101
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Pineda JMB, Bradley RK. Most human introns are recognized via multiple and tissue-specific branchpoints. Genes Dev 2018; 32:577-591. [PMID: 29666160 PMCID: PMC5959240 DOI: 10.1101/gad.312058.118] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/09/2018] [Indexed: 12/20/2022]
Abstract
Pineda and Bradley demonstrate that almost all human introns contain multiple branchpoints. Approximately three-quarters of constitutive introns exhibit tissue-specific branchpoint usage. Although branchpoint recognition is an essential component of intron excision during the RNA splicing process, the branchpoint itself is frequently assumed to be a basal, rather than regulatory, sequence feature. However, this assumption has not been systematically tested due to the technical difficulty of identifying branchpoints and quantifying their usage. Here, we analyzed ∼1.31 trillion reads from 17,164 RNA sequencing data sets to demonstrate that almost all human introns contain multiple branchpoints. This complexity holds even for constitutive introns, 95% of which contain multiple branchpoints, with an estimated five to six branchpoints per intron. Introns upstream of the highly regulated ultraconserved poison exons of SR genes contain twice as many branchpoints as the genomic average. Approximately three-quarters of constitutive introns exhibit tissue-specific branchpoint usage. In an extreme example, we observed a complete switch in branchpoint usage in the well-studied first intron of HBB (β-globin) in normal bone marrow versus metastatic prostate cancer samples. Our results indicate that the recognition of most introns is unexpectedly complex and tissue-specific and suggest that alternative splicing catalysis typifies the majority of introns even in the absence of differences in the mature mRNA.
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Affiliation(s)
- Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Genome Sciences, University of Washington, Seattle, Wasington 98195, USA.,Medical Scientist Training Program, University of Washington, Seattle, Wasington 98195, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Genome Sciences, University of Washington, Seattle, Wasington 98195, USA
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102
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Avsec Ž, Barekatain M, Cheng J, Gagneur J. Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. Bioinformatics 2018; 34:1261-1269. [PMID: 29155928 PMCID: PMC5905632 DOI: 10.1093/bioinformatics/btx727] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/16/2017] [Accepted: 11/15/2017] [Indexed: 12/01/2022] Open
Abstract
Motivation Regulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries or polyadenylation site. Deep learning has become the approach of choice for modeling regulatory sequences because of its strength to learn complex sequence features. However, modeling relative distances to genomic landmarks in deep neural networks has not been addressed. Results Here we developed spline transformation, a neural network module based on splines to flexibly and robustly model distances. Modeling distances to various genomic landmarks with spline transformations significantly increased state-of-the-art prediction accuracy of in vivo RNA-binding protein binding sites for 120 out of 123 proteins. We also developed a deep neural network for human splice branchpoint based on spline transformations that outperformed the current best, already distance-based, machine learning model. Compared to piecewise linear transformation, as obtained by composition of rectified linear units, spline transformation yields higher prediction accuracy as well as faster and more robust training. As spline transformation can be applied to further quantities beyond distances, such as methylation or conservation, we foresee it as a versatile component in the genomics deep learning toolbox. Availability and implementation Spline transformation is implemented as a Keras layer in the CONCISE python package: https://github.com/gagneurlab/concise. Analysis code is available at https://github.com/gagneurlab/Manuscript_Avsec_Bioinformatics_2017. Contact avsec@in.tum.de or gagneur@in.tum.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Žiga Avsec
- Department of Informatics, Technical University of Munich, Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Jun Cheng
- Department of Informatics, Technical University of Munich, Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
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103
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Boroni M, Sammeth M, Gava SG, Jorge NAN, Macedo AM, Machado CR, Mourão MM, Franco GR. Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. Sci Rep 2018; 8:3877. [PMID: 29497070 PMCID: PMC5832876 DOI: 10.1038/s41598-018-22093-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 02/12/2018] [Indexed: 11/09/2022] Open
Abstract
Spliced leader dependent trans-splicing (SLTS) has been described as an important RNA regulatory process that occurs in different organisms, including the trematode Schistosoma mansoni. We identified more than seven thousand putative SLTS sites in the parasite, comprising genes with a wide spectrum of functional classes, which underlines the SLTS as a ubiquitous mechanism in the parasite. Also, SLTS gene expression levels span several orders of magnitude, showing that SLTS frequency is not determined by the expression level of the target gene, but by the presence of particular gene features facilitating or hindering the trans-splicing mechanism. Our in-depth investigation of SLTS events demonstrates widespread alternative trans-splicing (ATS) acceptor sites occurring in different regions along the entire gene body, highlighting another important role of SLTS generating alternative RNA isoforms in the parasite, besides the polycistron resolution. Particularly for introns where SLTS directly competes for the same acceptor substrate with cis-splicing, we identified for the first time additional and important features that might determine the type of splicing. Our study substantially extends the current knowledge of RNA processing by SLTS in S. mansoni, and provide basis for future studies on the trans-splicing mechanism in other eukaryotes.
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Affiliation(s)
- Mariana Boroni
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
- Laboratório de Bioinformática e Biologia Computacional, Coordenação de Pesquisa, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, 20231-050, Brazil
| | - Michael Sammeth
- Bioinformatics in Transcriptomics and Functional Genomics (BITFUN), Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075, Brazil
| | - Sandra Grossi Gava
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Brazil
| | - Natasha Andressa Nogueira Jorge
- Laboratório de Bioinformática e Biologia Computacional, Coordenação de Pesquisa, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, 20231-050, Brazil
| | - Andréa Mara Macedo
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Carlos Renato Machado
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Marina Moraes Mourão
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Brazil.
| | - Glória Regina Franco
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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104
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Abstract
Since its discovery in 1977, much has been known about RNA splicing and how it plays a central role in human development, function, and, notably, disease. Defects in RNA splicing account for at least 10% of all genetic disorders, with the number expected to increase as more information is uncovered on the contribution of noncoding genomic regions to disease. Splice modulation through the use of antisense oligonucleotides (AOs) has emerged as a promising avenue for the treatment of these disorders. In fact, two splice-switching AOs have recently obtained approval from the US Food and Drug Administration: eteplirsen (Exondys 51) for Duchenne muscular dystrophy, and nusinersen (Spinraza) for spinal muscular atrophy. These work by exon skipping and exon inclusion, respectively. In this chapter, we discuss the early development of AO-based splice modulation therapy-its invention, first applications, and its evolution into the approach we are now familiar with. We give a more extensive history of exon skipping in particular, as it is the splice modulation approach given the most focus in this book.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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105
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Legendre M, Rodriguez-Ballesteros M, Rossi M, Abadie V, Amiel J, Revencu N, Blanchet P, Brioude F, Delrue MA, Doubaj Y, Sefiani A, Francannet C, Holder-Espinasse M, Jouk PS, Julia S, Melki J, Mur S, Naudion S, Fabre-Teste J, Busa T, Stamm S, Lyonnet S, Attie-Bitach T, Kitzis A, Gilbert-Dussardier B, Bilan F. CHARGE syndrome: a recurrent hotspot of mutations in CHD7 IVS25 analyzed by bioinformatic tools and minigene assays. Eur J Hum Genet 2017; 26:287-292. [PMID: 29255276 DOI: 10.1038/s41431-017-0007-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 08/17/2017] [Accepted: 08/29/2017] [Indexed: 11/09/2022] Open
Abstract
CHARGE syndrome is a rare genetic disorder mainly due to de novo and private truncating mutations of CHD7 gene. Here we report an intriguing hot spot of intronic mutations (c.5405-7G > A, c.5405-13G > A, c.5405-17G > A and c.5405-18C > A) located in CHD7 IVS25. Combining computational in silico analysis, experimental branch-point determination and in vitro minigene assays, our study explains this mutation hot spot by a particular genomic context, including the weakness of the IVS25 natural acceptor-site and an unconventional lariat sequence localized outside the common 40 bp upstream the acceptor splice site. For each of the mutations reported here, bioinformatic tools indicated a newly created 3' splice site, of which the existence was confirmed using pSpliceExpress, an easy-to-use and reliable splicing reporter tool. Our study emphasizes the idea that combining these two complementary approaches could increase the efficiency of routine molecular diagnosis.
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Affiliation(s)
- Marine Legendre
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France.,EA3808 CiMoTheMA Université Poitiers, Poitiers, France
| | | | - Massimiliano Rossi
- Service de génétique, Centre de Référence Anomalies du Développement, Hospices Civils de Lyon et INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Université Claude Bernard Lyon 1, Bron, France
| | - Véronique Abadie
- Service de Pédiatrie Générale, Hôpital Necker Enfants-Malades, AP-HP, Paris, France
| | - Jeanne Amiel
- Département de Génétique, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, UMR-1163 INSERM-Université Paris Descartes, Paris, France
| | - Nicole Revencu
- Center for Human Genetics, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium
| | - Patricia Blanchet
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHU Montpellier, France
| | - Frédéric Brioude
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S938, Centre de Recherche Saint Antoine and AP-HP, Hôpitaux Universitaires Paris Est, Hôpital Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, Paris, France
| | | | - Yassamine Doubaj
- Département de Génétique Médicale, Institut National d'Hygiène, Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie de Rabat, Mohammed V University in Rabat, Rabat, Morocco
| | - Abdelaziz Sefiani
- Département de Génétique Médicale, Institut National d'Hygiène, Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie de Rabat, Mohammed V University in Rabat, Rabat, Morocco
| | | | | | - Pierre-Simon Jouk
- Département Génétique & Procréation, Hôpital Couple-Enfant, CHU Grenoble, France
| | - Sophie Julia
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, France
| | - Judith Melki
- CHU Bicêtre, Unité de Génétique Médicale and UMR-1169, Inserm, Le Kremlin Bicêtre, France
| | - Sébastien Mur
- Clinique de médecine néonatale, Hôpital Jeanne de Flandre, CHU Lille, France
| | - Sophie Naudion
- Service de Génétique Médicale, GH Pellegrin, CHU Bordeaux, France
| | | | - Tiffany Busa
- Département de Génétique Médicale, Hôpital d'enfants de la Timone, Marseille, France
| | - Stephen Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, USA
| | - Stanislas Lyonnet
- Département de Génétique, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, UMR-1163 INSERM-Université Paris Descartes, Paris, France
| | - Tania Attie-Bitach
- Département de Génétique, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, UMR-1163 INSERM-Université Paris Descartes, Paris, France
| | - Alain Kitzis
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France.,EA3808 CiMoTheMA Université Poitiers, Poitiers, France
| | - Brigitte Gilbert-Dussardier
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France.,EA3808 CiMoTheMA Université Poitiers, Poitiers, France
| | - Frédéric Bilan
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France. .,EA3808 CiMoTheMA Université Poitiers, Poitiers, France.
