Hainaut
- International Prevention Research Institute, University of Strathclyde School of Global Public Health at iPRI, Lyon F-69006, France
| | - Jean-Louis Mergny
- Inserm U869, Institut Européen de Chimie et Biologie, Pessac F-33607, France, Univ. Bordeaux, ARNA Laboratory, Bordeaux F-33000, France
| | - Janet Hall
- Institut Curie, Centre de Recherche and Inserm, U612, Bât. 110-112, Centre Universitaire, Orsay F-91405, France,
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9
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Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y. GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data. Genome Biol 2013; 14:R74. [PMID: 23876401 PMCID: PMC4054007 DOI: 10.1186/gb-2013-14-7-r74] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 06/21/2013] [Accepted: 07/22/2013] [Indexed: 11/10/2022] Open
Abstract
To characterize the genetic variation of alternative splicing, we develop GLiMMPS, a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. GLiMMPS takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data. Analyses of simulated and real RNA-seq datasets demonstrate that GLiMMPS outperforms competing statistical models. Quantitative RT-PCR tests of 26 randomly selected GLiMMPS sQTLs yielded a validation rate of 100%. As population-scale RNA-seq studies become increasingly affordable and popular, GLiMMPS provides a useful tool for elucidating the genetic variation of alternative splicing in humans and model organisms.
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Affiliation(s)
- Keyan Zhao
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
| | - Zhi-xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
| | - Qing Zhou
- Department of Statistics, University of California, Los Angeles, 8125 Math
Sciences Building, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
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10
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Kallel R, Niasme-Grare M, Belguith-Maalej S, Mnif M, Abid M, Ayadi H, Masmoudi S, Jonard L, Hadj Kacem H. Screening of SLC26A4 gene in autoimmune thyroid diseases. Int J Immunogenet 2013; 40:284-91. [PMID: 23280318 DOI: 10.1111/iji.12035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 10/31/2012] [Accepted: 11/19/2012] [Indexed: 12/30/2022]
Abstract
The Pendred syndrome (PS) gene, SLC26A4, was involved in the genetic susceptibility of autoimmune thyroid disease (AITD) in Tunisian population. Recently, functional assays have shown a differential expression of SLC26A4 gene between Graves' disease (GD) and Hashimoto's thyroiditis (HT). Here, by the mean of DHPLC and HRM, we explored the 21 exons and their flanking intronic sequences of 128 patients affected with GD (n = 64) or HT (n = 64). The pathogenic effect of identified variations on splice was investigated using the web server HSF. Eighteen allelic variations were identified and ranged on missense, sens and splice variations. Nine identified variations (c.-66C>G, c.898A>C, c.1002-9A>C, c.1061T>C, c.1544 + 9G>T, c.1545-5T>G, c.1790T>C, c.1826T>G, c.2139T>G) were previously reported in hearing impairment studies. Forty-seven per cent (30/64) of GD patients and 37,5% (24/64) of HT patients present at least one variant in the explored sequences. Moreover, the analysis of the variant distribution between HT (9 (5'UTR), 12 exonic and 13 intronic) and GD (18 (5'UTR), 13 exonic and 5 intronic) patients showed a significant difference (χ² = 6.54, 2df, P = 0.03). Interestingly, missense changes (I300L, p.M283I, F354S and p.L597S) affected conserved residues of pendrin. On the other hand, the HSF analyses ascertain that some variants identified in HT disease are predicted to have a pathogenic effect on splice. In conclusion, our analysis of SLC26A4 sequence variations suggested a distinct genetics basis between HT and GD patients, which should be confirmed on a large cohort.
