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Hujová P, Souček P, Radová L, Kramárek M, Kováčová T, Freiberger T. Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites. Cell Mol Life Sci 2021; 78:6979-6993. [PMID: 34596691 PMCID: PMC11072513 DOI: 10.1007/s00018-021-03943-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/31/2022]
Abstract
Among alternative splicing events in the human transcriptome, tandem NAGNAG acceptor splice sites represent an appreciable proportion. Both proximal and distal NAG can be used to produce two splicing isoforms differing by three nucleotides. In some cases, the upstream exon can be alternatively spliced as well, which further increases the number of possible transcripts. In this study, we showed that NAG choice in tandem splice site depends considerably not only on the concerned acceptor, but also on the upstream donor splice site sequence. Using an extensive set of experiments with systematically modified two-exonic minigene systems of AFAP1L2 or CSTD gene, we recognized the third and fifth intronic upstream donor splice site position and the tandem acceptor splice site region spanning from -10 to +2, including NAGNAG itself, as the main drivers. In addition, competition between different branch points and their composition were also shown to play a significant role in NAG choice. All these nucleotide effects appeared almost additive, which explained the high variability in proximal versus distal NAG usage.
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Affiliation(s)
- Pavla Hujová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic.
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic.
| | - Lenka Radová
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
| | - Tatiana Kováčová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
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2
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Zafrir Z, Zur H, Tuller T. Selection for reduced translation costs at the intronic 5' end in fungi. DNA Res 2016; 23:377-94. [PMID: 27260512 PMCID: PMC4991832 DOI: 10.1093/dnares/dsw019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/26/2016] [Indexed: 12/12/2022] Open
Abstract
It is generally believed that introns are not translated; therefore, the potential intronic features that may be related to the translation step (occurring after splicing) have yet to be thoroughly studied. Here, focusing on four fungi, we performed for the first time a comprehensive study aimed at characterizing how translation efficiency is encoded in introns and affects their evolution. By analysing their intronome we provide evidence of selection for STOP codons close to the intronic 5′ end, and show that the beginning of introns are selected for significantly high translation, presumably to reduce translation and metabolic costs in cases of non-spliced introns. Ribosomal profiling data analysis in Saccharomyces cerevisiae supports the conjecture that in this organism intron retention frequently occurs, introns are partially translated, and their translation efficiency affects organismal fitness. We show that the reported results are more significant in highly translated and highly spliced genes, but are not associated only with genes with a specific function. We also discuss the potential relation of the reported signals to efficient nonsense-mediated decay due to splicing errors. These new discoveries are supported by population-genetics considerations. In addition, they are contributory steps towards a broader understanding of intron evolution and the effect of silent mutations on gene expression and organismal fitness.
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Affiliation(s)
- Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Hadas Zur
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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3
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Szafranski K, Kramer M. It's a bit over, is that ok? The subtle surplus from tandem alternative splicing. RNA Biol 2015; 12:115-22. [PMID: 25826565 DOI: 10.1080/15476286.2015.1017210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tandem alternative splice sites (TASS) form a defined class of alternative splicing and give rise to mRNA insertion/deletion variants with only small size differences. Previous work has confirmed evolutionary conservation of TASS elements while many cases show only low tissue specificity of isoform ratios. We pinpoint stochasticity and noise as important methodological issues for the dissection of TASS isoform patterns. Resolving such uncertainties, a recent report showed regulation in a cell culture system, with shifts of alternative splicing isoform ratios dependent on cell density. This novel type of regulation affects not only multiple TASS isoforms, but also other alternative splicing classes, in a concerted manner. Here, we discuss how specific regulatory network architectures may be realized through the novel regulation type and highlight the role of differential isoform functions as a key step in order to better understand the functional role of TASS.
