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Truong DJJ, Phlairaharn T, Eßwein B, Gruber C, Tümen D, Baligács E, Armbrust N, Vaccaro FL, Lederer EM, Beck EM, Geilenkeuser J, Göppert S, Krumwiede L, Grätz C, Raffl G, Schwarz D, Zirngibl M, Živanić M, Beyer M, Körner JD, Santl T, Evsyukov V, Strauß T, Schwarz SC, Höglinger GU, Heutink P, Doll S, Conrad M, Giesert F, Wurst W, Westmeyer GG. Non-invasive and high-throughput interrogation of exon-specific isoform expression. Nat Cell Biol 2021; 23:652-663. [PMID: 34083785 PMCID: PMC8189919 DOI: 10.1038/s41556-021-00678-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/01/2021] [Indexed: 02/05/2023]
Abstract
Expression of exon-specific isoforms from alternatively spliced mRNA is a fundamental mechanism that substantially expands the proteome of a cell. However, conventional methods to assess alternative splicing are either consumptive and work-intensive or do not quantify isoform expression longitudinally at the protein level. Here, we therefore developed an exon-specific isoform expression reporter system (EXSISERS), which non-invasively reports the translation of exon-containing isoforms of endogenous genes by scarlessly excising reporter proteins from the nascent polypeptide chain through highly efficient, intein-mediated protein splicing. We applied EXSISERS to quantify the inclusion of the disease-associated exon 10 in microtubule-associated protein tau (MAPT) in patient-derived induced pluripotent stem cells and screened Cas13-based RNA-targeting effectors for isoform specificity. We also coupled cell survival to the inclusion of exon 18b of FOXP1, which is involved in maintaining pluripotency of embryonic stem cells, and confirmed that MBNL1 is a dominant factor for exon 18b exclusion. EXSISERS enables non-disruptive and multimodal monitoring of exon-specific isoform expression with high sensitivity and cellular resolution, and empowers high-throughput screening of exon-specific therapeutic interventions.
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Affiliation(s)
- Dong-Jiunn Jeffery Truong
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Teeradon Phlairaharn
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Bianca Eßwein
- grid.4567.00000 0004 0483 2525Institute of Developmental Genetics, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Christoph Gruber
- grid.4567.00000 0004 0483 2525Institute of Developmental Genetics, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Deniz Tümen
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.411941.80000 0000 9194 7179Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Enikő Baligács
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Niklas Armbrust
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Francesco Leandro Vaccaro
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Eva-Maria Lederer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Eva Magdalena Beck
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Julian Geilenkeuser
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Simone Göppert
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Luisa Krumwiede
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Grätz
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Gerald Raffl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Dominic Schwarz
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Zirngibl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Milica Živanić
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Maren Beyer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Johann Dietmar Körner
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Santl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Valentin Evsyukov
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Munich, Germany ,grid.6936.a0000000123222966Department of Neurology, Technical University Munich, Munich, Germany ,grid.10423.340000 0000 9529 9877Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Tabea Strauß
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Munich, Germany ,grid.6936.a0000000123222966Department of Neurology, Technical University Munich, Munich, Germany
| | - Sigrid C. Schwarz
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Munich, Germany ,grid.6936.a0000000123222966Department of Neurology, Technical University Munich, Munich, Germany
| | - Günter U. Höglinger
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Munich, Germany ,grid.6936.a0000000123222966Department of Neurology, Technical University Munich, Munich, Germany ,grid.10423.340000 0000 9529 9877Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Peter Heutink
- grid.10392.390000 0001 2190 1447Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany ,grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Sebastian Doll
- grid.4567.00000 0004 0483 2525Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Marcus Conrad
- grid.4567.00000 0004 0483 2525Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.78028.350000 0000 9559 0613Laboratory of Experimental Oncology, National Research Medical University, Moscow, Russia
| | - Florian Giesert
- grid.4567.00000 0004 0483 2525Institute of Developmental Genetics, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Wolfgang Wurst