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Affiliation(s)
- R Kallel
- Laboratoire de Microorganismes et Biomolécules, équipe des Procédés de Criblage Moléculaires et Cellulaires, Center de Biotechnologie de Sfax, Sfax, Tunisie
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11
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Wang E, Aslanzadeh V, Papa F, Zhu H, de la Grange P, Cambi F. Global profiling of alternative splicing events and gene expression regulated by hnRNPH/F. PLoS One 2012; 7:e51266. [PMID: 23284676 PMCID: PMC3524136 DOI: 10.1371/journal.pone.0051266] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
In this study, we have investigated the global impact of heterogeneous nuclear Ribonuclear Protein (hnRNP) H/F-mediated regulation of splicing events and gene expression in oligodendrocytes. We have performed a genome-wide transcriptomic analysis at the gene and exon levels in Oli-neu cells treated with siRNA that targets hnRNPH/F compared to untreated cells using Affymetrix Exon Array. Gene expression levels and regulated exons were identified with the GenoSplice EASANA algorithm. Bioinformatics analyses were performed to determine the structural properties of G tracts that correlate with the function of hnRNPH/F as enhancers vs. repressors of exon inclusion. Different types of alternatively spliced events are regulated by hnRNPH/F. Intronic G tracts density, length and proximity to the 5′ splice site correlate with the hnRNPH/F enhancer function. Additionally, 6% of genes are differently expressed upon knock down of hnRNPH/F. Genes that regulate the transition of oligodendrocyte progenitor cells to oligodendrocytes are differentially expressed in hnRNPH/F depleted Oli-neu cells, resulting in a decrease of negative regulators and an increase of differentiation-inducing regulators. The changes were confirmed in developing oligodendrocytes in vivo. This is the first genome wide analysis of splicing events and gene expression regulated by hnRNPH/F in oligodendrocytes and the first report that hnRNPH/F regulate genes that are involved in the transition from oligodendrocyte progenitor cells to oligodendrocytes.
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Affiliation(s)
- Erming Wang
- Department of Neurology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Vahid Aslanzadeh
- Department of Biotechnology, Research Institute of Physiology and Biotechnology, University of Zanjan, Zanjan, Iran
| | - Filomena Papa
- Department of Neurology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Haiyan Zhu
- Department of Neurology, University of Kentucky, Lexington, Kentucky, United States of America
| | | | - Franca Cambi
- Department of Neurology, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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12
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Akan P, Alexeyenko A, Costea PI, Hedberg L, Solnestam BW, Lundin S, Hällman J, Lundberg E, Uhlén M, Lundeberg J. Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines. Genome Med 2012; 4:86. [PMID: 23158748 PMCID: PMC3580420 DOI: 10.1186/gm387] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 10/25/2012] [Accepted: 11/18/2012] [Indexed: 01/16/2023] Open
Abstract
We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.
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Affiliation(s)
- Pelin Akan
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Andrey Alexeyenko
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Paul Igor Costea
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Lilia Hedberg
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Beata Werne Solnestam
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Sverker Lundin
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Jimmie Hällman
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Emma Lundberg
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Mathias Uhlén
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
| | - Joakim Lundeberg
- KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden
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Zaphiropoulos PG. Genetic variations and alternative splicing: the Glioma associated oncogene 1, GLI1. Front Genet 2012; 3:119. [PMID: 22833753 PMCID: PMC3400943 DOI: 10.3389/fgene.2012.00119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 06/13/2012] [Indexed: 02/01/2023] Open
Abstract
Alternative splicing is a post-transcriptional regulatory process that is attaining stronger recognition as a modulator of gene expression. Alternative splicing occurs when the primary RNA transcript is differentially processed into more than one mature RNAs. This is the result of a variable definition/inclusion of the exons, the sequences that are excised from the primary RNA to form the mature RNAs. Consequently, RNA expression can generate a collection of differentially spliced RNAs, which may distinctly influence subsequent biological events, such as protein synthesis or other biomolecular interactions. Still the mechanisms that control exon definition and exon inclusion are not fully clarified. This mini-review highlights advances in this field as well as the impact of single nucleotide polymorphisms in affecting splicing decisions. The Glioma-associated oncogene 1, GLI1, is taken as an example in addressing the role of nucleotide substitutions for splicing regulation.