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Affiliation(s)
- Karol Szafranski
- a Fritz Lipmann Institute - Leibniz Institute on Aging ; Jena , Germany
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4
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Wang M, Zhang P, Shu Y, Yuan F, Zhang Y, Zhou Y, Jiang M, Zhu Y, Hu L, Kong X, Zhang Z. Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation. Nucleic Acids Res 2014; 42:13969-80. [PMID: 25428370 PMCID: PMC4267661 DOI: 10.1093/nar/gku1253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/29/2014] [Accepted: 11/12/2014] [Indexed: 12/28/2022] Open
Abstract
Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this issue, we studied the most common form of alternative 5' splice sites-GYNNGYs (Y = C/T), where both GYs can function as splice sites. Global analyses suggest that splicing noise (due to stochasticity of splicing process) can cause AS at GYNNGYs, evidenced by higher AS frequency in non-coding than in coding regions, in non-conserved than in conserved genes and in lowly expressed than in highly expressed genes. However, ∼20% AS GYNNGYs in humans and ∼3% in mice exhibit tissue-dependent regulation. Consistent with being functional, regulated GYNNGYs are more conserved than unregulated ones. And regulated GYNNGYs have distinctive sequence features which may confer regulation. Particularly, each regulated GYNNGY comprises two splice sites more resembling each other than unregulated GYNNGYs, and has more conserved downstream flanking intron. Intriguingly, most regulated GYNNGYs may tune gene expression through coupling with nonsense-mediated mRNA decay, rather than encode different proteins. In summary, AS at GYNNGY 5' splice sites is primarily splicing noise, and secondarily a way of regulation.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Peiwei Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yang Shu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Fei Yuan
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yuchao Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - You Zhou
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Min Jiang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yufei Zhu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Landian Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiangyin Kong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhenguo Zhang
- Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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Szafranski K, Fritsch C, Schumann F, Siebel L, Sinha R, Hampe J, Hiller M, Englert C, Huse K, Platzer M. Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons. Nucleic Acids Res 2014; 42:8895-904. [PMID: 25030907 PMCID: PMC4132704 DOI: 10.1093/nar/gku532] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Thousands of tandem alternative splice sites (TASS) give rise to mRNA insertion/deletion variants with small size differences. Recent work has concentrated on the question of biological relevance in general, and the physiological regulation of TASS in particular. We have quantitatively studied 11 representative TASS cases in comparison to one mutually exclusive exon case and two cassette exons (CEs) using a panel of human and mouse tissues, as well as cultured cell lines. Tissues show small but significant differences in TASS isoform ratios, with a variance 4- to 20-fold lower than seen for CEs. Remarkably, in cultured cells, all studied alternative splicing (AS) cases showed a cell-density-dependent shift of isoform ratios with similar time series profiles. A respective genome-wide co-regulation of TASS splicing was shown by next-generation mRNA sequencing data. Moreover, data from human and mouse organs indicate that this co-regulation of TASS occurs in vivo, with brain showing the strongest difference to other organs. Together, the results indicate a physiological AS regulation mechanism that functions almost independently from the splice site context and sequence.
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Affiliation(s)
- Karol Szafranski
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany
| | - Claudia Fritsch
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany Department of General Internal Medicine, Christian-Albrechts-University, Schittenhelmstrasse 12, 24105 Kiel, Germany
| | - Frank Schumann
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany Department of General Internal Medicine, Christian-Albrechts-University, Schittenhelmstrasse 12, 24105 Kiel, Germany
| | - Lisa Siebel
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany
| | - Rileen Sinha
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany
| | - Jochen Hampe
- Medical Department I, University Hospital, Technical University Dresden, Fetscherstr. 74, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics & Max Planck Institute for the Physics of Complex Systems, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Christoph Englert
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany
| | - Klaus Huse
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany
| | - Matthias Platzer
- Fritz Lipmann Institute-Institute for Age Research, Beutenbergstr. 11, 07745 Jena, Germany
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6
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A subtle alternative splicing event gives rise to a widely expressed human RNase k isoform. PLoS One 2014; 9:e96557. [PMID: 24797913 PMCID: PMC4010519 DOI: 10.1371/journal.pone.0096557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 04/09/2014] [Indexed: 12/30/2022] Open
Abstract
Subtle alternative splicing leads to the formation of RNA variants lacking or including a small number of nucleotides. To date, the impact of subtle alternative splicing phenomena on protein biosynthesis has been studied in frame-preserving incidents. On the contrary, mRNA isoforms derived from frame-shifting events were poorly studied and generally characterized as non-coding. This work provides evidence for a frame-shifting subtle alternative splicing event which results in the production of a novel protein isoform. We applied a combined molecular approach for the cloning and expression analysis of a human RNase κ transcript (RNase κ-02) which lacks four consecutive bases compared to the previously isolated RNase κ isoform. RNase κ-02 mRNA is expressed in all human cell lines tested end encodes the synthesis of a 134-amino-acid protein by utilizing an alternative initiation codon. The expression of RNase κ-02 in the cytoplasm of human cells was verified by Western blot and immunofluorescence analysis using a specific polyclonal antibody developed on the basis of the amino-acid sequence difference between the two protein isoforms. The results presented here show that subtle changes during mRNA splicing can lead to the expression of significantly altered protein isoforms.