- grid.4567.00000 0004 0483 2525Institute of Developmental Genetics, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Munich, Germany ,grid.6936.a0000000123222966TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Gil Gregor Westmeyer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Oberschleißheim, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
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2
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Mathur M, Kim CM, Munro SA, Rudina SS, Sawyer EM, Smolke CD. Programmable mutually exclusive alternative splicing for generating RNA and protein diversity. Nat Commun 2019; 10:2673. [PMID: 31209208 PMCID: PMC6572816 DOI: 10.1038/s41467-019-10403-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/01/2019] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing performs a central role in expanding genomic coding capacity and proteomic diversity. However, programming of splicing patterns in engineered biological systems remains underused. Synthetic approaches thus far have predominantly focused on controlling expression of a single protein through alternative splicing. Here, we describe a modular and extensible platform for regulating four programmable exons that undergo a mutually exclusive alternative splicing event to generate multiple functionally-distinct proteins. We present an intron framework that enforces the mutual exclusivity of two internal exons and demonstrate a graded series of consensus sequence elements of varying strengths that set the ratio of two mutually exclusive isoforms. We apply this framework to program the DNA-binding domains of modular transcription factors to differentially control downstream gene activation. This splicing platform advances an approach for generating diverse isoforms and can ultimately be applied to program modular proteins and increase coding capacity of synthetic biological systems.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Cameron M Kim
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Sarah A Munro
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Joint Initiative for Metrology in Biology, Stanford, CA, 94305, USA
- Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, 94305, USA
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Shireen S Rudina
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Eric M Sawyer
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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3
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An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5. Int J Mol Sci 2019; 20:ijms20051010. [PMID: 30813567 PMCID: PMC6429586 DOI: 10.3390/ijms20051010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
A set of tissue-specific splicing factors are thought to govern alternative splicing events during neural progenitor cell (NPC)-to-neuron transition by regulating neuron-specific exons. Here, we propose one such factor, RNA-binding protein Quaking 5 (Qki5), which is specifically expressed in the early embryonic neural stem cells. We performed mRNA-SEQ (Sequence) analysis using mRNAs obtained by developing cerebral cortices in Qk (Quaking) conditional knockout (cKO) mice. As expected, we found a large number of alternative splicing changes between control and conditional knockouts relative to changes in transcript levels. DAVID (The Database for Annotation, Visualization and Integrated Discovery) and Metascape analyses suggested that the affected spliced genes are involved in axon development and microtubule-based processes. Among these, the mRNA coding for the Ninein protein is listed as one of Qki protein-dependent alternative splicing targets. Interestingly, this exon encodes a very long polypeptide (2121 nt), and has been previously defined as a dynamic RNA switch during the NPC-to-neuron transition. Additionally, we validated that the regulation of this large exon is consistent with the Qki5-dependent alternative exon inclusion mode suggested by our previous Qki5 HITS-CLIP (high throughput sequencing-cross linking immunoprecipitation) analysis. Taken together, these data suggest that Qki5 is an important factor for alternative splicing in the NPC-to-neuron transition.
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Ipe J, Collins KS, Hao Y, Gao H, Bhatia P, Gaedigk A, Liu Y, Skaar TC. PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites. Front Genet 2018; 9:219. [PMID: 29963077 PMCID: PMC6013768 DOI: 10.3389/fgene.2018.00219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/29/2018] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) studies have identified large numbers of genetic variants that are predicted to alter miRNA–mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs). The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays. Fifty-five mirSNPs were functional in at least one of three cell lines (FDR ≤ 0.05); 11, 36, and 27 of them were functional in HEK293, HepG2, and HeLa cells, respectively. Only four of the variants were functional in all three cell lines, which demonstrates the cell-type specific effects of mirSNPs and the importance of testing the mirSNPs in multiple cell lines. Using PASSPORT-seq, we functionally tested 111 variants in the 3′ UTR of 17 pharmacogenes that are predicted to alter miRNA regulation. Thirty-three of the variants tested were functional in at least one cell line.
