1
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Steward RA, de Jong MA, Oostra V, Wheat CW. Alternative splicing in seasonal plasticity and the potential for adaptation to environmental change. Nat Commun 2022; 13:755. [PMID: 35136048 PMCID: PMC8825856 DOI: 10.1038/s41467-022-28306-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022] Open
Abstract
Seasonal plasticity is accomplished via tightly regulated developmental cascades that translate environmental cues into trait changes. Little is known about how alternative splicing and other posttranscriptional molecular mechanisms contribute to plasticity or how these mechanisms impact how plasticity evolves. Here, we use transcriptomic and genomic data from the butterfly Bicyclus anynana, a model system for seasonal plasticity, to compare the extent of differential expression and splicing and test how these axes of transcriptional plasticity differ in their potential for evolutionary change. Between seasonal morphs, we find that differential splicing affects a smaller but functionally unique set of genes compared to differential expression. Further, we find strong support for the novel hypothesis that spliced genes are more susceptible than differentially expressed genes to erosion of genetic variation due to selection on seasonal plasticity. Our results suggest that splicing plasticity is especially likely to experience genetic constraints that could affect the potential of wild populations to respond to rapidly changing environments.
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Affiliation(s)
| | | | - Vicencio Oostra
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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2
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Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes. Int J Mol Sci 2019; 20:ijms20153834. [PMID: 31390737 PMCID: PMC6695735 DOI: 10.3390/ijms20153834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.
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3
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Xiong J, Jiang X, Ditsiou A, Gao Y, Sun J, Lowenstein ED, Huang S, Khaitovich P. Predominant patterns of splicing evolution on human, chimpanzee and macaque evolutionary lineages. Hum Mol Genet 2019; 27:1474-1485. [PMID: 29452398 DOI: 10.1093/hmg/ddy058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/12/2018] [Indexed: 11/14/2022] Open
Abstract
Although splicing is widespread and evolves rapidly among species, the mechanisms driving this evolution, as well as its functional implications, are not yet fully understood. We analyzed the evolution of splicing patterns based on transcriptome data from five tissues of humans, chimpanzees, rhesus macaques and mice. In total, 1526 exons and exon sets from 1236 genes showed significant splicing differences among primates. More than 60% of these differences represent constitutive-to-alternative exon transitions while an additional 25% represent changes in exon inclusion frequency. These two dominant evolutionary patterns have contrasting conservation, regulation and functional features. The sum of these features indicates that, despite their prevalence, constitutive-to-alternative exon transitions do not substantially contribute to long-term functional transcriptome changes. Conversely, changes in exon inclusion frequency appear to be functionally relevant, especially for changes taking place in the brain on the human evolutionary lineage.
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Affiliation(s)
- Jieyi Xiong
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Xi Jiang
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Angeliki Ditsiou
- JBC/WTB Biocentre, University of Dundee, DD1 5EH Scotland, UK.,JMS Building, University of Sussex, BN1 9QG Brighton, UK
| | - Yang Gao
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Jing Sun
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Elijah D Lowenstein
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Freie Universität Berlin, 14195 Berlin, Germany
| | - Shuyun Huang
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia.,Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
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4
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Tranchevent LC, Aubé F, Dulaurier L, Benoit-Pilven C, Rey A, Poret A, Chautard E, Mortada H, Desmet FO, Chakrama FZ, Moreno-Garcia MA, Goillot E, Janczarski S, Mortreux F, Bourgeois CF, Auboeuf D. Identification of protein features encoded by alternative exons using Exon Ontology. Genome Res 2017; 27:1087-1097. [PMID: 28420690 PMCID: PMC5453322 DOI: 10.1101/gr.212696.116] [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: 07/13/2016] [Accepted: 03/28/2017] [Indexed: 12/16/2022]
Abstract
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information.