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106
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Hatje K, Rahman RU, Vidal RO, Simm D, Hammesfahr B, Bansal V, Rajput A, Mickael ME, Sun T, Bonn S, Kollmar M. The landscape of human mutually exclusive splicing. Mol Syst Biol 2017; 13:959. [PMID: 29242366 PMCID: PMC5740500 DOI: 10.15252/msb.20177728] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.
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Affiliation(s)
- Klas Hatje
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Raza-Ur Rahman
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ramon O Vidal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science Georg-August-University, Göttingen, Germany
| | - Björn Hammesfahr
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vikas Bansal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ashish Rajput
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Michel Edwar Mickael
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ting Sun
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany .,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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107
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Molecular basis of differential 3' splice site sensitivity to anti-tumor drugs targeting U2 snRNP. Nat Commun 2017; 8:2100. [PMID: 29235465 PMCID: PMC5727392 DOI: 10.1038/s41467-017-02007-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/30/2017] [Indexed: 01/21/2023] Open
Abstract
Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the differential sensitivity of 3′ splice sites to these drugs. Sequences 5′ from the branch point (BP) region strongly influence drug sensitivity, with additional functional BPs reducing, and BP-like sequences allowing, drug responses. Drug-induced retained introns are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs. Drug-induced exon skipping preferentially affects shorter alternatively spliced regions with weaker BPs. Remarkably, structurally similar drugs display both common and differential effects on splicing regulation, SSA generally displaying stronger effects on intron retention, and Sudemycins more acute effects on exon skipping. Collectively, our results illustrate how splicing modulation is exquisitely sensitive to the sequence context of 3′ splice sites and to small structural differences between drugs. Several families of natural compounds target core components of the pre-mRNA splicing machinery and display anti-tumor activity. Here the authors show that particular sequence features can be linked to drug response, and that drugs with very similar chemical structures display substantially different effects on splicing regulation.
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108
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Zhang W, Zhu X, Fu Y, Tsuji J, Weng Z. Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. BMC Bioinformatics 2017; 18:464. [PMID: 29219070 PMCID: PMC5773893 DOI: 10.1186/s12859-017-1875-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order to guide wet experiments, we develop computational methods to predict human splicing branchpoints. Results Considering the fact that an intron may have multiple branchpoints, we transform the branchpoint prediction as the multi-label learning problem, and attempt to predict branchpoint sites from intron sequences. First, we investigate a variety of intron sequence-derived features, such as sparse profile, dinucleotide profile, position weight matrix profile, Markov motif profile and polypyrimidine tract profile. Second, we consider several multi-label learning methods: partial least squares regression, canonical correlation analysis and regularized canonical correlation analysis, and use them as the basic classification engines. Third, we propose two ensemble learning schemes which integrate different features and different classifiers to build ensemble learning systems for the branchpoint prediction. One is the genetic algorithm-based weighted average ensemble method; the other is the logistic regression-based ensemble method. Conclusions In the computational experiments, two ensemble learning methods outperform benchmark branchpoint prediction methods, and can produce high-accuracy results on the benchmark dataset.
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Affiliation(s)
- Wen Zhang
- School of Computer, Wuhan University, Wuhan, 430072, China.
| | - Xiaopeng Zhu
- School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Yu Fu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Junko Tsuji
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
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109
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Wen J, Wang J, Zhang Q, Guo D. A heuristic model for computational prediction of human branch point sequence. BMC Bioinformatics 2017; 18:459. [PMID: 29065858 PMCID: PMC5655975 DOI: 10.1186/s12859-017-1864-9] [Citation(s) in RCA: 6] [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: 02/20/2017] [Accepted: 10/09/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Pre-mRNA splicing is the removal of introns from precursor mRNAs (pre-mRNAs) and the concurrent ligation of the flanking exons to generate mature mRNA. This process is catalyzed by the spliceosome, where the splicing factor 1 (SF1) specifically recognizes the seven-nucleotide branch point sequence (BPS) and the U2 snRNP later displaces the SF1 and binds to the BPS. In mammals, the degeneracy of BPS motifs together with the lack of a large set of experimentally verified BPSs complicates the task of BPS prediction in silico. RESULTS In this paper, we develop a simple and yet efficient heuristic model for human BPS prediction based on a novel scoring scheme, which quantifies the splicing strength of putative BPSs. The candidate BPS is restricted exclusively within a defined BPS search region to avoid the influences of other elements in the intron and therefore the prediction accuracy is improved. Moreover, using two types of relative frequencies for human BPS prediction, we demonstrate our model outperformed other current implementations on experimentally verified human introns. CONCLUSION We propose that the binding energy contributes to the molecular recognition involved in human pre-mRNA splicing. In addition, a genome-wide human BPS prediction is carried out. The characteristics of predicted BPSs are in accordance with experimentally verified human BPSs, and branch site positions relative to the 3'ss and the 5'end of the shortened AGEZ are consistent with the results of published papers. Meanwhile, a webserver for BPS predictor is freely available at http://biocomputer.bio.cuhk.edu.hk/BPS .
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Affiliation(s)
- Jia Wen
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jue Wang
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Qing Zhang
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Dianjing Guo
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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110
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Ohno K, Takeda JI, Masuda A. Rules and tools to predict the splicing effects of exonic and intronic mutations. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [DOI: 10.1002/wrna.1451] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Jun-ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
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111
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Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ. Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol Cell 2017; 65:539-553.e7. [PMID: 28157508 DOI: 10.1016/j.molcel.2017.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulatory events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one-third of the regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large "missing cache" of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.
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Affiliation(s)
- Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | | | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Calley L Hirsch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Juli Wang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frederick Vizeacoumar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Alessandro Datti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lilia Magomedova
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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112
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Mendes de Almeida R, Tavares J, Martins S, Carvalho T, Enguita FJ, Brito D, Carmo-Fonseca M, Lopes LR. Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PLoS One 2017; 12:e0182946. [PMID: 28797094 PMCID: PMC5552324 DOI: 10.1371/journal.pone.0182946] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/27/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High throughput sequencing technologies have revolutionized the identification of mutations responsible for genetic diseases such as hypertrophic cardiomyopathy (HCM). However, approximately 50% of individuals with a clinical diagnosis of HCM have no causal mutation identified. This may be due to the presence of pathogenic mutations located deep within the introns, which are not detected by conventional sequencing analysis restricted to exons and exon-intron boundaries. OBJECTIVE The aim of this study was to develop a whole-gene sequencing strategy to prioritize deep intronic variants that may play a role in HCM pathogenesis. METHODS AND RESULTS The full genomic DNA sequence of 26 genes previously associated with HCM was analysed in 16 unrelated patients. We identified likely pathogenic deep intronic variants in VCL, PRKAG2 and TTN genes. These variants, which are predicted to act through disruption of either splicing or transcription factor binding sites, are 3-fold more frequent in our cohort of probands than in normal European populations. Moreover, we found a patient that is compound heterozygous for a splice site mutation in MYBPC3 and the deep intronic VCL variant. Analysis of family members revealed that carriers of the MYBPC3 mutation alone do not manifest the disease, while family members that are compound heterozygous are clinically affected. CONCLUSION This study provides a framework for scrutinizing variation along the complete intronic sequence of HCM-associated genes and prioritizing candidates for mechanistic and functional analysis. Our data suggest that deep intronic variation contributes to HCM phenotype.
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Affiliation(s)
- Rita Mendes de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Tavares
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Dulce Brito
- Departamento de Cardiologia, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Rocha Lopes
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
- Institute of Cardiovascular Science, University College London, London, United Kingdom
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113
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Milek M, Imami K, Mukherjee N, Bortoli FD, Zinnall U, Hazapis O, Trahan C, Oeffinger M, Heyd F, Ohler U, Selbach M, Landthaler M. DDX54 regulates transcriptome dynamics during DNA damage response. Genome Res 2017; 27:1344-1359. [PMID: 28596291 PMCID: PMC5538551 DOI: 10.1101/gr.218438.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveillance pathways. The contribution of post-transcriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing radiation (IR). Interestingly, more than 260 proteins, including many nucleolar proteins, showed increased binding to poly(A)+ RNA in IR-exposed cells. The functional analysis of DDX54, a candidate genotoxic stress responsive RNA helicase, revealed that this protein is an immediate-to-early DDR regulator required for the splicing efficacy of its target IR-induced pre-mRNAs. Upon IR exposure, DDX54 acts by increased interaction with a well-defined class of pre-mRNAs that harbor introns with weak acceptor splice sites, as well as by protein-protein contacts within components of U2 snRNP and spliceosomal B complex, resulting in lower intron retention and higher processing rates of its target transcripts. Because DDX54 promotes survival after exposure to IR, its expression and/or mutation rate may impact DDR-related pathologies. Our work indicates the relevance of many uncharacterized RBPs potentially involved in the DDR.