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Affiliation(s)
- Joseph Ipe
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kimberly S Collins
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yangyang Hao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Puja Bhatia
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Todd C Skaar
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
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5
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Zhu BH, Xiao J, Xue W, Xu GC, Sun MY, Li JT. P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. BMC Genomics 2018; 19:175. [PMID: 29499650 PMCID: PMC5834899 DOI: 10.1186/s12864-018-4567-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/22/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transcripts can be used to scaffold genomes and complete transcribed regions. RESULTS We present P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs. Tested in various species, P_RNA_scaffolder exhibited higher speed and efficiency than the existing state-of-the-art scaffolders. This tool also improved the contiguity of genome assemblies generated by current mate-pair scaffolding and third-generation single-molecule sequencing assembly. CONCLUSIONS The P_RNA_scaffolder can improve the contiguity of genome assembly and benefit gene prediction. This tool is available at http://www.fishbrowser.org/software/P_RNA_scaffolder .
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Affiliation(s)
- Bai-Han Zhu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Jun Xiao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Wei Xue
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Gui-Cai Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.,College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ming-Yuan Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
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6
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Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. eLife 2017; 6:32537. [PMID: 29280736 PMCID: PMC5762160 DOI: 10.7554/elife.32537] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Production of most eukaryotic mRNAs requires splicing of introns from pre-mRNA. The splicing reaction requires definition of splice sites, which are initially recognized in either intron-spanning (‘intron definition’) or exon-spanning (‘exon definition’) pairs. To understand how exon and intron length and splice site recognition mode impact splicing, we measured splicing rates genome-wide in Drosophila, using metabolic labeling/RNA sequencing and new mathematical models to estimate rates. We found that the modal intron length range of 60–70 nt represents a local maximum of splicing rates, but that much longer exon-defined introns are spliced even faster and more accurately. We observed unexpectedly low variation in splicing rates across introns in the same gene, suggesting the presence of gene-level influences, and we identified multiple gene level variables associated with splicing rate. Together our data suggest that developmental and stress response genes may have preferentially evolved exon definition in order to enhance the rate or accuracy of splicing.
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Affiliation(s)
- Athma A Pai
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Kayla McCue
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Adam Burkholder
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle, United States
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
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Bolisetty MT, Beemon KL. Splicing of internal large exons is defined by novel cis-acting sequence elements. Nucleic Acids Res 2012; 40:9244-54. [PMID: 22790982 PMCID: PMC3467050 DOI: 10.1093/nar/gks652] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Human internal exons have an average size of 147 nt, and most are <300 nt. This small size is thought to facilitate exon definition. A small number of large internal exons have been identified and shown to be alternatively spliced. We identified 1115 internal exons >1000 nt in the human genome; these were found in 5% of all protein-coding genes, and most were expressed and translated. Surprisingly, 40% of these were expressed at levels similar to the flanking exons, suggesting they were constitutively spliced. While all of the large exons had strong splice sites, the constitutively spliced large exons had a higher ratio of splicing enhancers/silencers and were more conserved across mammals than the alternatively spliced large exons. We asked if large exons contain specific sequences that promote splicing and identified 38 sequences enriched in the large exons relative to small exons. The consensus sequence is C-rich with a central invariant CA dinucleotide. Mutation of these sequences in a candidate large exon indicated that these are important for recognition of large exons by the splicing machinery. We propose that these sequences are large exon splicing enhancers (LESEs).