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Affiliation(s)
- Léon-Charles Tranchevent
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fabien Aubé
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Louis Dulaurier
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Clara Benoit-Pilven
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Amandine Rey
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Arnaud Poret
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Emilie Chautard
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, INRIA Erable, Villeurbanne, F-69622, France
| | - Hussein Mortada
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - François-Olivier Desmet
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fatima Zahra Chakrama
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Maira Alejandra Moreno-Garcia
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Evelyne Goillot
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, F-69007 France
| | - Stéphane Janczarski
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Franck Mortreux
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Didier Auboeuf
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
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5
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Morata J, Béjar S, Talavera D, Riera C, Lois S, de Xaxars GM, de la Cruz X. The relationship between gene isoform multiplicity, number of exons and protein divergence. PLoS One 2013; 8:e72742. [PMID: 24023641 PMCID: PMC3758341 DOI: 10.1371/journal.pone.0072742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/14/2013] [Indexed: 11/18/2022] Open
Abstract
At present we know that phenotypic differences between organisms arise from a variety of sources, like protein sequence divergence, regulatory sequence divergence, alternative splicing, etc. However, we do not have yet a complete view of how these sources are related. Here we address this problem, studying the relationship between protein divergence and the ability of genes to express multiple isoforms. We used three genome-wide datasets of human-mouse orthologs to study the relationship between isoform multiplicity co-occurrence between orthologs (the fact that two orthologs have more than one isoform) and protein divergence. In all cases our results showed that there was a monotonic dependence between these two properties. We could explain this relationship in terms of a more fundamental one, between exon number of the largest isoform and protein divergence. We found that this last relationship was present, although with variations, in other species (chimpanzee, cow, rat, chicken, zebrafish and fruit fly). In summary, we have identified a relationship between protein divergence and isoform multiplicity co-occurrence and explained its origin in terms of a simple gene-level property. Finally, we discuss the biological implications of these findings for our understanding of inter-species phenotypic differences.
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Affiliation(s)
- Jordi Morata
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB)-Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Santi Béjar
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB)-Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - David Talavera
- Faculty of Life Sciences, Manchester University, Manchester, United Kingdom
| | - Casandra Riera
- Laboratory of Translational Bioinformatics in Neuroscience, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
| | - Sergio Lois
- Laboratory of Translational Bioinformatics in Neuroscience, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
| | - Gemma Mas de Xaxars
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB)-Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
- Laboratory of Translational Bioinformatics in Neuroscience, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail:
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6
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Choi SS, Hannenhalli S. Three independent determinants of protein evolutionary rate. J Mol Evol 2013; 76:98-111. [PMID: 23400388 DOI: 10.1007/s00239-013-9543-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/16/2013] [Indexed: 12/15/2022]
Abstract
One of the most widely accepted ideas related to the evolutionary rates of proteins is that functionally important residues or regions evolve slower than other regions, a reasonable outcome of which should be a slower evolutionary rate of the proteins with a higher density of functionally important sites. Oddly, the role of functional importance, mainly measured by essentiality, in determining evolutionary rate has been challenged in recent studies. Several variables other than protein essentiality, such as expression level, gene compactness, protein-protein interactions, etc., have been suggested to affect protein evolutionary rate. In the present review, we try to refine the concept of functional importance of a gene, and consider three factors-functional importance, expression level, and gene compactness, as independent determinants of evolutionary rate of a protein, based not only on their known correlation with evolutionary rate but also on a reasonable mechanistic model. We suggest a framework based on these mechanistic models to correctly interpret the correlations between evolutionary rates and the various variables as well as the interrelationships among the variables.
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Affiliation(s)
- Sun Shim Choi
- Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, South Korea.
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7
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Lawson CB, Niino T, Hermansen RA, Brok-Volchanskaya V, Jackson MF, Garikipati DK, Liberles DA, Rodgers BD. The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate. BMC Evol Biol 2012; 12:202. [PMID: 23043301 PMCID: PMC3557186 DOI: 10.1186/1471-2148-12-202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most fishes possess two paralogs for myostatin, a muscle growth inhibitor, while salmonids are presumed to have four: mstn1a, mstn1b, mstn2a and mstn2b, a pseudogene. The mechanisms responsible for preserving these duplicates as well as the depth of mstn2b nonfunctionalization within the family remain unknown. We therefore characterized several genomic clones in order to better define species and gene phylogenies. RESULTS Gene organization and sequence conservation was particularly evident among paralog groupings and within salmonid subfamilies. All mstn2b sequences included in-frame stop codons, confirming its nonfunctionalization across taxa, although the indels and polymorphisms responsible often differed. For example, the specific indels within the Onchorhynchus tshawytscha and O. nerka genes were remarkably similar and differed equally from other mstn2b orthologs. A phylogenetic analysis weakly established a mstn2b clade including only these species, which coupled with a shared 51 base pair deletion might suggest a history involving hybridization or a shared phylogenetic history. Furthermore, mstn2 introns all lacked conserved splice site motifs, suggesting that the tissue-specific processing of mstn2a transcripts, but not those of mstn2b, is due to alternative cis regulation and is likely a common feature in salmonids. It also suggests that limited transcript processing may have contributed to mstn2b nonfunctionalization. CONCLUSIONS Previous studies revealed divergence within gene promoters while the current studies provide evidence for relaxed or positive selection in some coding sequence lineages. These results together suggest that the salmonid myostatin gene family is a novel resource for investigating mechanisms that regulate duplicate gene fate as paralog specific differences in gene expression, transcript processing and protein structure are all suggestive of active divergence.