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Affiliation(s)
- Miha Milek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Koshi Imami
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Neelanjan Mukherjee
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Francesca De Bortoli
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, 14195 Berlin, Germany
| | - Ulrike Zinnall
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Orsalia Hazapis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, H2W 1R7 Montréal, Quebec, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, H3A 1A3 Montréal, Quebec, Canada
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, H2W 1R7 Montréal, Quebec, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, H3A 1A3 Montréal, Quebec, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, H3T 1J4 Montréal, Quebec, Canada
| | - Florian Heyd
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, 14195 Berlin, Germany
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
- Department of Computer Science, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
- Charite-Universitätsmedizin Berlin, 10115 Berlin, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
- IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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114
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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115
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Protein 4.1R Exon 16 3' Splice Site Activation Requires Coordination among TIA1, Pcbp1, and RBM39 during Terminal Erythropoiesis. Mol Cell Biol 2017; 37:MCB.00446-16. [PMID: 28193846 DOI: 10.1128/mcb.00446-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/03/2017] [Indexed: 12/18/2022] Open
Abstract
Exon 16 of protein 4.1R encodes a spectrin/actin-binding peptide critical for erythrocyte membrane stability. Its expression during erythroid differentiation is regulated by alternative pre-mRNA splicing. A UUUUCCCCCC motif situated between the branch point and the 3' splice site is crucial for inclusion. We show that the UUUU region and the last three C residues in this motif are necessary for the binding of splicing factors TIA1 and Pcbp1 and that these proteins appear to act in a collaborative manner to enhance exon 16 inclusion. This element also activates an internal exon when placed in a corresponding intronic position in a heterologous reporter. The impact of these two factors is further enhanced by high levels of RBM39, whose expression rises during erythroid differentiation as exon 16 inclusion increases. TIA1 and Pcbp1 associate in a complex containing RBM39, which interacts with U2AF65 and SF3b155 and promotes U2 snRNP recruitment to the branch point. Our results provide a mechanism for exon 16 3' splice site activation in which a coordinated effort among TIA1, Pcbp1, and RBM39 stabilizes or increases U2 snRNP recruitment, enhances spliceosome A complex formation, and facilitates exon definition through RBM39-mediated splicing regulation.
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116
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Nozu K, Iijima K, Igarashi T, Yamada S, Kralovicova J, Nozu Y, Yamamura T, Minamikawa S, Morioka I, Ninchoji T, Kaito H, Nakanishi K, Vorechovsky I. A birth of bipartite exon by intragenic deletion. Mol Genet Genomic Med 2017; 5:287-294. [PMID: 28546999 PMCID: PMC5441408 DOI: 10.1002/mgg3.277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/03/2017] [Accepted: 01/06/2017] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome. The deletion encompassed exons 38 through 41 and activated a cryptic 3' and 5' splice site that were derived from intron 37 and intron 41, respectively. The deletion breakpoint was in the middle of the new exon, with considerable complementarity between the two exonic parts, potentially bringing the cryptic 3' and 5' splice site into proximity. The 3' splice site, polypyrimidine tract and the branch site of the new exon were derived from an inactive, 5' truncated LINE-1 retrotransposon. This ancient LINE-1 copy sustained a series of mutations that created the highly conserved AG dinucleotide at the 3' splice site early in primate development. The exon was fully included in mature transcripts and introduced a stop codon in the shortened COL4A5 mRNA, illustrating pitfalls of inferring disease severity from DNA mutation alone. CONCLUSION These results expand the repertoire of mutational mechanisms that alter RNA processing in genetic disease and illustrate the extraordinary versatility of transposed elements in shaping the new exon-intron structure and the phenotypic variability.
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Affiliation(s)
- Kandai Nozu
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Kazumoto Iijima
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Toru Igarashi
- Department of PediatricsNippon Medical School HospitalTokyoJapan
| | - Shiro Yamada
- Department of PediatricsTokai University Oiso HospitalOisoJapan.,Division of Human GeneticsNational Institute of GeneticsMishimaJapan
| | | | - Yoshimi Nozu
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Tomohiko Yamamura
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Shogo Minamikawa
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Ichiro Morioka
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Takeshi Ninchoji
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Hiroshi Kaito
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Koichi Nakanishi
- Department of PediatricsWakayama Medical UniversityWakayamaJapan
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Yue Y, Hou S, Wang X, Zhan L, Cao G, Li G, Shi Y, Zhang P, Hong W, Lin H, Liu B, Shi F, Yang Y, Jin Y. Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing. RNA Biol 2017; 14:1399-1410. [PMID: 28277933 DOI: 10.1080/15476286.2017.1294308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.
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Affiliation(s)
- Yuan Yue
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Shouqing Hou
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Xiu Wang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China.,b Institute of Ecology, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Leilei Zhan
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Guozheng Cao
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Guoli Li
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yang Shi
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Peng Zhang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Weiling Hong
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Hao Lin
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Baoping Liu
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Feng Shi
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yun Yang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yongfeng Jin
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
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118
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Taggart AJ, Lin CL, Shrestha B, Heintzelman C, Kim S, Fairbrother WG. Large-scale analysis of branchpoint usage across species and cell lines. Genome Res 2017; 27:639-649. [PMID: 28119336 PMCID: PMC5378181 DOI: 10.1101/gr.202820.115] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/18/2017] [Indexed: 02/03/2023]
Abstract
The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5′ splice site, a branch site, and a 3′ splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2–5 linkage. Here, we report large-scale mapping of the branchpoints from deep sequencing data in three different species and in the SF3B1 K700E oncogenic mutant background. We have developed a novel method whereby raw lariat reads are refined by U2snRNP/pre-mRNA base-pairing models to return the largest current data set of branchpoint sequences with quality metrics. This analysis discovers novel modes of U2snRNA:pre-mRNA base-pairing conserved in yeast and provides insight into the biogenesis of intron circles. Finally, matching branch site usage with isoform selection across the extensive panel of ENCODE RNA-seq data sets offers insight into the mechanisms by which branchpoint usage drives alternative splicing.
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Affiliation(s)
- Allison J Taggart
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Chien-Ling Lin
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Barsha Shrestha
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Claire Heintzelman
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Seongwon Kim
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.,Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA.,Hassenfeld Child Health Innovation Institute of Brown University, Providence, Rhode Island 02912, USA
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119
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Yoshimoto R, Kaida D, Furuno M, Burroughs AM, Noma S, Suzuki H, Kawamura Y, Hayashizaki Y, Mayeda A, Yoshida M. Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA (NEW YORK, N.Y.) 2017; 23:47-57. [PMID: 27754875 PMCID: PMC5159648 DOI: 10.1261/rna.058065.116] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/03/2016] [Indexed: 05/27/2023]
Abstract
Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, a potent antitumor compound isolated from a culture broth of Pseudomonas sp no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, a subcomplex of the U2 snRNP, to inhibit pre-mRNA splicing. However, the mechanism of SSA's antitumor activity is unknown. It is noteworthy that SSA causes accumulation of a truncated form of the CDK inhibitor protein p27 translated from CDKN1B pre-mRNA, which is involved in SSA-induced cell-cycle arrest. However, it is still unclear whether pre-mRNAs are uniformly exported from the nucleus following SSA treatment. We performed RNA-seq analysis on nuclear and cytoplasmic fractions of SSA-treated cells. Our statistical analyses showed that intron retention is the major consequence of SSA treatment, and a small number of intron-containing pre-mRNAs leak into the cytoplasm. Using a series of reporter plasmids to investigate the roles of intronic sequences in the pre-mRNA leakage, we showed that the strength of the 5' splice site affects pre-mRNA leakage. Additionally, we found that the level of pre-mRNA leakage is related to transcript length. These results suggest that the strength of the 5' splice site and the length of the transcripts are determinants of the pre-mRNA leakage induced by SF3b inhibitors.
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Affiliation(s)
- Rei Yoshimoto
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Daisuke Kaida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Frontier Research Core for Life Sciences, University of Toyama, Toyama-shi, Toyama 930-0194, Japan
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama-shi, Toyama 930-0194, Japan
| | - Masaaki Furuno
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - A Maxwell Burroughs
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Shohei Noma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Kawamura
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Japan Science and Technology Corporation, CREST Research Project, Kawaguchi, Saitama 332-0012, Japan
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120
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Abstract
The functional capacity of cells is defined by the transcriptome. Many recent studies have identified variations in the transcriptome of tumors due to alternative splicing changes, as well as mutations in splicing factors and regulatory signals in most tumor types. Some of these alterations have been linked to tumor progression, metastasis, therapy resistance, and other oncogenic processes. Here, we describe the different mechanisms that drive splicing changes in tumors and their impact in cancer. Motivated by the current evidence, we propose a model whereby a subset of the splicing patterns contributes to the definition of specific tumor phenotypes, and may hold potential for the development of novel clinical biomarkers and therapeutic approaches.