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Affiliation(s)
- Mohan T Bolisetty
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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8
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Weir M, Eaton M, Rice M. Challenging the spliceosome machine. Genome Biol 2006; 7:R3. [PMID: 16507135 PMCID: PMC1431713 DOI: 10.1186/gb-2006-7-1-r3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 11/07/2005] [Accepted: 12/15/2005] [Indexed: 11/10/2022] Open
Abstract
Analysis of a set of almost 25,000 donor and acceptor splice sites in Drosophila shows that information content increases near splice sites flanking very long of very short introns and exons. Background Using cDNA copies of transcripts and corresponding genomic sequences from the Berkeley Drosophila Genome Project, a set of 24,753 donor and acceptor splice sites were computed with a scanning algorithm that tested for single nucleotide insertion, deletion and substitution polymorphisms. Using this dataset, we developed a progressive partitioning approach to examining the effects of challenging the spliceosome system. Results Our analysis shows that information content increases near splice sites flanking progressively longer introns and exons, suggesting that longer splice elements require stronger binding of spliceosome components. Information also increases at splice sites near very short introns and exons, suggesting that short splice elements have crowding problems. We observe that the information found at individual splice sites depends upon a balance of splice element lengths in the vicinity, including both flanking and non-adjacent introns and exons. Conclusion These results suggest an interdependence of multiple splicing events along the pre-mRNA, which may have implications for how the macromolecular spliceosome machine processes sets of neighboring splice sites.
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Affiliation(s)
- Michael Weir
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA
| | - Matthew Eaton
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA
| | - Michael Rice
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA
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9
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Zhang XHF, Chasin LA. Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 2004; 18:1241-50. [PMID: 15145827 PMCID: PMC420350 DOI: 10.1101/gad.1195304] [Citation(s) in RCA: 338] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Accepted: 04/09/2004] [Indexed: 12/23/2022]
Abstract
We have searched for sequence motifs that contribute to the recognition of human pre-mRNA splice sites by comparing the frequency of 8-mers in internal noncoding exons versus unspliced pseudo exons and 5' untranslated regions (5' untranslated regions [UTRs]) of transcripts of intronless genes. This type of comparison avoids the isolation of sequences that are distinguished by their protein-coding information. We classified sequence families comprising 2069 putative exonic enhancers and 974 putative exonic silencers. Representatives of each class functioned as enhancers or silencers when inserted into a test exon and assayed in transfected mammalian cells. As a class, the enhancer sequencers were more prevalent and the silencer elements less prevalent in all exons compared with introns. A survey of 58 reported exonic splicing mutations showed good agreement between the splicing phenotype and the effect of the mutation on the motifs defined here. The large number of effective sequences implied by these results suggests that sequences that influence splicing may be very abundant in pre-mRNA.
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Affiliation(s)
- Xiang H-F Zhang
- Department of Biological Sciences, MC2433, Columbia University, New York, New York 10027, USA
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10
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Romano M, Marcucci R, Baralle FE. Splicing of constitutive upstream introns is essential for the recognition of intra-exonic suboptimal splice sites in the thrombopoietin gene. Nucleic Acids Res 2001; 29:886-94. [PMID: 11160920 PMCID: PMC29620 DOI: 10.1093/nar/29.4.886] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The human thrombopoietin (TPO) gene, which codes for the principal cytokine involved in platelet maturation, shows a peculiar alternative splicing of its last exon, where an intra-exonic 116 nt alternative intron is spliced out in a fraction of its mRNA. To characterize the molecular mechanism underlying this alternative splicing, minigenes of TPO genomic constructs with variable exon-intron configurations or carrying exclusively the TPO cDNA were generated and transiently transfected in the Hep3B cell line. We have found that the final rate of the alternative intron splicing is determined by three elements: the presence of upstream constitutive introns, the suboptimal splice sites of the alternative intron and the length of the alternative intron itself. Our results indicate that the recognition of suboptimal intra-exonic splice junctions in the TPO gene is influenced by the assembly of the spliceosome complex on constitutive introns and by a qualitative scanning of the sequence by the transcriptional/splicing machinery complex primed by upstream splicing signals.