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The single nucleotide polymorphism g.1548A >G (K469E) of the ICAM-1 gene is associated with worse prognosis in non-small cell lung cancer. Tumour Biol 2012; 33:1429-36. [DOI: 10.1007/s13277-012-0393-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 03/27/2012] [Indexed: 01/01/2023] Open
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Kim J, Zhao K, Jiang P, Lu ZX, Wang J, Murray JC, Xing Y. Transcriptome landscape of the human placenta. BMC Genomics 2012; 13:115. [PMID: 22448651 PMCID: PMC3368734 DOI: 10.1186/1471-2164-13-115] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 03/27/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The placenta is a key component in understanding the physiological processes involved in pregnancy. Characterizing genes critical for placental function can serve as a basis for identifying mechanisms underlying both normal and pathologic pregnancies. Detailing the placental tissue transcriptome could provide a valuable resource for genomic studies related to placental disease. RESULTS We have conducted a deep RNA sequencing (RNA-Seq) study on three tissue components (amnion, chorion, and decidua) of 5 human placentas from normal term pregnancies. We compared the placental RNA-Seq data to that of 16 other human tissues and observed a wide spectrum of transcriptome differences both between placenta and other human tissues and between distinct compartments of the placenta. Exon-level analysis of the RNA-Seq data revealed a large number of exons with differential splicing activities between placenta and other tissues, and 79% (27 out of 34) of the events selected for RT-PCR test were validated. The master splicing regulator ESRP1 is expressed at a proportionately higher level in amnion compared to all other analyzed human tissues, and there is a significant enrichment of ESRP1-regulated exons with tissue-specific splicing activities in amnion. This suggests an important role of alternative splicing in regulating gene function and activity in specific placental compartments. Importantly, genes with differential expression or splicing in the placenta are significantly enriched for genes implicated in placental abnormalities and preterm birth. In addition, we identified 604-1007 novel transcripts and 494-585 novel exons expressed in each of the three placental compartments. CONCLUSIONS Our data demonstrate unique aspects of gene expression and splicing in placental tissues that provide a basis for disease investigation related to disruption of these mechanisms. These data are publicly available providing the community with a rich resource for placental physiology and disease-related studies.
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Affiliation(s)
- Jinsil Kim
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA52242, USA
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Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 2012; 40:e61. [PMID: 22266656 PMCID: PMC3333886 DOI: 10.1093/nar/gkr1291] [Citation(s) in RCA: 259] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (multivariate analysis of transcript splicing), a Bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P-value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern. We evaluated the performance of MATS using simulated and real RNA-Seq data sets. In the RNA-Seq analysis of alternative splicing events regulated by the epithelial-specific splicing factor ESRP1, we obtained a high RT–PCR validation rate of 86% for differential exon skipping events with a MATS FDR of <10%. Additionally, over the full list of RT–PCR tested exons, the MATS FDR estimates matched well with the experimental validation rate. Our results demonstrate that MATS is an effective and flexible approach for detecting differential alternative splicing from RNA-Seq data.
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Affiliation(s)
- Shihao Shen
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
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Lu ZX, Jiang P, Xing Y. Genetic variation of pre-mRNA alternative splicing in human populations. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:581-92. [PMID: 22095823 DOI: 10.1002/wrna.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The precise splicing outcome of a transcribed gene is controlled by complex interactions between cis regulatory splicing signals and trans-acting regulators. In higher eukaryotes, alternative splicing is a prevalent mechanism for generating transcriptome and proteome diversity. Alternative splicing can modulate gene function, affect organismal phenotype and cause disease. Common genetic variation that affects splicing regulation can lead to differences in alternative splicing between human individuals and consequently impact expression level or protein function. In several well-documented examples, such natural variation of alternative splicing has indeed been shown to influence disease susceptibility and drug response. With new microarray and sequencing-based genomic technologies that can analyze eukaryotic transcriptomes at the exon or nucleotide level, it has become possible to globally compare the alternative splicing profiles across human individuals in any tissue or cell type of interest. Recent large-scale transcriptome studies using high-density splicing-sensitive microarray and deep RNA sequencing (RNA-Seq) have revealed widespread genetic variation of alternative splicing in humans. In the future, an extensive catalog of alternative splicing variation in human populations will help elucidate the molecular underpinnings of complex traits and human diseases, and shed light on the mechanisms of splicing regulation in human cells.
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Affiliation(s)
- Zhi-Xiang Lu
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
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