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Affiliation(s)
- Babita Singh
- a Pompeu Fabra University, PRBB , Barcelona , Spain
| | - Eduardo Eyras
- a Pompeu Fabra University, PRBB , Barcelona , Spain.,b ICREA , Barcelona , Spain
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121
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Dolatshad H, Pellagatti A, Liberante FG, Llorian M, Repapi E, Steeples V, Roy S, Scifo L, Armstrong RN, Shaw J, Yip BH, Killick S, Kušec R, Taylor S, Mills KI, Savage KI, Smith CWJ, Boultwood J. Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes. Leukemia 2016; 30:2322-2331. [PMID: 27211273 PMCID: PMC5029572 DOI: 10.1038/leu.2016.149] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/04/2016] [Accepted: 05/16/2016] [Indexed: 02/08/2023]
Abstract
The splicing factor SF3B1 is the most frequently mutated gene in myelodysplastic syndromes (MDS), and is strongly associated with the presence of ring sideroblasts (RS). We have performed a systematic analysis of cryptic splicing abnormalities from RNA sequencing data on hematopoietic stem cells (HSCs) of SF3B1-mutant MDS cases with RS. Aberrant splicing events in many downstream target genes were identified and cryptic 3' splice site usage was a frequent event in SF3B1-mutant MDS. The iron transporter ABCB7 is a well-recognized candidate gene showing marked downregulation in MDS with RS. Our analysis unveiled aberrant ABCB7 splicing, due to usage of an alternative 3' splice site in MDS patient samples, giving rise to a premature termination codon in the ABCB7 mRNA. Treatment of cultured SF3B1-mutant MDS erythroblasts and a CRISPR/Cas9-generated SF3B1-mutant cell line with the nonsense-mediated decay (NMD) inhibitor cycloheximide showed that the aberrantly spliced ABCB7 transcript is targeted by NMD. We describe cryptic splicing events in the HSCs of SF3B1-mutant MDS, and our data support a model in which NMD-induced downregulation of the iron exporter ABCB7 mRNA transcript resulting from aberrant splicing caused by mutant SF3B1 underlies the increased mitochondrial iron accumulation found in MDS patients with RS.
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Affiliation(s)
- H Dolatshad
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - A Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - F G Liberante
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - M Llorian
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, UK
| | - E Repapi
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - V Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - S Roy
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - L Scifo
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - R N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - J Shaw
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - B H Yip
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - S Killick
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - R Kušec
- Dubrava University hospital and Zagreb School of Medicine, University of Zagreb, Zagreb, Croatia
| | - S Taylor
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - K I Mills
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - K I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - C W J Smith
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, UK
| | - J Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
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Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. eLife 2016; 5. [PMID: 27882870 PMCID: PMC5122456 DOI: 10.7554/elife.19743] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022] Open
Abstract
Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition. The active early complex formed in the absence of PTBP1 proceeded to assemble an EDC with the eviction of hnRNP proteins, the late recruitment of SR proteins, and binding of the U2 snRNP. These results demonstrate that during early stages of splicing, exon RNP complexes are highly dynamic with many proteins failing to bind during PTBP1 arrest. DOI:http://dx.doi.org/10.7554/eLife.19743.001
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Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Ajay Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, Phoenix, United States
| | - Darryl Chui
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
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123
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Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nat Struct Mol Biol 2016; 24:86-96. [PMID: 27870833 DOI: 10.1038/nsmb.3325] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/18/2016] [Indexed: 12/26/2022]
Abstract
Pervasive transcription of the human genome results in a heterogeneous mix of coding RNAs and long noncoding RNAs (lncRNAs). Only a small fraction of lncRNAs have demonstrated regulatory functions, thus making functional lncRNAs difficult to distinguish from nonfunctional transcriptional byproducts. This difficulty has resulted in numerous competing human lncRNA classifications that are complicated by a steady increase in the number of annotated lncRNAs. To address these challenges, we quantitatively examined transcription, splicing, degradation, localization and translation for coding and noncoding human genes. We observed that annotated lncRNAs had lower synthesis and higher degradation rates than mRNAs and discovered mechanistic differences explaining slower lncRNA splicing. We grouped genes into classes with similar RNA metabolism profiles, containing both mRNAs and lncRNAs to varying extents. These classes exhibited distinct RNA metabolism, different evolutionary patterns and differential sensitivity to cellular RNA-regulatory pathways. Our classification provides an alternative to genomic context-driven annotations of lncRNAs.
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Rodor J, FitzPatrick DR, Eyras E, Cáceres JF. The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development. RNA Biol 2016; 14:45-57. [PMID: 27763814 PMCID: PMC5270529 DOI: 10.1080/15476286.2016.1247148] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease.
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Affiliation(s)
- Julie Rodor
- a Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital , Edinburgh , EH4 2XU , UK
| | - David R FitzPatrick
- a Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital , Edinburgh , EH4 2XU , UK
| | - Eduardo Eyras
- b Computational Genomics Group, Universitat Pompeu Fabra , E08003 , Barcelona , Spain.,c Catalan Institution for Research and Advanced Studies (ICREA) , E08010 , Barcelona , Spain
| | - Javier F Cáceres
- a Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital , Edinburgh , EH4 2XU , UK
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125
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Kralovicova J, Vorechovsky I. Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons. Nucleic Acids Res 2016; 45:417-434. [PMID: 27566151 PMCID: PMC5224494 DOI: 10.1093/nar/gkw733] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 12/30/2022] Open
Abstract
The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3′ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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126
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Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3' splice sites within RNA secondary structures. Oncogene 2016; 36:1123-1133. [PMID: 27524419 PMCID: PMC5311031 DOI: 10.1038/onc.2016.279] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/14/2016] [Accepted: 07/01/2016] [Indexed: 02/08/2023]
Abstract
Recurrent mutations in core splicing factors have been reported in several clonal disorders, including cancers. Mutations in SF3B1, a component of the U2 splicing complex, are the most common. SF3B1 mutations are associated with aberrant pre-mRNA splicing using cryptic 3’ splice sites (3’SS) but the mechanism of their selection is not clear. To understand how cryptic 3’SS are selected, we performed comprehensive analysis of transcriptome-wide changes to splicing and gene expression associated with SF3B1 mutations in patient samples as well as an experimental model of inducible expression. Hundreds of cryptic 3’SS were detectable across the genome in cells expressing mutant SF3B1. These 3’SS are typically sequestered within RNA secondary structures and poorly accessible compared to their corresponding canonical 3’SS. We hypothesized that these cryptic 3’SS are inaccessible during normal splicing catalysis and that this constraint is overcome in spliceosomes containing mutant SF3B1. This model of secondary structure-dependent selection of cryptic 3’SS was found across multiple clonal processes associated with SF3B1 mutations (myelodysplastic syndrome and chronic lymphocytic leukemia). We validated our model predictions in mini-gene splicing assays. Additionally, we found deregulated expression of proteins with relevant functions in splicing factor-related diseases both in association with aberrant splicing and without corresponding splicing changes. Our results show that SF3B1 mutations are associated with a distinct splicing program shared across multiple clonal processes and define a biochemical mechanism for altered 3’SS choice.
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127
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Lo CL, Lossie AC, Liang T, Liu Y, Xuei X, Lumeng L, Zhou FC, Muir WM. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model. PLoS Genet 2016; 12:e1006178. [PMID: 27490364 PMCID: PMC4973992 DOI: 10.1371/journal.pgen.1006178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/15/2016] [Indexed: 12/30/2022] Open
Abstract
Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits. Alcohol Used Disorder (AUD) or Alcoholism extracts a great societal cost in terms of human suffering. Understanding the genetic basis is critical to comprehend, treat and prevent this disease, but difficult in humans, as choice is influenced by nature and nurture. To discover its genetic basis, we used an animal model system that controlled for genetic and non-genetic factors through randomization, study replication, long-term divergent selection, and a controlled environment. We conducted whole genome sequencing in breeds that were either compulsive excessive drinkers or completely abstinent. We discovered consistent alterations in several genes and neurological pathways previously unassociated with alcoholism. These results strengthened our understanding of the genetic basis of alcoholism and revealed potential genetic- and neurological-based treatments.
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Affiliation(s)
- Chiao-Ling Lo
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Amy C. Lossie
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Tiebing Liang
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Yunlong Liu
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medical Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Xiaoling Xuei
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Lawrence Lumeng
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Feng C. Zhou
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail: (FCZ); (WMM)
| | - William M. Muir
- Indiana Alcohol Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail: (FCZ); (WMM)
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128
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Llorian M, Gooding C, Bellora N, Hallegger M, Buckroyd A, Wang X, Rajgor D, Kayikci M, Feltham J, Ule J, Eyras E, Smith CWJ. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators. Nucleic Acids Res 2016; 44:8933-8950. [PMID: 27317697 PMCID: PMC5062968 DOI: 10.1093/nar/gkw560] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 06/08/2016] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is a key component of gene expression programs that drive cellular differentiation. Smooth muscle cells (SMCs) are important in the function of a number of physiological systems; however, investigation of SMC AS has been restricted to a handful of events. We profiled transcriptome changes in mouse de-differentiating SMCs and observed changes in hundreds of AS events. Exons included in differentiated cells were characterized by particularly weak splice sites and by upstream binding sites for Polypyrimidine Tract Binding protein (PTBP1). Consistent with this, knockdown experiments showed that that PTBP1 represses many smooth muscle specific exons. We also observed coordinated splicing changes predicted to downregulate the expression of core components of U1 and U2 snRNPs, splicing regulators and other post-transcriptional factors in differentiated cells. The levels of cognate proteins were lower or similar in differentiated compared to undifferentiated cells. However, levels of snRNAs did not follow the expression of splicing proteins, and in the case of U1 snRNP we saw reciprocal changes in the levels of U1 snRNA and U1 snRNP proteins. Our results suggest that the AS program in differentiated SMCs is orchestrated by the combined influence of auxiliary RNA binding proteins, such as PTBP1, along with altered activity and stoichiometry of the core splicing machinery.