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Affiliation(s)
- Casey B Lawson
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
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8
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Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis. Hum Genet 2011; 131:87-97. [PMID: 21735172 PMCID: PMC7088416 DOI: 10.1007/s00439-011-1053-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 06/21/2011] [Indexed: 01/17/2023]
Abstract
Contrasting results have been reported concerning the association of a splice-site polymorphism (rs10774671) in OAS1 with multiple sclerosis (MS). We analysed two OAS1 regions encompassing alternatively spliced exons. While the region carrying the splice-site variant is neutrally evolving, a signature of long-standing balancing selection was observed across an alternative exon 7. Analysis of variants in this exon identified an insertion/deletion polymorphism (rs11352835, A/−) that originates predicted products with distinct C termini. This variant is located along the major branch of the haplotype genealogy, suggesting that it may represent the selection target. A case/control study for MS indicated that rs11352835 is associated with disease susceptibility (for an allelic model with the deleted allele predisposing to MS, OR 1.27, 95% CI 1.072–1.513, p = 0.010). No association was found between rs10774671 and MS. As the two SNPs are in linkage disequilibrium in Europeans, the previously reported association between rs10774671 and MS susceptibility might be driven by rs11352835, possibly explaining the contrasting results previously observed for the splice-site polymorphism. Thus, we describe a novel susceptibility variant for MS in OAS1 and show that population genetic analyses can be instrumental to the identification of selection targets and, consequently, of functional polymorphisms with an effect on phenotypic traits.
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9
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Zago P, Buratti E, Stuani C, Baralle FE. Evolutionary connections between coding and splicing regulatory regions in the fibronectin EDA exon. J Mol Biol 2011; 411:1-15. [PMID: 21663748 DOI: 10.1016/j.jmb.2011.05.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/16/2011] [Accepted: 05/20/2011] [Indexed: 01/03/2023]
Abstract
Research on exonic coding sequences has demonstrated that many substitutions at the amino acid level may also reflect profound changes at the level of splicing regulatory regions. These results have revealed that, for many alternatively spliced exons, there is considerable pressure to strike a balance between two different and sometimes conflicting forces: the drive to improve the quality and production efficiency of proteins and the maintenance of proper exon recognition by the splicing machinery. Up to now, the systems used to investigate these connections have mostly focused on short alternatively spliced exons that contain a high density of splicing regulatory elements. Although this is obviously a desirable feature in order to maximize the chances of spotting connections, it also complicates the process of drawing straightforward evolutionary pathways between different species (because of the numerous alternative pathways through which the same end point can be achieved). The alternatively spliced fibronectin extra domain A exon (also referred to as EDI or EIIIA) does not have these limitations, as its inclusion is already known to depend on a single exonic splicing enhancer element within its sequence. In this study, we have compared the rat and human fibronectin EDA exons with regard to RNA structure, exonic splicing enhancer strengths, and SR protein occupancy. The results gained from these analyses have then been used to perform an accurate evaluation of EDA sequences observed in a wide range of animal species. This comparison strongly suggests the existence of an evolutionary connection between changes at the nucleotide levels and the need to maintain efficient EDA recognition in different species.
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Affiliation(s)
- Paola Zago
- International Center for Genetic Engineering and Biotechnology, Trieste, Italy
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10
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Igea J, Juste J, Castresana J. Novel intron markers to study the phylogeny of closely related mammalian species. BMC Evol Biol 2010; 10:369. [PMID: 21118501 PMCID: PMC3087552 DOI: 10.1186/1471-2148-10-369] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 11/30/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. RESULTS In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. CONCLUSIONS We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification and enough variability in most species, indicating that this marker set can be very helpful in multilocus phylogenetics of mammals. Due to the lower variability and stronger stochasticity of nuclear markers with respect to mitochondrial genes, studies should be designed to make use of several markers like the ones designed here.