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7
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Nishimura Y, Shimono N, Yoshimoto T, Kamiguchi H, Nishikawa Y. Cloning and transcriptional expression of mouse mannosyltransferase IV/V cDNA, which is involved in the synthesis of lipid-linked oligosaccharides. Biosci Biotechnol Biochem 2014; 78:400-9. [PMID: 25036826 DOI: 10.1080/09168451.2014.890026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We cloned the mouse mannosyltransferase IV/V gene (mALG11) from FM3A cells by a bioinformatic approach. The ORF contained 1476 bp encoding 492 amino acids. The cloned mALG11 complemented the growth defect of the Saccharomyces cerevisiae ALG11Δ mutant. In addition, we detected a variant cDNA by alternate splicing that had an additional four-nucleotide ATGC insertion at base 276 of the ORF. Consequently the variant cDNA encoded a truncated protein with 92 amino acids, lacking the glycosyltransferase group-1 domain. The variant cDNA occurs in many mouse strains according to EST database searches. Moreover, we detected it in FM3A cDNA, but we did not detect any such variants in the human EST database or in HeLa cDNA, although human ALG11 (hALG11) genomic DNA has the same sequence around the intron-exon boundaries as those of mALG11 genomic DNA. Hence, we concluded that there is different transcriptional control mechanism between mALG11 and hALG11.
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Affiliation(s)
- Yuuki Nishimura
- a Department of Applied Biochemistry , School of Engineering, Tokai University , Hiratsuka , Japan
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8
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Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol 2012; 10:e1001229. [PMID: 22235189 PMCID: PMC3250501 DOI: 10.1371/journal.pbio.1001229] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 11/18/2011] [Indexed: 11/19/2022] Open
Abstract
Thousands of human genes contain introns ending in NAGNAG (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms that differ by inclusion/exclusion of three bases. However, few models exist for how such splicing might be regulated, and some studies have concluded that NAGNAG splicing is purely stochastic and nonfunctional. Here, we used deep RNA-Seq data from 16 human and eight mouse tissues to analyze the regulation and evolution of NAGNAG splicing. Using both biological and technical replicates to estimate false discovery rates, we estimate that at least 25% of alternatively spliced NAGNAGs undergo tissue-specific regulation in mammals, and alternative splicing of strongly tissue-specific NAGNAGs was 10 times as likely to be conserved between species as was splicing of non-tissue-specific events, implying selective maintenance. Preferential use of the distal NAG was associated with distinct sequence features, including a more distal location of the branch point and presence of a pyrimidine immediately before the first NAG, and alteration of these features in a splicing reporter shifted splicing away from the distal site. Strikingly, alignments of orthologous exons revealed a ∼15-fold increase in the frequency of three base pair gaps at 3' splice sites relative to nearby exon positions in both mammals and in Drosophila. Alternative splicing of NAGNAGs in human was associated with dramatically increased frequency of exon length changes at orthologous exon boundaries in rodents, and a model involving point mutations that create, destroy, or alter NAGNAGs can explain both the increased frequency and biased codon composition of gained/lost sequence observed at the beginnings of exons. This study shows that NAGNAG alternative splicing generates widespread differences between the proteomes of mammalian tissues, and suggests that the evolutionary trajectories of mammalian proteins are strongly biased by the locations and phases of the introns that interrupt coding sequences.