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Affiliation(s)
- Miriam Llorian
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Nicolas Bellora
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK Catalan Institute for Research and Advanced Studies (ICREA), E08010 Barcelona, Spain
| | - Martina Hallegger
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK Computational Genomics, Universitat Pompeu Fabra, E08003 Barcelona, Spain
| | - Adrian Buckroyd
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Xiao Wang
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Dipen Rajgor
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Melis Kayikci
- INIBIOMA, CONICET-UNComahue, Bariloche 8400 Río Negro, Argentina
| | - Jack Feltham
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Jernej Ule
- Computational Genomics, Universitat Pompeu Fabra, E08003 Barcelona, Spain
| | - Eduardo Eyras
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
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129
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Quinn JJ, Zhang QC, Georgiev P, Ilik IA, Akhtar A, Chang HY. Rapid evolutionary turnover underlies conserved lncRNA-genome interactions. Genes Dev 2016; 30:191-207. [PMID: 26773003 PMCID: PMC4719309 DOI: 10.1101/gad.272187.115] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many long noncoding RNAs (lncRNAs) can regulate chromatin states, but the evolutionary origin and dynamics driving lncRNA-genome interactions are unclear. We adapted an integrative strategy that identifies lncRNA orthologs in different species despite limited sequence similarity, which is applicable to mammalian and insect lncRNAs. Analysis of the roX lncRNAs, which are essential for dosage compensation of the single X chromosome in Drosophila males, revealed 47 new roX orthologs in diverse Drosophilid species across ∼40 million years of evolution. Genetic rescue by roX orthologs and engineered synthetic lncRNAs showed that altering the number of focal, repetitive RNA structures determines roX ortholog function. Genomic occupancy maps of roX RNAs in four species revealed conserved targeting of X chromosome neighborhoods but rapid turnover of individual binding sites. Many new roX-binding sites evolved from DNA encoding a pre-existing RNA splicing signal, effectively linking dosage compensation to transcribed genes. Thus, dynamic change in lncRNAs and their genomic targets underlies conserved and essential lncRNA-genome interactions.
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Affiliation(s)
- Jeffrey J Quinn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California 94305, USA
| | - Qiangfeng C Zhang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| | - Ibrahim A Ilik
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
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130
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Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, Joshi RS, Mittelman D, Sharp AJ. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids Res 2016; 44:3750-62. [PMID: 27060133 PMCID: PMC4857002 DOI: 10.1093/nar/gkw219] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/22/2016] [Indexed: 01/23/2023] Open
Abstract
Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome.
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Affiliation(s)
- Javier Quilez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Audrey Guilmatre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gareth Highnam
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Melissa Gymrek
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA New York Genome Center, New York, NY 10038, USA
| | - Yaniv Erlich
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY 10027, USA
| | - Ricky S Joshi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Mittelman
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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131
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IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome. J Hum Genet 2016; 61:633-40. [PMID: 27009626 DOI: 10.1038/jhg.2016.23] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 01/20/2023]
Abstract
Precise spatiotemporal regulation of splicing is mediated by splicing cis-elements on pre-mRNA. Single-nucleotide variations (SNVs) affecting intronic cis-elements possibly compromise splicing, but no efficient tool has been available to identify them. Following an effect-size analysis of each intronic nucleotide on annotated alternative splicing, we extracted 105 parameters that could affect the strength of the splicing signals. However, we could not generate reliable support vector regression models to predict the percent-splice-in (PSI) scores for normal human tissues. Next, we generated support vector machine (SVM) models using 110 parameters to directly differentiate pathogenic SNVs in the Human Gene Mutation Database and normal SNVs in the dbSNP database, and we obtained models with a sensitivity of 0.800±0.041 (mean and s.d.) and a specificity of 0.849±0.021. Our IntSplice models were more discriminating than SVM models that we generated with Shapiro-Senapathy score and MaxEntScan::score3ss. We applied IntSplice to a naturally occurring and nine artificial intronic mutations in RAPSN causing congenital myasthenic syndrome. IntSplice correctly predicted the splicing consequences for nine of the ten mutants. We created a web service program, IntSplice (http://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice) to predict splicing-affecting SNVs at intronic positions from -50 to -3.
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Wang Z, Iida A, Miyake N, Nishiguchi KM, Fujita K, Nakazawa T, Alswaid A, Albalwi MA, Kim OH, Cho TJ, Lim GY, Isidor B, David A, Rustad CF, Merckoll E, Westvik J, Stattin EL, Grigelioniene G, Kou I, Nakajima M, Ohashi H, Smithson S, Matsumoto N, Nishimura G, Ikegawa S. Axial Spondylometaphyseal Dysplasia Is Caused by C21orf2 Mutations. PLoS One 2016; 11:e0150555. [PMID: 26974433 PMCID: PMC4790905 DOI: 10.1371/journal.pone.0150555] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/15/2016] [Indexed: 12/19/2022] Open
Abstract
Axial spondylometaphyseal dysplasia (axial SMD) is an autosomal recessive disease characterized by dysplasia of axial skeleton and retinal dystrophy. We conducted whole exome sequencing and identified C21orf2 (chromosome 21 open reading frame 2) as a disease gene for axial SMD. C21orf2 mutations have been recently found to cause isolated retinal degeneration and Jeune syndrome. We found a total of five biallelic C21orf2 mutations in six families out of nine: three missense and two splicing mutations in patients with various ethnic backgrounds. The pathogenic effects of the splicing (splice-site and branch-point) mutations were confirmed on RNA level, which showed complex patterns of abnormal splicing. C21orf2 mutations presented with a wide range of skeletal phenotypes, including cupped and flared anterior ends of ribs, lacy ilia and metaphyseal dysplasia of proximal femora. Analysis of patients without C21orf2 mutation indicated genetic heterogeneity of axial SMD. Functional data in chondrocyte suggest C21orf2 is implicated in cartilage differentiation. C21orf2 protein was localized to the connecting cilium of the cone and rod photoreceptors, confirming its significance in retinal function. Our study indicates that axial SMD is a member of a unique group of ciliopathy affecting skeleton and retina.
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Affiliation(s)
- Zheng Wang
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, 108–8639, Japan
- McKusick-Zhang Center for Genetic Medicine and State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Aritoshi Iida
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, 108–8639, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236–0004, Japan
| | - Koji M. Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, 980–8574, Japan
| | - Kosuke Fujita
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Sendai, 980–8574, Japan
| | - Toru Nakazawa
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, 980–8574, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Sendai, 980–8574, Japan
- Department of Opthalmology, Tohoku University Graduate School of Medicine, Sendai, 980–8574, Japan
| | - Abdulrahman Alswaid
- Department of Pediatrics, King Abdulaziz Medical City for National Guard Health Affairs, Riyadh, 22490, Saudi Arabia
| | - Mohammed A. Albalwi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, National Guard Health Affairs, Riyadh, 22490, Saudi Arabia
| | - Ok-Hwa Kim
- Department of Radiology, Woorisoa Children's Hospital, Seoul, 08291, Republic of Korea
| | - Tae-Joon Cho
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Gye-Yeon Lim
- Department of Radiology, St. Mary’s Hospital, The Catholic University, Seoul, 07345, Republic of Korea
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale and INSERM, UMR-S 957, Nantes, 44093, France
| | - Albert David
- CHU Nantes, Service de Génétique Médicale and INSERM, UMR-S 957, Nantes, 44093, France
| | - Cecilie F. Rustad
- Department of Medical Genetics, Section for Clinical Genetics, Oslo University Hospital, Oslo, 0424, Norway
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, Oslo, 0424, Norway
| | - Jostein Westvik
- Department of Radiology, Oslo University Hospital, Oslo, 0424, Norway
| | - Eva-Lena Stattin
- Department of Medical Biosciences, Medical and Clinical Genetics, Umeå University, Umeå, 90187, Sweden
| | - Giedre Grigelioniene
- Department of Clinical Genetics and Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm, 17176, Sweden
| | - Ikuyo Kou
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, 108–8639, Japan
| | - Masahiro Nakajima
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, 108–8639, Japan
| | - Hirohumi Ohashi
- Division of Medical Genetics, Saitama Children’s Medical Center, Saitama, 339–8551, Japan
| | - Sarah Smithson
- Department of Clinical Genetics, St. Michaels Hospital, Bristol, BS2 8EG, United Kingdom
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236–0004, Japan
| | - Gen Nishimura
- Department of Pediatric Imaging, Tokyo Metropolitan Children's Medical Center, Fuchu, 183–8561, Japan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, 108–8639, Japan
- * E-mail:
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Voorter CEM, Gerritsen KEH, Groeneweg M, Wieten L, Tilanus MGJ. The role of gene polymorphism in HLA class I splicing. Int J Immunogenet 2016; 43:65-78. [PMID: 26920492 DOI: 10.1111/iji.12256] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/28/2016] [Accepted: 02/04/2016] [Indexed: 01/15/2023]
Abstract
Among the large number of human leucocyte antigen (HLA) alleles, only a few have been identified with a nucleotide polymorphism impairing correct splicing. Those alleles show aberrant expression levels, due to either a direct effect of the polymorphism on the normal splice site or to the creation of an alternative splice site. Furthermore, in several studies, the presence of alternatively spliced HLA transcripts co-expressed with the mature spliced transcripts was reported. We evaluated the splice site sequences of all known HLA class I alleles and found that, beside the consensus GT and AG sequences at the intron borders, there were some other highly conserved nucleotides for the different class I genes. In this review, we summarize the splicing mechanism and evaluate what is known today about alternative splicing of HLA class I genes.