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Affiliation(s)
- Javier Igea
- Institute of Evolutionary Biology (CSIC-UPF), Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Javier Juste
- Estacion Biologica de Donana (CSIC), Avda. Americo Vespucio s/n, 41092 Seville, Spain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-UPF), Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
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11
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Shimada MK, Hayakawa Y, Takeda JI, Gojobori T, Imanishi T. A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing. BMC Evol Biol 2010; 10:122. [PMID: 20433709 PMCID: PMC2882926 DOI: 10.1186/1471-2148-10-122] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 04/30/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) is a key molecular process that endows biological functions with diversity and complexity. Generally, functional redundancy leads to the generation of new functions through relaxation of selective pressure in evolution, as exemplified by duplicated genes. It is also known that alternatively spliced exons (ASEs) are subject to relaxed selective pressure. Within consensus sequences at the splice junctions, the most conserved sites are dinucleotides at both ends of introns (splice dinucleotides). However, a small number of single nucleotide polymorphisms (SNPs) occur at splice dinucleotides. An intriguing question relating to the evolution of AS diversity is whether mutations at splice dinucleotides are maintained as polymorphisms and produce diversity in splice patterns within the human population. We therefore surveyed validated SNPs in the database dbSNP located at splice dinucleotides of all human genes that are defined by the H-Invitational Database. RESULTS We found 212 validated SNPs at splice dinucleotides (sdSNPs); these were confirmed to be consistent with the GT-AG rule at either allele. Moreover, 53 of them were observed to neighbor ASEs (AE dinucleotides). No significant differences were observed between sdSNPs at AE dinucleotides and those at constitutive exons (CE dinucleotides) in SNP properties including average heterozygosity, SNP density, ratio of predicted alleles consistent with the GT-AG rule, and scores of splice sites formed with the predicted allele. We also found that the proportion of non-conserved exons was higher for exons with sdSNPs than for other exons. CONCLUSIONS sdSNPs are found at CE dinucleotides in addition to those at AE dinucleotides, suggesting two possibilities. First, sdSNPs at CE dinucleotides may be robust against sdSNPs because of unknown mechanisms. Second, similar to sdSNPs at AE dinucleotides, those at CE dinucleotides cause differences in AS patterns because of the arbitrariness in the classification of exons into alternative and constitutive type that varies according to the dataset. Taking into account the absence of differences in sdSNP properties between those at AE and CE dinucleotides, the increased proportion of non-conserved exons found in exons flanked by sdSNPs suggests the hypothesis that sdSNPs are maintained at the splice dinucleotides of newly generated exons at which negative selection pressure is relaxed.
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Affiliation(s)
- Makoto K Shimada
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-45 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Yosuke Hayakawa
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-45 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Hitachi Software Engineering Co., Ltd., 1-1-43 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jun-ichi Takeda
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-45 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Takashi Gojobori
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Tadashi Imanishi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo135-0064, Japan
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12
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Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010; 11:345-55. [DOI: 10.1038/nrg2776] [Citation(s) in RCA: 756] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Karambataki M, Malousi A, Maglaveras N, Kouidou S. Synonymous polymorphisms at splicing regulatory sites are associated with CpGs in neurodegenerative disease-related genes. Neuromolecular Med 2010; 12:260-9. [PMID: 20077034 DOI: 10.1007/s12017-009-8111-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 12/17/2009] [Indexed: 01/10/2023]
Abstract
Neuronal plasticity is associated with alternative splicing and epigenetic modulation. Recent evidence reveals the association of cytosine methylation with alternative splicing and splicing regulatory mechanisms. Single nucleotide polymorphisms (SNPs) are generally less frequent in conserved coding regions and probably in splice sites, compared to non-coding regions. CpG polymorphisms in coding regions and splice sites and their association with splicing regulatory elements have not been investigated till presently. We currently analyzed the CpG variability in 28 genes (361 constitutive and 105 alternative exons and the corresponding splice sites) associated with neurodegenerative diseases (ND). CpG polymorphisms in the splice sites of these genes are particularly frequent when compared to those at AG sequences. Moreover, in both constitutive and alternative exons, polymorphisms in CpGs are more frequent than in AG, GT sequences. On the contrary, in the polypyrimidine acceptor sequence C/T conservation is prominent indicating that in this locus the sequence of cytosines and thymines is preserved. Bioinformatic analysis of the splicing-associated regulatory elements in these exons and splice sites reveals that 18 out of a total of 39 SNPs which could strongly affect splicing (>1.5 score difference) contain CpG sequences. Cytosines are considerably more frequent and variable than expected at the position preceding the GT splice donors, while sites of epigenetic modification are absent from acceptors. The high CpG frequency in polymorphic splicing-associated sites implicates the involvement of epigenetic mechanisms in splicing selection decisions regulated by these sites, and indicates the complexity of genetic studies involving these, tentatively critical, polymorphisms in ND.