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Tsai KW, Chan WC, Hsu CN, Lin WC. Sequence features involved in the mechanism of 3' splice junction wobbling. BMC Mol Biol 2010; 11:34. [PMID: 20459675 PMCID: PMC2875228 DOI: 10.1186/1471-2199-11-34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 05/07/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative splicing is an important mechanism mediating the diversified functions of genes in multicellular organisms, and such event occurs in around 40-60% of human genes. Recently, a new splice-junction wobbling mechanism was proposed that subtle modifications exist in mRNA maturation by alternatively choosing at 5'- GTNGT and 3'- NAGNAG, which created single amino acid insertion and deletion isoforms. RESULTS By browsing the Alternative Splicing Database information, we observed that most 3' alternative splice site choices occur within six nucleotides of the dominant splice site and the incidence significantly decreases further away from the dominant acceptor site. Although a lower frequency of alternative splicing occurs within the intronic region (alternative splicing at the proximal AG) than in the exonic region (alternative splicing at the distal AG), alternative AG sites located within the intronic region show stronger potential as the acceptor. These observations revealed that the choice of 3' splice sites during 3' splicing junction wobbling could depend on the distance between the duplicated AG and the branch point site (BPS). Further mutagenesis experiments demonstrated that the distance of AG-to-AG and BPS-to-AG can greatly influence 3' splice site selection. Knocking down a known alternative splicing regulator, hSlu7, failed to affect wobble splicing choices. CONCLUSION Our results implied that nucleotide distance between proximal and distal AG sites has an important regulatory function. In this study, we showed that occurrence of 3' wobble splicing occurs in a distance-dependent manner and that most of this wobble splicing is probably caused by steric hindrance from a factor bound at the neighboring tandem motif sequence.
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Affiliation(s)
- Kuo-Wang Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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10
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Sinha R, Lenser T, Jahn N, Gausmann U, Friedel S, Szafranski K, Huse K, Rosenstiel P, Hampe J, Schuster S, Hiller M, Backofen R, Platzer M. TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinformatics 2010; 11:216. [PMID: 20429909 PMCID: PMC2878309 DOI: 10.1186/1471-2105-11-216] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 04/29/2010] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the complexity of transcriptomes and proteomes. However, these events have been either omitted altogether in databases on alternative splicing, or only the cases of experimentally confirmed alternative splicing have been reported. Thus, a database which covers all confirmed cases of subtle alternative splicing as well as the numerous putative tandem splice sites (which might be confirmed once more transcript data becomes available), and allows to search for tandem splice sites with specific features and download the results, is a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites. Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species. DESCRIPTION We have substantially revised and extended TassDB. The currently available version 2 contains extensive information about tandem splice sites separated by 2-12 nt for the human and mouse transcriptomes including data on the conservation of the tandem motifs in five vertebrates. TassDB2 offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. For example, users can search for cases of alternative splicing where the proportion of EST/mRNA evidence supporting the minor isoform exceeds a specific threshold, or where the difference in splice site scores is specified by the user. The predicted impact of each event on the protein is also reported, along with information about being a putative target for the nonsense-mediated decay (NMD) pathway. Links are provided to the UCSC genome browser and other external resources. CONCLUSION TassDB2, available via http://www.tassdb.info, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.