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Affiliation(s)
- C E M Voorter
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - K E H Gerritsen
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - M Groeneweg
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - L Wieten
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - M G J Tilanus
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
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Alsafadi S, Houy A, Battistella A, Popova T, Wassef M, Henry E, Tirode F, Constantinou A, Piperno-Neumann S, Roman-Roman S, Dutertre M, Stern MH. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Nat Commun 2016; 7:10615. [PMID: 26842708 DOI: 10.1038/ncomms10615] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/05/2016] [Indexed: 12/20/2022] Open
Abstract
Hotspot mutations in the spliceosome gene SF3B1 are reported in ∼20% of uveal melanomas. SF3B1 is involved in 3'-splice site (3'ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1(R625/K666) mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3'ss. Modelling the differential junctions in SF3B1(WT) and SF3B1(R625/K666) cell lines demonstrates that the deregulated splice pattern strictly depends on SF3B1 status and on the 3'ss-sequence context. SF3B1(WT) knockdown or overexpression do not reproduce the SF3B1(R625/K666) splice pattern, qualifying SF3B1(R625/K666) as change-of-function mutants. Mutagenesis of predicted branchpoints reveals that the SF3B1(R625/K666)-promoted splice pattern is a direct result of alternative branchpoint usage. Altogether, this study provides a better understanding of the mechanisms underlying splicing alterations induced by mutant SF3B1 in cancer, and reveals a role for alternative branchpoints in disease.
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Affiliation(s)
- Samar Alsafadi
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Alexandre Houy
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Aude Battistella
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Tatiana Popova
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Michel Wassef
- Depatment of Developmental Biology and Genetics, CNRS UMR 3215/INSERM U934, Institut Curie, PSL Research University, Paris 75248, France
| | - Emilie Henry
- Translational Research Department, Institut Curie, PSL Research University, Paris 75248, France
| | - Franck Tirode
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Angelos Constantinou
- Department of Molecular Bases of Human Diseases, CNRS UPR 1142, IGH-Institute of Human Genetics, Montpellier 34090, France
| | | | - Sergio Roman-Roman
- Translational Research Department, Institut Curie, PSL Research University, Paris 75248, France
| | - Martin Dutertre
- Department of Genotoxic stress and Cancer, CNRS UMR 3348, Institut Curie, PSL Research University, Orsay 91400, France
| | - Marc-Henri Stern
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
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Ajiro M, Zheng ZM. Vemurafenib-resistant BRAF selects alternative branch points different from its wild-type BRAF in intron 8 for RNA splicing. Cell Biosci 2015; 5:70. [PMID: 26697165 PMCID: PMC4687071 DOI: 10.1186/s13578-015-0061-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/14/2015] [Indexed: 12/19/2022] Open
Abstract
One mechanism of resistance of the melanoma-associated BRAF kinase to its small molecule inhibitor vemurafenib is by point mutations in its intron 8 resulting in exons 4–8 skipping. In this report, we carried out in vitro BRAF RNA splicing assays and lariat RT-PCR to map the intron 8 branch points in wild-type and BRAF mutants. We identify multiple branch points (BP) in intron 8 of both wild-type (wt) and vemurafenib-resistant BRAF RNA. In wt BRAF, BPs are located at -29A, -28A and -26A, whereas in a vemurafenib-resistant BRAF splicing mutant, BPs map to -22A, -18A and -15A, proximal to the intron 8 3′ splice site. This finding of a distal-to-proximal shift of the branch point sequence in BRAF splicing in response to point-mutations in intron 8 provides insight into the regulation of BRAF alternative splicing upon vemurafenib resistance.
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Affiliation(s)
- Masahiko Ajiro
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 USA
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Sakuma M, Iida K, Hagiwara M. Deciphering targeting rules of splicing modulator compounds: case of TG003. BMC Mol Biol 2015; 16:16. [PMID: 26400733 PMCID: PMC4580995 DOI: 10.1186/s12867-015-0044-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired effect of genetic mutations. However, the knowledge and tools to understand factors contributing to splicing modulator compound sensitivity have been lacking. Our goal was to establish a method to characterize sequence features found in compound sensitive exons. Results Here we developed a comparative transcriptomic approach to explore features that make an exon sensitive to a chemical compound. In this study, we chose TG003, a potential drug for Duchenne muscular dystrophy, and performed RNA-sequencing on samples from human and mouse skeletal muscle cells, with and without TG003 treatments. We compared TG003 responsiveness between homologous exon pairs and identified 21 pairs in which human exons were skip-enhanced but not mouse exons. We compared the sequence features; splice site scores, number of splicing factor binding sites, and properties of branch sequence and polypyrimidine tracts, and found that polypyrimidine tracts were stronger (longer stretches and richer content of consecutive polypyrimidine) in the mouse TG003 insensitive exons. We also compared the features between TG003 skip-enhanced and insensitive exons within the species, and discovered that human TG003 skip-enhanced exons were shorter and had less splicing factor binding sites than the group of human TG003 insensitive exons. Mouse insensitive exons homologous to human TG003 skip-enhanced exons shared these properties. Our results suggested that these features are prerequisites for TG003 skip-enhanced exons and weak polypyrimidine tracts are defining features, which were supported by a decision tree analysis on all cassette exons in human. Conclusions In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0044-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maki Sakuma
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan. .,Medical Research Support Center, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
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Chaudhry AS, Prasad B, Shirasaka Y, Fohner A, Finkelstein D, Fan Y, Wang S, Wu G, Aklillu E, Sim SC, Thummel KE, Schuetz EG. The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2 Alleles. Drug Metab Dispos 2015; 43:1226-35. [PMID: 26021325 DOI: 10.1124/dmd.115.064428] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/28/2015] [Indexed: 12/13/2022] Open
Abstract
CYP2C19 rs12769205 alters an intron 2 branch point adenine leading to an alternative mRNA in human liver with complete inclusion of intron 2 (exon 2B). rs12769205 changes the mRNA reading frame, introduces 87 amino acids, and leads to a premature stop codon. The 1000 Genomes project (http://browser.1000genomes.org/index.html) indicated rs12769205 is in linkage disequilibrium with rs4244285 on CYP2C19*2, but found alone on CYP2C19*35 in Blacks. Minigenes containing rs12769205 transfected into HepG2 cells demonstrated this single nucleotide polymorphism (SNP) alone leads to exon 2B and decreases CYP2C19 canonical mRNA. A residual amount of CYP2C19 protein was detectable by quantitative proteomics with tandem mass spectrometry in CYP2C19*2/*2 and *1/*35 liver microsomes with an exon 2 probe. However, an exon 4 probe, downstream from rs12769205, but upstream of rs4244285, failed to detect CYP2C19 protein in livers homozygous for rs12769205, demonstrating rs12769205 alone can lead to complete loss of CYP2C19 protein. CYP2C19 genotypes and mephenytoin phenotype were compared in 104 Ethiopians. Poor metabolism of mephenytoin was seen in persons homozygous for both rs12769205 and rs4244285 (CYP2C19*2/*2), but with little effect on mephenytoin disposition of CYP2C19*1/*2, CYP2C19*1/*3, or CYP2C19*1/*35 heterozygous alleles. Extended haplotype homozygosity tests of the HapMap Yorubans (YRI) showed both haplotypes carrying rs12769205 (CYP2C19*35 and CYP2C19*2) are under significant natural selection, with CYP2C19*35 having a higher relative extended haplotype homozygosity score. The phylogenetic tree of the YRI CYP2C19 haplotypes revealed rs12769205 arose first on CYP2C19*35 and that rs4244285 was added later, creating CYP2C19*2. In conclusion, rs12769205 is the ancestral polymorphism leading to aberrant splicing of CYP2C19*35 and CYP2C19*2 alleles in liver.
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Affiliation(s)
- Amarjit S Chaudhry
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Yoshiyuki Shirasaka
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Alison Fohner
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - David Finkelstein
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Yiping Fan
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Shuoguo Wang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Gang Wu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Eleni Aklillu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Sarah C Sim
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Kenneth E Thummel
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
| | - Erin G Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee (A.S.C., E.G.S.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (B.P., Y.S., A.F., K.E.T.); Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee (D.F., Y.F., S.W., G.W.); Department of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden (E.A.); and Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.C.S.)
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Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 2015; 348:666-9. [PMID: 25954003 PMCID: PMC4537935 DOI: 10.1126/science.1261877] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Accurate prediction of the functional effect of genetic variation is critical for clinical genome interpretation. We systematically characterized the transcriptome effects of protein-truncating variants, a class of variants expected to have profound effects on gene function, using data from the Genotype-Tissue Expression (GTEx) and Geuvadis projects. We quantitated tissue-specific and positional effects on nonsense-mediated transcript decay and present an improved predictive model for this decay. We directly measured the effect of variants both proximal and distal to splice junctions. Furthermore, we found that robustness to heterozygous gene inactivation is not due to dosage compensation. Our results illustrate the value of transcriptome data in the functional interpretation of genetic variants.