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Affiliation(s)
- M Romano
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34012 Trieste, Italy
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11
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Abstract
Mammalian genes are characterized by relatively small exons surrounded by variable lengths of intronic sequence. Sequences similar to the splice signals that define the 5' and 3' boundaries of these exons are also present in abundance throughout the surrounding introns. What causes the real sites to be distinguished from the multitude of pseudosites in pre-mRNA is unclear. Much progress has been made in defining additional sequence elements that enhance the use of particular sites. Less work has been done on sequences that repress the use of particular splice sites. To find additional examples of sequences that inhibit splicing, we searched human genomic DNA libraries for sequences that would inhibit the inclusion of a constitutively spliced exon. Genetic selection experiments suggested that such sequences were common, and we subsequently tested randomly chosen restriction fragments of about 100 bp. When inserted into the central exon of a three-exon minigene, about one in three inhibited inclusion, revealing a high frequency of inhibitory elements in human DNA. In contrast, only 1 in 27 Escherichia coli DNA fragments was inhibitory. Several previously identified silencing elements derived from alternatively spliced exons functioned weakly in this constitutively spliced exon. In contrast, a high-affinity site for U2AF65 strongly inhibited exon inclusion. Together, our results suggest that splicing occurs in a background of repression and, since many of our inhibitors contain splice like signals, we suggest that repression of some pseudosites may occur through an inhibitory arrangement of these sites.
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Affiliation(s)
- W G Fairbrother
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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12
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Abstract
Exon/intron architecture varies across the eukaryotic kingdom with large introns and small exons the rule in vertebrates and the opposite in lower eukaryotes. To investigate the relationship between exon and intron size in pre-mRNA processing, internally expanded exons were placed in vertebrate genes with small and large introns. Both exon and intron size influenced splicing phenotype. Intron size dictated if large exons were efficiently recognized. When introns were large, large exons were skipped; when introns were small, the same large exons were included. Thus, large exons were incompatible for splicing if and only if they were flanked by large introns. Both intron and exon size became problematic at approximately 500 nt, although both exon and intron sequence influenced the size at which exons and introns failed to be recognized. These results indicate that present-day gene architecture reflects at least in part limitations on exon recognition. Furthermore, these results strengthen models that invoke pairing of splice sites during recognition of pre-mRNAs, and suggest that vertebrate consensus sequences support pairing across either introns or exons.
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Affiliation(s)
- D A Sterner
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
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Tian H, Kole R. Selection of novel exon recognition elements from a pool of random sequences. Mol Cell Biol 1995; 15:6291-8. [PMID: 7565782 PMCID: PMC230881 DOI: 10.1128/mcb.15.11.6291] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A 20-nucleotide sequence close to the 3' end of the internal exon of a model two-intron, three-exon pre-mRNA (DUP184 [Z. Dominski and R. Kole, J. Biol. Chem. 269:23590-23596, 1994]) was replaced by a random 20-mer, resulting in a pool of pre-mRNAs which, like the initial DUP184 construct, were spliced in vitro by a pathway leading to predominant skipping of the internal exon. The randomized pre-mRNAs were subjected to a selection protocol, resulting in a pool enriched in pre-mRNAs that efficiently included the internal exon. Isolation and sequencing of a number of clones corresponding to the selected pre-mRNAs showed that two classes of sequences were selected from the initial pool. Most abundant among these were sequences with purine tracts similar to those in the recently identified exon-splicing enhancers while a smaller class included sequences lacking discernible purine tracts within the 20-nucleotide region. Splicing of selected pre-mRNAs showed that the purine tracts vary in their ability to promote exon inclusion and, more important, that sequences lacking purine tracts stimulate inclusion of the internal exon as efficiently as their purine-rich counterparts. The latter result indicates the existence of a novel class of exon recognition sequences or splicing enhancers.