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Affiliation(s)
- Maria Karambataki
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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Lu H, Lin L, Sato S, Xing Y, Lee CJ. Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PLoS Comput Biol 2009; 5:e1000608. [PMID: 20019791 PMCID: PMC2784930 DOI: 10.1371/journal.pcbi.1000608] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 11/12/2009] [Indexed: 12/31/2022] Open
Abstract
High-throughput methods such as EST sequencing, microarrays and deep sequencing have identified large numbers of alternative splicing (AS) events, but studies have shown that only a subset of these may be functional. Here we report a sensitive bioinformatics approach that identifies exons with evidence of a strong RNA selection pressure ratio (RSPR)--i.e., evolutionary selection against mutations that change only the mRNA sequence while leaving the protein sequence unchanged--measured across an entire evolutionary family, which greatly amplifies its predictive power. Using the UCSC 28 vertebrate genome alignment, this approach correctly predicted half to three-quarters of AS exons that are known binding targets of the NOVA splicing regulatory factor, and predicted 345 strongly selected alternative splicing events in human, and 262 in mouse. These predictions were strongly validated by several experimental criteria of functional AS such as independent detection of the same AS event in other species, reading frame-preservation, and experimental evidence of tissue-specific regulation: 75% (15/20) of a sample of high-RSPR exons displayed tissue specific regulation in a panel of ten tissues, vs. only 20% (4/20) among a sample of low-RSPR exons. These data suggest that RSPR can identify exons with functionally important splicing regulation, and provides biologists with a dataset of over 600 such exons. We present several case studies, including both well-studied examples (GRIN1) and novel examples (EXOC7). These data also show that RSPR strongly outperforms other approaches such as standard sequence conservation (which fails to distinguish amino acid selection pressure from RNA selection pressure), or pairwise genome comparison (which lacks adequate statistical power for predicting individual exons).
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Affiliation(s)
- Hongchao Lu
- Molecular Biology Institute, Center for Computational Biology, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lan Lin
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Seiko Sato
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yi Xing
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
| | - Christopher J. Lee
- Molecular Biology Institute, Center for Computational Biology, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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15
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Corvelo A, Eyras E. Exon creation and establishment in human genes. Genome Biol 2009; 9:R141. [PMID: 18811936 PMCID: PMC2592719 DOI: 10.1186/gb-2008-9-9-r141] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 08/16/2008] [Accepted: 09/23/2008] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND A large proportion of species-specific exons are alternatively spliced. In primates, Alu elements play a crucial role in the process of exon creation but many new exons have appeared through other mechanisms. Despite many recent studies, it is still unclear which are the splicing regulatory requirements for de novo exonization and how splicing regulation changes throughout an exon's lifespan. RESULTS Using comparative genomics, we have defined sets of exons with different evolutionary ages. Younger exons have weaker splice-sites and lower absolute values for the relative abundance of putative splicing regulators between exonic and adjacent intronic regions, indicating a less consolidated splicing regulation. This relative abundance is shown to increase with exon age, leading to higher exon inclusion. We show that this local difference in the density of regulators might be of biological significance, as it outperforms other measures in real exon versus pseudo-exon classification. We apply this new measure to the specific case of the exonization of anti-sense Alu elements and show that they are characterized by a general lack of exonic splicing silencers. CONCLUSIONS Our results suggest that specific sequence environments are required for exonization and that these can change with time. We propose a model of exon creation and establishment in human genes, in which splicing decisions depend on the relative local abundance of regulatory motifs. Using this model, we provide further explanation as to why Alu elements serve as a major substrate for exon creation in primates. Finally, we discuss the benefits of integrating such information in gene prediction.