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Affiliation(s)
- Manuel A Rivas
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
| | - Matti Pirinen
- FInstitute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Monkol Lek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Emily K Tsang
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA. Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Julian B Maller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kimberly R Kukurba
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Menachem Fromer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. Department of Psychiatry, Mt. Sinai Hospital, NY, USA
| | - Pedro G Ferreira
- Department of Genetic Medicine and Development,University of Geneva, Geneva, Switzerland. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland. Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Kevin S Smith
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rui Zhang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Fengmei Zhao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Banks
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan Poplin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Douglas M Ruderfer
- Department of Psychiatry, Mt. Sinai Hospital, NY, USA. Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Shaun M Purcell
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. Department of Psychiatry, Mt. Sinai Hospital, NY, USA. Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Taru Tukiainen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric V Minikel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | | | | | - Jared Nedzel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Roderic Guigo
- Center for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. Department of Statistics, University of Oxford, Oxford, UK
| | | | - Michael Sammeth
- Center for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain. National Institute for Scientific Computing (LNCC), Petropolis, Rio de Janeiro, Brazil
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development,University of Geneva, Geneva, Switzerland. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland. Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA
| | - Tuuli Lappalainen
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Genetic Medicine and Development,University of Geneva, Geneva, Switzerland. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland. Swiss Institute of Bioinformatics, Geneva, Switzerland. New York Genome Center, New York, NY, USA. Department of Systems Biology, Columbia University, New York, NY, USA.
| | - Daniel G MacArthur
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. Department of Medicine, Harvard Medical School, Boston, MA, USA.
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139
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Kralovicova J, Knut M, Cross NCP, Vorechovsky I. Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins. Nucleic Acids Res 2015; 43:3747-63. [PMID: 25779042 PMCID: PMC4402522 DOI: 10.1093/nar/gkv194] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 02/24/2015] [Indexed: 01/05/2023] Open
Abstract
The auxiliary factor of U2 small nuclear RNA (U2AF) is a heterodimer consisting of 65- and 35-kD proteins that bind the polypyrimidine tract (PPT) and AG dinucleotides at the 3′ splice site (3′ss). The gene encoding U2AF35 (U2AF1) is alternatively spliced, giving rise to two isoforms U2AF35a and U2AF35b. Here, we knocked down U2AF35 and each isoform and characterized transcriptomes of HEK293 cells with varying U2AF35/U2AF65 and U2AF35a/b ratios. Depletion of both isoforms preferentially modified alternative RNA processing events without widespread failure to recognize 3′ss or constitutive exons. Over a third of differentially used exons were terminal, resulting largely from the use of known alternative polyadenylation (APA) sites. Intronic APA sites activated in depleted cultures were mostly proximal whereas tandem 3′UTR APA was biased toward distal sites. Exons upregulated in depleted cells were preceded by longer AG exclusion zones and PPTs than downregulated or control exons and were largely activated by PUF60 and repressed by CAPERα. The U2AF(35) repression and activation was associated with a significant interchange in the average probabilities to form single-stranded RNA in the optimal PPT and branch site locations and sequences further upstream. Although most differentially used exons were responsive to both U2AF subunits and their inclusion correlated with U2AF levels, a small number of transcripts exhibited distinct responses to U2AF35a and U2AF35b, supporting the existence of isoform-specific interactions. These results provide new insights into function of U2AF and U2AF35 in alternative RNA processing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Marcin Knut
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Nicholas C P Cross
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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140
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DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, Jamieson CHM, Carson D, Kipps TJ, Frazer KA. Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PLoS Comput Biol 2015; 11:e1004105. [PMID: 25768983 PMCID: PMC4358997 DOI: 10.1371/journal.pcbi.1004105] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/29/2014] [Indexed: 01/12/2023] Open
Abstract
Mutations in the splicing factor SF3B1 are found in several cancer types and have been associated with various splicing defects. Using transcriptome sequencing data from chronic lymphocytic leukemia, breast cancer and uveal melanoma tumor samples, we show that hundreds of cryptic 3’ splice sites (3’SSs) are used in cancers with SF3B1 mutations. We define the necessary sequence context for the observed cryptic 3’ SSs and propose that cryptic 3’SS selection is a result of SF3B1 mutations causing a shift in the sterically protected region downstream of the branch point. While most cryptic 3’SSs are present at low frequency (<10%) relative to nearby canonical 3’SSs, we identified ten genes that preferred out-of-frame cryptic 3’SSs. We show that cancers with mutations in the SF3B1 HEAT 5-9 repeats use cryptic 3’SSs downstream of the branch point and provide both a mechanistic model consistent with published experimental data and affected targets that will guide further research into the oncogenic effects of SF3B1 mutation. A key goal of cancer genomics studies is to identify genes that are recurrently mutated at a rate above background and likely contribute to cancer development. Many such recurrently mutated genes have been identified over the last few years, but we often do not know the underlying mechanisms by which they contribute to cancer growth. Unexpectedly, several genes in the spliceosome, the collection of RNAs and proteins that remove introns from transcribed RNAs, are recurrently mutated in different cancers. Here, we have examined mutations in the splicing factor SF3B1, a key component of the spliceosome, and identified a global splicing defect present in different cancers with SF3B1 mutations by comparing the expression of splice junctions using generalized linear models. While prior studies have reported a limited number of aberrant splicing events in SF3B1-mutated cancers, we have established that SF3B1 mutations are associated with usage of hundreds of atypical splice sites at the 3’ end of the intron. We have identified nucleotide sequence requirements for these cryptic splice sites that are consistent with a proposed mechanistic model. These findings greatly expand our understanding of the effect of SF3B1 mutations on splicing and provide new targets for determining the oncogenic effect of SF3B1 mutations.
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Affiliation(s)
- Christopher DeBoever
- Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California, United States of America
| | - Emanuela M. Ghia
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Peter J. Shepard
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, California, United States of America
| | - Laura Rassenti
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Christian L. Barrett
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Catriona H. M. Jamieson
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Dennis Carson
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Kelly A. Frazer
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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141
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Zhang X, Joehanes R, Chen BH, Huan T, Ying S, Munson PJ, Johnson AD, Levy D, O'Donnell CJ. Identification of common genetic variants controlling transcript isoform variation in human whole blood. Nat Genet 2015; 47:345-52. [PMID: 25685889 DOI: 10.1038/ng.3220] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 01/20/2015] [Indexed: 12/17/2022]
Abstract
An understanding of the genetic variation underlying transcript splicing is essential to dissect the molecular mechanisms of common disease. The available evidence from splicing quantitative trait locus (sQTL) studies has been limited to small samples. We performed genome-wide screening to identify SNPs that might control mRNA splicing in whole blood collected from 5,257 Framingham Heart Study participants. We identified 572,333 cis sQTLs involving 2,650 unique genes. Many sQTL-associated genes (40%) undergo alternative splicing. Using the National Human Genome Research Institute (NHGRI) genome-wide association study (GWAS) catalog, we determined that 528 unique sQTLs were significantly enriched for 8,845 SNPs associated with traits in previous GWAS. In particular, we found 395 (4.5%) GWAS SNPs with evidence of cis sQTLs but not gene-level cis expression quantitative trait loci (eQTLs), suggesting that sQTL analysis could provide additional insights into the functional mechanism underlying GWAS results. Our findings provide an informative sQTL resource for further characterizing the potential functional roles of SNPs that control transcript isoforms relevant to common diseases.
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Affiliation(s)
- Xiaoling Zhang
- 1] Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. [2] National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA
| | - Roby Joehanes
- 1] Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. [2] National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA. [3] Mathematical and Statistical Computing Laboratory, Center for Information Technology, US National Institutes of Health, Bethesda, Maryland, USA
| | - Brian H Chen
- 1] Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. [2] National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA
| | - Tianxiao Huan
- 1] Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. [2] National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA
| | - Saixia Ying
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, US National Institutes of Health, Bethesda, Maryland, USA
| | - Peter J Munson
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, US National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew D Johnson
- 1] Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. [2] National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA
| | - Daniel Levy
- 1] Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. [2] National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA
| | - Christopher J O'Donnell
- 1] Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. [2] National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA. [3] Division of Cardiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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142
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Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Genome-wide discovery of human splicing branchpoints. Genome Res 2015; 25:290-303. [PMID: 25561518 PMCID: PMC4315302 DOI: 10.1101/gr.182899.114] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During the splicing reaction, the 5′ intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3′ splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron–exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.
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Affiliation(s)
- Tim R Mercer
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Michael B Clark
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Stacey B Andersen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marion E Brunck
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; Illumina, Inc., San Diego, California 92122, USA; School of Medicine and Health Services, Department of Integrated Systems Biology and Department of Pediatrics, George Washington University, Washington DC 20037, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia;
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143
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Starke S, Jost I, Rossbach O, Schneider T, Schreiner S, Hung LH, Bindereif A. Exon circularization requires canonical splice signals. Cell Rep 2014; 10:103-11. [PMID: 25543144 DOI: 10.1016/j.celrep.2014.12.002] [Citation(s) in RCA: 567] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/30/2014] [Accepted: 11/28/2014] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs), an abundant class of noncoding RNAs in higher eukaryotes, are generated from pre-mRNAs by circularization of adjacent exons. Using a set of 15 circRNAs, we demonstrated their cell-type-specific expression and circular versus linear processing in mammalian cells. Northern blot analysis combined with RNase H cleavage conclusively proved a circular configuration for two examples, LPAR1 and HIPK3. To address the circularization mechanism, we analyzed the sequence requirements using minigenes derived from natural circRNAs. Both canonical splice sites are required for circularization, although they vary in flexibility and potential use of cryptic sites. Surprisingly, we found that no specific circRNA exon sequence is necessary and that potential flanking intron structures can modulate circularization efficiency. In combination with splice inhibitor assays, our results argue that the canonical spliceosomal machinery functions in circRNA biogenesis, constituting an alternative splicing mode.