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Affiliation(s)
- Rileen Sinha
- Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Thorsten Lenser
- Bio Systems Analysis Group, Friedrich Schiller University Jena, Ernst-Abbe-Platz 1-4, D-07743 Jena, Germany
| | - Niels Jahn
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Ulrike Gausmann
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Swetlana Friedel
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Systems Biology/Bioinformatics, Beutenbergstrasse. 11a, 07745 Jena, Germany
| | - Karol Szafranski
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Klaus Huse
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany
| | - Jochen Hampe
- Department of General Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Michael Hiller
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Rolf Backofen
- Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
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11
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Sinha R, Zimmer AD, Bolte K, Lang D, Reski R, Platzer M, Rensing SA, Backofen R. Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens. BMC PLANT BIOLOGY 2010; 10:76. [PMID: 20426810 PMCID: PMC3095350 DOI: 10.1186/1471-2229-10-76] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 04/28/2010] [Indexed: 05/05/2023]
Abstract
BACKGROUND Alternative splicing (AS) involving tandem acceptors that are separated by three nucleotides (NAGNAG) is an evolutionarily widespread class of AS, which is well studied in Homo sapiens (human) and Mus musculus (mouse). It has also been shown to be common in the model seed plants Arabidopsis thaliana and Oryza sativa (rice). In one of the first studies involving sequence-based prediction of AS in plants, we performed a genome-wide identification and characterization of NAGNAG AS in the model plant Physcomitrella patens, a moss. RESULTS Using Sanger data, we found 295 alternatively used NAGNAG acceptors in P. patens. Using 31 features and training and test datasets of constitutive and alternative NAGNAGs, we trained a classifier to predict the splicing outcome at NAGNAG tandem splice sites (alternative splicing, constitutive at the first acceptor, or constitutive at the second acceptor). Our classifier achieved a balanced specificity and sensitivity of >or= 89%. Subsequently, a classifier trained exclusively on data well supported by transcript evidence was used to make genome-wide predictions of NAGNAG splicing outcomes. By generation of more transcript evidence from a next-generation sequencing platform (Roche 454), we found additional evidence for NAGNAG AS, with altogether 664 alternative NAGNAGs being detected in P. patens using all currently available transcript evidence. The 454 data also enabled us to validate the predictions of the classifier, with 64% (80/125) of the well-supported cases of AS being predicted correctly. CONCLUSION NAGNAG AS is just as common in the moss P. patens as it is in the seed plants A. thaliana and O. sativa (but not conserved on the level of orthologous introns), and can be predicted with high accuracy. The most informative features are the nucleotides in the NAGNAG and in its immediate vicinity, along with the splice sites scores, as found earlier for NAGNAG AS in animals. Our results suggest that the mechanism behind NAGNAG AS in plants is similar to that in animals and is largely dependent on the splice site and its immediate neighborhood.
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Affiliation(s)
- Rileen Sinha
- Bioinformatics group, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
| | - Andreas D Zimmer
- Faculty of Biology, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Kathrin Bolte
- Faculty of Biology, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Philipps-Universität Marburg, Laboratorium für Zellbiologie, Karl-von-Frisch Str., 35032 Marburg, Germany
| | - Daniel Lang
- Faculty of Biology, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Stefan A Rensing
- Faculty of Biology, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics group, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
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12
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Hartmann B, Valcárcel J. Decrypting the genome's alternative messages. Curr Opin Cell Biol 2009; 21:377-86. [PMID: 19307111 DOI: 10.1016/j.ceb.2009.02.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 02/19/2009] [Accepted: 02/20/2009] [Indexed: 12/12/2022]
Abstract
Alternative splicing of messenger RNA (mRNA) precursors affects the majority of human genes, has a considerable impact on eukaryotic gene function and offers distinct opportunities for regulation. Alterations in alternative splicing can cause or modify the progression of a significant number of pathologies. Recent high-throughput technologies have uncovered a wealth of transcript diversity generated by alternative splicing, as well as examples for how this diversity can be established and become misregulated. A variety of mechanisms modulate splice site choice coordinately with other cellular processes, from transcription and mRNA editing or decay to miRNA-based regulation and telomerase function. Alternative splicing studies can contribute to our understanding of multiple biological processes, including genetic diversity, speciation, cell/stem cell differentiation, nervous system function, neuromuscular disorders and tumour progression.