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Affiliation(s)
- André Corvelo
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
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16
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Irimia M, Rukov JL, Roy SW, Vinther J, Garcia-Fernandez J. Quantitative regulation of alternative splicing in evolution and development. Bioessays 2009; 31:40-50. [DOI: 10.1002/bies.080092] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Roy M, Kim N, Xing Y, Lee C. The effect of intron length on exon creation ratios during the evolution of mammalian genomes. RNA (NEW YORK, N.Y.) 2008; 14:2261-73. [PMID: 18796579 PMCID: PMC2578852 DOI: 10.1261/rna.1024908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Recent studies report that alternatively spliced exons tend to occur in longer introns, which is attributed to the length constraints for splice site pairing for the two major splicing mechanisms, intron definition versus exon definition. Using genome-wide studies of EST and microarray data from human and mouse, we have analyzed the distribution of various subsets of alternatively spliced exons, based on their inclusion level and evolutionary history, versus increasing intron length. Alternative exons may be included in either a major or minor fraction of all transcripts (known as major-form and minor-form exons, respectively). We find that major-form exons are seven- to eightfold more likely to be contained in short introns (<400 nt) than minor-form exons, which occur preferentially in longer introns. Since minor-form exons are more likely to be novel (approximately 75%), this implied that novel exons arise more frequently in longer introns. To test this hypothesis, we used whole genome alignments to classify exons according to their phylogenetic age. We find that older exons, i.e., exons that are conserved in all mammals, predominate at shorter intron lengths, for both major- and minor-form exons. In contrast, exons that arose recently during primate evolution are more prevalent at longer intron lengths (>1000 nt). This suggests that the observed correlation of longer intron lengths with alternatively spliced exons may be at least partly due to biases in the probability of exon creation, which is higher in long introns.
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Affiliation(s)
- Meenakshi Roy
- Molecular Biology Institute, University of California, Los Angeles, California 90024, USA
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18
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Lev-Maor G, Goren A, Sela N, Kim E, Keren H, Doron-Faigenboim A, Leibman-Barak S, Pupko T, Ast G. The "alternative" choice of constitutive exons throughout evolution. PLoS Genet 2008; 3:e203. [PMID: 18020709 PMCID: PMC2077895 DOI: 10.1371/journal.pgen.0030203] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Accepted: 10/01/2007] [Indexed: 12/23/2022] Open
Abstract
Alternative cassette exons are known to originate from two processes—exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons during evolution. We compiled a dataset of orthologous exons from human and mouse that are constitutively spliced in one species but alternatively spliced in the other. Examination of these exons suggests that the common ancestors were constitutively spliced. We show that relaxation of the 5′ splice site during evolution is one of the molecular mechanisms by which exons shift from constitutive to alternative splicing. This shift is associated with the fixation of exonic splicing regulatory sequences (ESRs) that are essential for exon definition and control the inclusion level only after the transition to alternative splicing. The effect of each ESR on splicing and the combinatorial effects between two ESRs are conserved from fish to human. Our results uncover an evolutionary pathway that increases transcriptome diversity by shifting exons from constitutive to alternative splicing. Alternative splicing is believed to play a major role in the creation of transcriptomic diversification leading to higher order of organismal complexity, especially in mammals. As much as 80% of human genes generate more than one type of mRNA by alternative splicing. Thus, alternative splicing can bridge the low number of protein coding genes (∼24,500) and the total number of proteins generated in the human proteome (∼90,000). The correlation between the higher order of phenotypic diversity and alternative splicing was recently demonstrated and thus the origin of alternative splicing is of great interest. There are currently two models regarding the origin of alternatively spliced exons—exonization of intronic sequences and exon shuffling. According to these two mechanisms, a protein-coding gene was first established and only then a new alternative exon appeared within it or was added to the gene. Our current study provides evidences for a new mechanism indicating that during evolution constitutively spliced exons became alternatively spliced. Large-scale bioinformatic analyses reveal the magnitude of this process and experimental validation systems provide insights into its mechanisms.