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Affiliation(s)
- H Tian
- Lineberger Comprehensive Cancer Center, Department of Pharmacology, University of North Carolina, Chapel Hill 27599, USA
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14
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Sequences homologous to 5' splice sites are required for the inhibitory activity of papillomavirus late 3' untranslated regions. Mol Cell Biol 1994. [PMID: 8035806 DOI: 10.1128/mcb.14.8.5278] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of bovine papillomavirus type 1 (BPV-1) late genes is limited to terminally differentiated keratinocytes in an infected epithelium. We have previously shown that although the BPV-1 late polyadenylation site is functional in nonpermissive cells, a 53-nucleotide (nt) fragment of the late 3' untranslated region acts posttranscriptionally to reduce polyadenylated cytoplasmic RNA levels. This 53-nt fragment does not appear to function by destabilizing polyadenylated cytoplasmic RNA (P. A. Furth and C. C. Baker, J. Virol. 65:5806-5812, 1991). In this study, we used site-directed mutagenesis and deletion analysis to demonstrate that the sequence AAG/GUAAGU, which is identical to the consensus 5' splice site sequence, was both necessary and sufficient for the inhibitory activity of the 53-nt fragment. Furthermore, base pairing between the 5' end of the U1 small nuclear RNA and this 5' splice site-like sequence was shown to be required for the inhibitory activity in vivo. We have also further mapped the human papillomavirus type 16 late 3' inhibitory element (I. M. Kennedy, J. K. Haddow, and J. B. Clements, J. Virol. 65:2093-2097, 1991) to a 51-nt region containing four overlapping sequence motifs with partial homology to 5' splice sites. Mutation of each of these motifs demonstrated that only one of these motifs is required for the inhibitory activity. However, the presence of the other motifs may contribute to the full inhibitory activity of the element. No BPV-1 or human papillomavirus type 16 mRNAs which are spliced by using the potential 5' splice sites present in the viral late 3' untranslated regions have been identified. This suggests that the primary function of these 5' splice site-like sequences is the inhibition of late gene expression. The most likely mechanism of action of these elements is reduction of polyadenylation efficiency, perhaps through interference with 3'-terminal exon definition.
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15
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Furth PA, Choe WT, Rex JH, Byrne JC, Baker CC. Sequences homologous to 5' splice sites are required for the inhibitory activity of papillomavirus late 3' untranslated regions. Mol Cell Biol 1994; 14:5278-89. [PMID: 8035806 PMCID: PMC359047 DOI: 10.1128/mcb.14.8.5278-5289.1994] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Expression of bovine papillomavirus type 1 (BPV-1) late genes is limited to terminally differentiated keratinocytes in an infected epithelium. We have previously shown that although the BPV-1 late polyadenylation site is functional in nonpermissive cells, a 53-nucleotide (nt) fragment of the late 3' untranslated region acts posttranscriptionally to reduce polyadenylated cytoplasmic RNA levels. This 53-nt fragment does not appear to function by destabilizing polyadenylated cytoplasmic RNA (P. A. Furth and C. C. Baker, J. Virol. 65:5806-5812, 1991). In this study, we used site-directed mutagenesis and deletion analysis to demonstrate that the sequence AAG/GUAAGU, which is identical to the consensus 5' splice site sequence, was both necessary and sufficient for the inhibitory activity of the 53-nt fragment. Furthermore, base pairing between the 5' end of the U1 small nuclear RNA and this 5' splice site-like sequence was shown to be required for the inhibitory activity in vivo. We have also further mapped the human papillomavirus type 16 late 3' inhibitory element (I. M. Kennedy, J. K. Haddow, and J. B. Clements, J. Virol. 65:2093-2097, 1991) to a 51-nt region containing four overlapping sequence motifs with partial homology to 5' splice sites. Mutation of each of these motifs demonstrated that only one of these motifs is required for the inhibitory activity. However, the presence of the other motifs may contribute to the full inhibitory activity of the element. No BPV-1 or human papillomavirus type 16 mRNAs which are spliced by using the potential 5' splice sites present in the viral late 3' untranslated regions have been identified. This suggests that the primary function of these 5' splice site-like sequences is the inhibition of late gene expression. The most likely mechanism of action of these elements is reduction of polyadenylation efficiency, perhaps through interference with 3'-terminal exon definition.
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Affiliation(s)
- P A Furth
- Laboratory of Tumor Virus Biology, National Cancer Institute, Bethesda, Maryland 20892
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