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Tress ML, Abascal F, Valencia A. Alternative Splicing May Not Be the Key to Proteome Complexity. Trends Biochem Sci 2016; 42:98-110. [PMID: 27712956 DOI: 10.1016/j.tibs.2016.08.008] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/19/2016] [Accepted: 08/15/2016] [Indexed: 12/21/2022]
Abstract
Alternative splicing is commonly believed to be a major source of cellular protein diversity. However, although many thousands of alternatively spliced transcripts are routinely detected in RNA-seq studies, reliable large-scale mass spectrometry-based proteomics analyses identify only a small fraction of annotated alternative isoforms. The clearest finding from proteomics experiments is that most human genes have a single main protein isoform, while those alternative isoforms that are identified tend to be the most biologically plausible: those with the most cross-species conservation and those that do not compromise functional domains. Indeed, most alternative exons do not seem to be under selective pressure, suggesting that a large majority of predicted alternative transcripts may not even be translated into proteins.
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Affiliation(s)
- Michael L Tress
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Federico Abascal
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain; Human Genetics Department, Sandhu Group, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alfonso Valencia
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain; National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain.
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52
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Hartley SW, Mullikin JC, Klein DC, Park M, Coon SL. Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation. PLoS One 2016; 11:e0163590. [PMID: 27684375 PMCID: PMC5042479 DOI: 10.1371/journal.pone.0163590] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/12/2016] [Indexed: 01/23/2023] Open
Abstract
Alternative isoform regulation (AIR) vastly increases transcriptome diversity and plays an important role in numerous biological processes and pathologies. However, the detection and analysis of isoform-level differential regulation is difficult, particularly in the face of complex and incompletely-annotated transcriptomes. Here we have used Illumina short-read/high-throughput RNA-Seq to identify 55 genes that exhibit neurally-regulated AIR in the pineal gland, and then used two other complementary experimental platforms to further study and characterize the Ttc8 gene, which is involved in Bardet-Biedl syndrome and non-syndromic retinitis pigmentosa. Use of the JunctionSeq analysis tool led to the detection of several novel exons and splice junctions in this gene, including two novel alternative transcription start sites which were found to display disproportionately strong neurally-regulated differential expression in several independent experiments. These high-throughput sequencing results were validated and augmented via targeted qPCR and long-read Pacific Biosciences SMRT sequencing. We confirmed the existence of numerous novel splice junctions and the selective upregulation of the two novel start sites. In addition, we identified more than 20 novel isoforms of the Ttc8 gene that are co-expressed in this tissue. By using information from multiple independent platforms we not only greatly reduce the risk of errors, biases, and artifacts influencing our results, we also are able to characterize the regulation and splicing of the Ttc8 gene more deeply and more precisely than would be possible via any single platform. The hybrid method outlined here represents a powerful strategy in the study of the transcriptome.
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Affiliation(s)
- Stephen W. Hartley
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail:
| | - James C. Mullikin
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - David C. Klein
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Morgan Park
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, 20852, United States of America
| | - NISC Comparative Sequencing Program
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, 20852, United States of America
| | - Steven L. Coon
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
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53
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Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol 2016; 34:1287-1291. [PMID: 27669167 PMCID: PMC5143225 DOI: 10.1038/nbt.3682] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 08/22/2016] [Indexed: 11/17/2022]
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Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AMP, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A. Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res 2016; 44:D746-52. [PMID: 26481351 PMCID: PMC4702781 DOI: 10.1093/nar/gkv1045] [Citation(s) in RCA: 396] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 09/25/2015] [Accepted: 09/29/2015] [Indexed: 11/12/2022] Open
Abstract
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.
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Affiliation(s)
- Robert Petryszak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Maria Keays
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Y Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Nuno A Fonseca
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Elisabet Barrera
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | - Simon Jupp
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Satu Koskinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Oliver Mannion
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Laura Huerta
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Karine Megy
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Catherine Snow
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Eleanor Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Mitra Barzine
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | | | | | - Wolfgang Huber
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | - Helen E Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
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Roux J, Rosikiewicz M, Robinson-Rechavi M. What to compare and how: Comparative transcriptomics for Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:372-82. [PMID: 25864439 PMCID: PMC4949521 DOI: 10.1002/jez.b.22618] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/19/2015] [Indexed: 12/30/2022]
Abstract
Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372–382, 2015. © 2015 The Authors. J. Exp. Zool. (Mol. Dev. Evol.) published by Wiley Periodicals, Inc.
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Affiliation(s)
- Julien Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Marta Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Liu R, Loraine AE, Dickerson JA. Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. BMC Bioinformatics 2014; 15:364. [PMID: 25511303 PMCID: PMC4271460 DOI: 10.1186/s12859-014-0364-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 10/29/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Alternative Splicing (AS) as a post-transcription regulation mechanism is an important application of RNA-seq studies in eukaryotes. A number of software and computational methods have been developed for detecting AS. Most of the methods, however, are designed and tested on animal data, such as human and mouse. Plants genes differ from those of animals in many ways, e.g., the average intron size and preferred AS types. These differences may require different computational approaches and raise questions about their effectiveness on plant data. The goal of this paper is to benchmark existing computational differential splicing (or transcription) detection methods so that biologists can choose the most suitable tools to accomplish their goals. RESULTS This study compares the eight popular public available software packages for differential splicing analysis using both simulated and real Arabidopsis thaliana RNA-seq data. All software are freely available. The study examines the effect of varying AS ratio, read depth, dispersion pattern, AS types, sample sizes and the influence of annotation. Using a real data, the study looks at the consistences between the packages and verifies a subset of the detected AS events using PCR studies. CONCLUSIONS No single method performs the best in all situations. The accuracy of annotation has a major impact on which method should be chosen for AS analysis. DEXSeq performs well in the simulated data when the AS signal is relative strong and annotation is accurate. Cufflinks achieve a better tradeoff between precision and recall and turns out to be the best one when incomplete annotation is provided. Some methods perform inconsistently for different AS types. Complex AS events that combine several simple AS events impose problems for most methods, especially for MATS. MATS stands out in the analysis of real RNA-seq data when all the AS events being evaluated are simple AS events.
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Affiliation(s)
- Ruolin Liu
- Department of Electrical and Computational Engineering, Iowa State University, Howe Hall, Ames, 50011-3060, USA.
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, 600 Laureate Way, Kannapolis, 28081, NC, USA.
| | - Julie A Dickerson
- Department of Electrical and Computational Engineering, Iowa State University, Howe Hall, Ames, 50011-3060, USA.
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