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Affiliation(s)
- Galit Lev-Maor
- Department of Human Molecular Genetics, Tel Aviv University, Tel Aviv, Israel
| | - Amir Goren
- Department of Human Molecular Genetics, Tel Aviv University, Tel Aviv, Israel
| | - Noa Sela
- Department of Human Molecular Genetics, Tel Aviv University, Tel Aviv, Israel
| | - Eddo Kim
- Department of Human Molecular Genetics, Tel Aviv University, Tel Aviv, Israel
| | - Hadas Keren
- Department of Human Molecular Genetics, Tel Aviv University, Tel Aviv, Israel
| | - Adi Doron-Faigenboim
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
| | | | - Tal Pupko
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Gil Ast
- Department of Human Molecular Genetics, Tel Aviv University, Tel Aviv, Israel
- * To whom correspondence should be addressed. E-mail:
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Peng T, Xue C, Bi J, Li T, Wang X, Zhang X, Li Y. Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse. BMC Genomics 2008; 9:191. [PMID: 18439302 PMCID: PMC2432081 DOI: 10.1186/1471-2164-9-191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 04/26/2008] [Indexed: 12/19/2022] Open
Abstract
Background Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments indicate that multiple cassette exons within a gene may interact with each other. This interaction can increase the potential to generate various transcripts and adds an extra layer of complexity to gene regulation. Several cases of exon interaction have been discovered. However, the extent to which the cassette exons coordinate with each other remains unknown. Results Based on EST data, we employed a metric of correlation coefficients to describe the interaction between two adjacent cassette exons and then categorized these exon pairs into three different groups by their interaction (correlation) patterns. Sequence analysis demonstrates that strongly-correlated groups are more conserved and contain a higher proportion of pairs with reading frame preservation in a combinatorial manner. Multiple genome comparison further indicates that different groups of correlated pairs have different evolutionary courses: (1) The vast majority of positively-correlated pairs are old, (2) most of the weakly-correlated pairs are relatively young, and (3) negatively-correlated pairs are a mixture of old and young events. Conclusion We performed a large-scale analysis of interactions between adjacent cassette exons. Compared with weakly-correlated pairs, the strongly-correlated pairs, including both the positively and negatively correlated ones, show more evidence that they are under delicate splicing control and tend to be functionally important. Additionally, the positively-correlated pairs bear strong resemblance to constitutive exons, which suggests that they may evolve from ancient constitutive exons, while negatively and weakly correlated pairs are more likely to contain newly emerging exons.
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Affiliation(s)
- Tao Peng
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, PRoC.
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20
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Chern TM, Paul N, van Nimwegen E, Zavolan M. Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA Res 2008; 15:63-72. [PMID: 18276623 PMCID: PMC2650624 DOI: 10.1093/dnares/dsm036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
High-throughput sequencing studies revealed that the majority of human and mouse multi-exon genes have multiple splice forms. High-density oligonucleotide array-based measurements have further established that many exons are expressed in a tissue-specific manner. The mechanisms underlying the tissue-dependent expression of most alternative exons remain, however, to be understood. In this study, we focus on one possible mechanism, namely the coupling of (tissue specific) transcription regulation with alternative splicing. We analyzed the FANTOM3 and H-Invitational datasets of full-length mouse and human cDNAs, respectively, and found that in transcription units with multiple start sites, the inclusion of at least 15% and possibly up to 30% of the ‘cassette’ exons correlates with the use of specific transcription start sites (TSS). The vast majority of TSS-associated exons are conserved between human and mouse, yet the conservation is weaker when compared with TSS-independent exons. Additionally, the currently available data only support a weak correlation between the probabilities of TSS association of orthologous exons. Our analysis thus suggests frequent coupling of transcriptional and splicing programs, and provides a large dataset of exons on which the molecular basis of this coupling can be further studied.