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Affiliation(s)
- Stefan Starke
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Isabelle Jost
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Tim Schneider
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Silke Schreiner
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Albrecht Bindereif
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
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144
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Paronetto M, Bernardis I, Volpe E, Bechara E, Sebestyén E, Eyras E, Valcárcel J. Regulation of FAS Exon Definition and Apoptosis by the Ewing Sarcoma Protein. Cell Rep 2014; 7:1211-26. [DOI: 10.1016/j.celrep.2014.03.077] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 02/16/2014] [Accepted: 03/31/2014] [Indexed: 12/18/2022] Open
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145
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Li Q, Xiao G, Zhu YX. Single-nucleotide resolution mapping of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns. MOLECULAR PLANT 2014; 7:829-40. [PMID: 24398628 DOI: 10.1093/mp/sst175] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Alternative splicing (AS) is a vital genetic mechanism that enhances the diversity of eukaryotic transcriptomes. Here, we generated 8.3 Gb high-quality RNA-sequencing data from cotton (Gossypium raimondii) and performed a systematic, comparative analysis of AS events. We mapped 85% of the RNA-sequencing data onto the reference genome and identified 154368 splice junctions with 16437 as events in 10197 genes. Intron retention constituted the majority (40%) of all AS events in G. raimondii. Comparison across 11 eukaryote species showed that intron retention is the most common AS type in higher plants. Although transposable elements (TEs) were found in only 2.9% of all G. raimondii introns, they are present in 43% of the retained introns, suggesting that TE-insertion may be an important mechanism for intron retention during AS. The majority of the TE insertions are concentrated 0-40 nt upstream of the 3'-splice site, substantially altering the distribution of branch points from preferred positions and reducing the efficiency of intron splicing by decreasing RNA secondary structure flexibility. Our data suggest that TE-insertion-induced changes in branch point-site distribution are important for intron retention-type AS. Our findings may help explain the vast differences in intron-retention frequencies between vertebrates and higher plants.
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Affiliation(s)
- Qin Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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146
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Abstract
How do cis and trans elements involved in pre-mRNA splicing come together to form a splicing "code"? This question has been a driver of much of the research involving RNA biogenesis. The variability of splicing outcome across developmental stages and between tissues coupled with association of splicing defects with numerous diseases highlights the importance of such a code. However, the sheer number of elements involved in splicing regulation and the context-specific manner of their operation have made the derivation of such a code challenging. Recently, machine learning-based methods have been developed to infer computational models for a splicing code. These methods use high-throughput experiments measuring mRNA expression at exonic resolution and binding locations of RNA-binding proteins (RBPs) to infer what the regulatory elements that control the inclusion of a given pre-mRNA segment are. The inferred regulatory models can then be applied to genomic sequences or experimental conditions that have not been measured to predict splicing outcome. Moreover, the models themselves can be interrogated to identify new regulatory mechanisms, which can be subsequently tested experimentally. In this chapter, we survey the current state of this technology, and illustrate how it can be applied by non-computational or RNA splicing experts to study regulation of specific exons by using the AVISPA web tool.
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147
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Gazzara MR, Vaquero-Garcia J, Lynch KW, Barash Y. In silico to in vivo splicing analysis using splicing code models. Methods 2013; 67:3-12. [PMID: 24321485 DOI: 10.1016/j.ymeth.2013.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 02/03/2023] Open
Abstract
With the growing appreciation of RNA splicing's role in gene regulation, development, and disease, researchers from diverse fields find themselves investigating exons of interest. Commonly, researchers are interested in knowing if an exon is alternatively spliced, if it is differentially included in specific tissues or in developmental stages, and what regulatory elements control its inclusion. An important step towards the ability to perform such analysis in silico was made with the development of computational splicing code models. Aimed as a practical how-to guide, we demonstrate how researchers can now use these code models to analyze a gene of interest, focusing on Bin1 as a case study. Bridging integrator 1 (BIN1) is a nucleocytoplasmic adaptor protein known to be functionally regulated through alternative splicing in a tissue-specific manner. Specific Bin1 isoforms have been associated with muscular diseases and cancers, making the study of its splicing regulation of wide interest. Using AVISPA, a recently released web tool based on splicing code models, we show that many Bin1 tissue-dependent isoforms are correctly predicted, along with many of its known regulators. We review the best practices and constraints of using the tool, demonstrate how AVISPA is used to generate high confidence novel regulatory hypotheses, and experimentally validate predicted regulators of Bin1 alternative splicing.
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Affiliation(s)
- Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jorge Vaquero-Garcia
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Kannan R, Hartnett S, Voelker RB, Berglund JA, Staley JP, Baumann P. Intronic sequence elements impede exon ligation and trigger a discard pathway that yields functional telomerase RNA in fission yeast. Genes Dev 2013; 27:627-38. [PMID: 23468430 DOI: 10.1101/gad.212738.112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The fission yeast telomerase RNA (TER1) precursor harbors an intron immediately downstream from its mature 3' end. Unlike most introns, which are removed from precursor RNAs by the spliceosome in two sequential but tightly coupled transesterification reactions, TER1 only undergoes the first cleavage reaction during telomerase RNA maturation. The mechanism underlying spliceosome-mediated 3' end processing has remained unclear. We now demonstrate that a strong branch site (BS), a long distance to the 3' splice site (3' SS), and a weak polypyrimidine (Py) tract act synergistically to attenuate the transition from the first to the second step of splicing. The observation that a strong BS antagonizes the second step of splicing in the context of TER1 suggests that the BS-U2 snRNA interaction is disrupted after the first step and thus much earlier than previously thought. The slow transition from first to second step triggers the Prp22 DExD/H-box helicase-dependent rejection of the cleaved products and Prp43-dependent "discard" of the splicing intermediates. Our findings explain how the spliceosome can function in 3' end processing and provide new insights into the mechanism of splicing.
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Affiliation(s)
- Ram Kannan
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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149
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Popović M, Nelson JD, Schroeder KT, Greenbaum NL. Impact of base pair identity 5' to the spliceosomal branch site adenosine on branch site conformation. RNA (NEW YORK, N.Y.) 2012; 18:2093-2103. [PMID: 23002123 PMCID: PMC3479398 DOI: 10.1261/rna.035782.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
The branch site helix from Saccharomyces cerevisiae with pseudouridine (ψ) incorporated in a phylogenetically conserved position of U2 snRNA features an extrahelical branch site adenosine (A) that forms a base triple interaction with the minor groove edge of a widely conserved purine(U2 strand)-pyrimidine(intron strand) (R(U2)-Y(intron)) base pair two positions upstream. In these studies, NMR spectra of a duplex in which 2-aminopurine (2ap), a fluorescent analog of adenine lacking the proposed hydrogen bond donor, was substituted for the branch site A, indicated that the substitution does not alter the extrahelical position of the branch site residue; thus, it appears that a hydrogen bond between the adenine amino group and the R-Y pair is not obligatory for stabilization of the extrahelical conformation. In contrast, reversal of the orientation of A(U2)-U(intron) to U(U2)-A(intron) resulted in an intrahelical position for the branch site A or 2ap. Fluorescence intensity of 2ap substituted for the branch site A with the original R(U2)-Y(intron) orientation (AU or GC) was high, consistent with an extrahelical position, whereas fluorescence in helices with the reversed R-Y orientation, or with a mismatched pair (A-U → G•A or U•C), was markedly quenched, implying that the residue was stacked in the helix. The A 5' to the branch site residue was not extrahelical in any of the duplexes. These findings suggest that the R(U2)-Y(intron) base pair orientation in the ψ-dependent branch site helix plays an important role in positioning the branch site A for recognition and/or function.
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Affiliation(s)
- Milena Popović
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, USA
| | - Joycelynn D. Nelson
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, USA
| | - Kersten T. Schroeder
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, USA
| | - Nancy L. Greenbaum
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- The Graduate Center, City University of New York, New York, New York 10016, USA
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150
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Änkö ML, Müller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol 2012; 13:R17. [PMID: 22436691 PMCID: PMC3439968 DOI: 10.1186/gb-2012-13-3-r17] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 01/03/2023] Open
Abstract
Background The SR proteins comprise a family of essential, structurally related RNA binding proteins. The complexity of their RNA targets and specificity of RNA recognition in vivo is not well understood. Here we use iCLIP to globally analyze and compare the RNA binding properties of two SR proteins, SRSF3 and SRSF4, in murine cells. Results SRSF3 and SRSF4 binding sites mapped to largely non-overlapping target genes, and in vivo consensus binding motifs were distinct. Interactions with intronless and intron-containing mRNAs as well as non-coding RNAs were detected. Surprisingly, both SR proteins bound to the 3' ends of the majority of intronless histone transcripts, implicating SRSF3 and SRSF4 in histone mRNA metabolism. In contrast, SRSF3 but not SRSF4 specifically bound transcripts encoding numerous RNA binding proteins. Remarkably, SRSF3 was shown to modulate alternative splicing of its own as well as three other transcripts encoding SR proteins. These SRSF3-mediated splicing events led to downregulation of heterologous SR proteins via nonsense-mediated decay. Conclusions SRSF3 and SRSF4 display unique RNA binding properties underlying diverse cellular regulatory mechanisms, with shared as well as unique coding and non-coding targets. Importantly, CLIP analysis led to the discovery that SRSF3 cross-regulates the expression of other SR protein family members.
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Affiliation(s)
- Minna-Liisa Änkö
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany.
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