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Affiliation(s)
- Britta Hartmann
- Centre de Regulació Genómica, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
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13
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Lv J, Yang Y, Yin H, Chu F, Wang H, Zhang W, Zhang Y, Jin Y. Molecular determinants and evolutionary dynamics of wobble splicing. Mol Biol Evol 2009; 26:1081-92. [PMID: 19221008 PMCID: PMC2668829 DOI: 10.1093/molbev/msp023] [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: 01/11/2023] Open
Abstract
Alternative splicing at tandem splice sites (wobble splicing) is widespread in many species, but the mechanisms specifying the tandem sites remain poorly understood. Here, we used synaptotagmin I as a model to analyze the phylogeny of wobble splicing spanning more than 300 My of insect evolution. Phylogenetic analysis indicated that the occurrence of species-specific wobble splicing was related to synonymous variation at tandem splice sites. Further mutagenesis experiments demonstrated that wobble splicing could be lost by artificially induced synonymous point mutations due to destruction of splice acceptor sites. In contrast, wobble splicing could not be correctly restored through mimicking an ancestral tandem acceptor by artificial synonymous mutation in in vivo splicing assays, which suggests that artificial tandem splice sites might be incompatible with normal wobble splicing. Moreover, combining comparative genomics with hybrid minigene analysis revealed that alternative splicing has evolved from the 3′ tandem donor to the 5′ tandem acceptor in Culex pipiens, as a result of an evolutionary shift of cis element sequences from 3′ to 5′ splice sites. These data collectively suggest that the selection of tandem splice sites might not simply be an accident of history but rather in large part the result of coevolution between splice site and cis element sequences as a basis for wobble splicing. An evolutionary model of wobble splicing is proposed.
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Affiliation(s)
- Jianning Lv
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
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14
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Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics 2008; 9:159. [PMID: 18402682 PMCID: PMC2375911 DOI: 10.1186/1471-2164-9-159] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 04/10/2008] [Indexed: 11/10/2022] Open
Abstract
Background Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes. Results In a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes. Conclusion NAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
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15
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Hiller M, Platzer M. Widespread and subtle: alternative splicing at short-distance tandem sites. Trends Genet 2008; 24:246-55. [PMID: 18394746 DOI: 10.1016/j.tig.2008.03.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 03/05/2008] [Accepted: 03/06/2008] [Indexed: 12/11/2022]
Abstract
Alternative splicing at donor or acceptor sites located just a few nucleotides apart is widespread in many species. It results in subtle changes in the transcripts and often in the encoded proteins. Several of these tandem splice events contribute to the repertoire of functionally different proteins, whereas many are neutral or deleterious. Remarkably, some of the functional events are differentially spliced in tissues or developmental stages, whereas others exhibit constant splicing ratios, indicating that function is not always associated with differential splicing. Stochastic splice site selection seems to play a major role in these processes. Here, we review recent progress in understanding functional and evolutionary aspects as well as the mechanism of splicing at short-distance tandem sites.
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Affiliation(s)
- Michael Hiller
- Bioinformatics Group, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany.
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Hiller M, Szafranski K, Huse K, Backofen R, Platzer M. Selection against tandem splice sites affecting structured protein regions. BMC Evol Biol 2008; 8:89. [PMID: 18366714 PMCID: PMC2279118 DOI: 10.1186/1471-2148-8-89] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 03/21/2008] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Alternative selection of splice sites in tandem donors and acceptors is a major mode of alternative splicing. Here, we analyzed whether in-frame tandem sites leading to subtle mRNA insertions/deletions of 3, 6, or 9 nucleotides are under natural selection. RESULTS We found multiple lines of evidence that the human protein coding sequences are under selection against such in-frame tandem splice events, indicating that these events are often deleterious. The strength of selection is not homogeneous within the coding sequence as protein regions that fold into a fixed 3D structure (intrinsically ordered) are under stronger selection, especially against sites with a strong minor splice site. Investigating structures of functional protein domains, we found that tandem acceptors are preferentially located at the domain surface and outside structural elements such as helices and sheets. Using three-species comparisons, we estimate that more than half of all mutations that create NAGNAG acceptors in the coding region have been eliminated by selection. CONCLUSION We estimate that ~2,400 introns are under selection against possessing a tandem site.
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Affiliation(s)
- Michael Hiller
- Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.
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