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Affiliation(s)
- Tzu-Ming Chern
- Division of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel CH-4056, Switzerland
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21
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Nurtdinov RN, Neverov AD, Favorov AV, Mironov AA, Gelfand MS. Conserved and species-specific alternative splicing in mammalian genomes. BMC Evol Biol 2007; 7:249. [PMID: 18154685 PMCID: PMC2231371 DOI: 10.1186/1471-2148-7-249] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 12/22/2007] [Indexed: 11/30/2022] Open
Abstract
Background Alternative splicing has been shown to be one of the major evolutionary mechanisms for protein diversification and proteome expansion, since a considerable fraction of alternative splicing events appears to be species- or lineage-specific. However, most studies were restricted to the analysis of cassette exons in pairs of genomes and did not analyze functionality of the alternative variants. Results We analyzed conservation of human alternative splice sites and cassette exons in the mouse and dog genomes. Alternative exons, especially minor-isofom ones, were shown to be less conserved than constitutive exons. Frame-shifting alternatives in the protein-coding regions are less conserved than frame-preserving ones. Similarly, the conservation of alternative sites is highest for evenly used alternatives, and higher when the distance between the sites is divisible by three. The rate of alternative-exon and site loss in mouse is slightly higher than in dog, consistent with faster evolution of the former. The evolutionary dynamics of alternative sites was shown to be consistent with the model of random activation of cryptic sites. Conclusion Consistent with other studies, our results show that minor cassette exons are less conserved than major-alternative and constitutive exons. However, our study provides evidence that this is caused not only by exon birth, but also lineage-specific loss of alternative exons and sites, and it depends on exon functionality.
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Affiliation(s)
- Ramil N Nurtdinov
- Faculty of Bioengineering and Bioinformatics, M,V, Lomonosov Moscow State University, Vorbyevy Gory 1-73, Moscow, 119992, Russia.
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Artamonova II, Gelfand MS. Comparative Genomics and Evolution of Alternative Splicing: The Pessimists' Science. Chem Rev 2007; 107:3407-30. [PMID: 17645315 DOI: 10.1021/cr068304c] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irena I Artamonova
- Group of Bioinformatics, Vavilov Institute of General Genetics, RAS, Gubkina 3, Moscow 119991, Russia
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23
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Parmley JL, Hurst LD. How common are intragene windows with KA > KS owing to purifying selection on synonymous mutations? J Mol Evol 2007; 64:646-55. [PMID: 17557167 DOI: 10.1007/s00239-006-0207-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 03/07/2007] [Indexed: 12/14/2022]
Abstract
One method for diagnosing the mode of sequence evolution considers the ratio of nonsynonymous substitutions per nonsynonymous site (K (A)) to the corresponding figure for synonymous substitutions (K (S)). A ratio (K (A)/K (S)) greater than unity is taken as evidence for positive selection. This, however, need not necessarily be the case. Notably, there is one instance of a high intragenic K (A)/K (S) peak, revealed by sliding window analysis and observed in two pairwise comparisons, better accounted for by localised purifying selection on synonymous mutations that affect splicing. Is this example exceptional? To address this we isolate intragenic domains with K (A)/K (S) > 1 from more than 1000 long mouse-rat orthologues. Approximately one K (A)/K (S) > 1 peak is found per 12-15 kb of coding sequence. Surprisingly, low synonymous substitution rates underpin more incidences than do high nonsynonymous rates. Several reasons, however, prevent us from supposing that the low synonymous rates reflect purifying selection on synonymous mutations. First, for many peaks, the null that the peak is no higher than expected given the underlying rates of evolution, cannot be rejected. Second, of 18 statistically significant incidences with unusually low K (S) values, only 3 are repeatable across independent comparisons. At least two of these are within alternatively spliced exons. We conclude that repeatable statistically significant intragenic domains of low intragenic K (S) are rare. As so few K (A)/K (S) peaks reflect increased rates of protein evolution and so few hold statistical support, we additionally conclude that sliding window analysis to infer domains of positive selection is highly error-prone.
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Affiliation(s)
- Joanna L Parmley
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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24
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Xing Y, Lee C. Relating alternative splicing to proteome complexity and genome evolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:36-49. [PMID: 18380339 DOI: 10.1007/978-0-387-77374-2_3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Prior to genomics, studies of alternative splicing primarily focused on the function and mechanism of alternative splicing in individual genes and exons. This has changed dramatically since the late 1990s. High-throughput genomics technologies, such as EST sequencing and microarrays designed to detect changes in splicing, led to genome-wide discoveries and quantification of alternative splicing in a wide range of species from human to Arabidopsis. Consensus estimates of AS frequency in the human genome grew from less than 5% in mid-1990s to as high as 60-74% now. The rapid growth in sequence and microarray data for alternative splicing has made it possible to look into the global impact of alternative splicing on protein function and evolution of genomes. In this chapter, we review recent research on alternative splicing's impact on proteomic complexity and its role in genome evolution.
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Affiliation(s)
- Yi Xing
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, USA
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