1
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Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
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Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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2
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Keuthan CJ, Karma S, Zack DJ. Alternative RNA Splicing in the Retina: Insights and Perspectives. Cold Spring Harb Perspect Med 2023; 13:a041313. [PMID: 36690463 PMCID: PMC10547393 DOI: 10.1101/cshperspect.a041313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alternative splicing is a fundamental and highly regulated post-transcriptional process that enhances transcriptome and proteome diversity. This process is particularly important in neuronal tissues, such as the retina, which exhibit some of the highest levels of differentially spliced genes in the body. Alternative splicing is regulated both temporally and spatially during neuronal development, can be cell-type-specific, and when altered can cause a number of pathologies, including retinal degeneration. Advancements in high-throughput sequencing technologies have facilitated investigations of the alternative splicing landscape of the retina in both healthy and disease states. Additionally, innovations in human stem cell engineering, specifically in the generation of 3D retinal organoids, which recapitulate many aspects of the in vivo retinal microenvironment, have aided studies of the role of alternative splicing in human retinal development and degeneration. Here we review these advances and discuss the ongoing development of strategies for the treatment of alternative splicing-related retinal disease.
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Affiliation(s)
- Casey J Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Sadik Karma
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Donald J Zack
- Departments of Ophthalmology, Wilmer Eye Institute, Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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3
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Lio CT, Grabert G, Louadi Z, Fenn A, Baumbach J, Kacprowski T, List M, Tsoy O. Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics 2022; 39:6965022. [PMID: 36579860 PMCID: PMC9831059 DOI: 10.1093/bioinformatics/btac846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. RESULTS Here, we propose Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection. AVAILABILITY AND IMPLEMENTATION The Spycone package is available as a PyPI package. The source code of Spycone is available under the GPLv3 license at https://github.com/yollct/spycone and the documentation at https://spycone.readthedocs.io/en/latest/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chit Tong Lio
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Gordon Grabert
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | - Zakaria Louadi
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Amit Fenn
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Institute of Mathematics and Computer Science, University of Southern Denmark, Odense 5000, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | | | - Olga Tsoy
- To whom correspondence should be addressed.
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4
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Chen K, Chen C, Li H, Yang J, Xiang M, Wang H, Xie Z. Widespread translational control regulates retinal development in mouse. Nucleic Acids Res 2021; 49:9648-9664. [PMID: 34469513 PMCID: PMC8464051 DOI: 10.1093/nar/gkab749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022] Open
Abstract
Retinal development is tightly regulated to ensure the generation of appropriate cell types and the assembly of functional neuronal circuitry. Despite remarkable advances have been made in understanding regulation of gene expression during retinal development, how translational regulation guides retinogenesis is less understood. Here, we conduct a comprehensive translatome and transcriptome survey to the mouse retinogenesis from the embryonic to the adult stages. We discover thousands of genes that have dynamic changes at the translational level and pervasive translational regulation in a developmental stage-specific manner with specific biological functions. We further identify genes whose translational efficiencies are frequently controlled by changing usage in upstream open reading frame during retinal development. These genes are enriched for biological functions highly important to neurons, such as neuron projection organization and microtubule-based protein transport. Surprisingly, we discover hundreds of previously uncharacterized micropeptides, translated from putative long non-coding RNAs and circular RNAs. We validate their protein products in vitro and in vivo and demonstrate their potentials in regulating retinal development. Together, our study presents a rich and complex landscape of translational regulation and provides novel insights into their roles during retinogenesis.
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Affiliation(s)
- Kaining Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Congying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Huihui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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5
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Li J, Liu F, Lv Y, Sun K, Zhao Y, Reilly J, Zhang Y, Tu J, Yu S, Liu X, Qin Y, Huang Y, Gao P, Jia D, Chen X, Han Y, Shu X, Luo D, Tang Z, Liu M. Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing. Nucleic Acids Res 2021; 49:2027-2043. [PMID: 33476374 PMCID: PMC7913766 DOI: 10.1093/nar/gkab003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis, especially in neural tissues. Mutations in pre-mRNAs processing factor 31 (PRPF31) cause autosomal dominant retinitis pigmentosa, a progressive retinal degeneration disease. The transcriptome-wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here, we showed that the differentiation and viability of retinal progenitor cells (RPCs) are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level, significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild-type human PRPF31 rather than the disease-associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak 5′ splicing site. Moreover, genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events, which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis.
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Affiliation(s)
- Jingzhen Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuntong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Science, Wuhan 430072, PR China
| | - Jamas Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, UK
| | - Yangjun Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yayun Qin
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, UK
| | - Daji Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Science, Wuhan 430072, PR China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
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6
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The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease. Int J Mol Sci 2021; 22:ijms22041855. [PMID: 33673358 PMCID: PMC7917623 DOI: 10.3390/ijms22041855] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing of mRNA is an essential mechanism to regulate and increase the diversity of the transcriptome and proteome. Alternative splicing frequently occurs in a tissue- or time-specific manner, contributing to differential gene expression between cell types during development. Neural tissues present extremely complex splicing programs and display the highest number of alternative splicing events. As an extension of the central nervous system, the retina constitutes an excellent system to illustrate the high diversity of neural transcripts. The retina expresses retinal specific splicing factors and produces a large number of alternative transcripts, including exclusive tissue-specific exons, which require an exquisite regulation. In fact, a current challenge in the genetic diagnosis of inherited retinal diseases stems from the lack of information regarding alternative splicing of retinal genes, as a considerable percentage of mutations alter splicing or the relative production of alternative transcripts. Modulation of alternative splicing in the retina is also instrumental in the design of novel therapeutic approaches for retinal dystrophies, since it enables precision medicine for specific mutations.
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7
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874
expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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8
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2020; 80:100874. [PMID: 32553897 DOI: 10.1016/j.preteyeres.2020.100874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
Abstract
Mutations which induce aberrant transcript splicing represent a distinct class of disease-causing genetic variants in retinal disease genes. Such mutations may either weaken or erase regular splice sites or create novel splice sites which alter exon recognition. While mutations affecting the canonical GU-AG dinucleotides at the splice donor and splice acceptor site are highly predictive to cause a splicing defect, other variants in the vicinity of the canonical splice sites or those affecting additional cis-acting regulatory sequences within exons or introns are much more difficult to assess or even to recognize and require additional experimental validation. Splicing mutations are unique in that the actual outcome for the transcript (e.g. exon skipping, pseudoexon inclusion, intron retention) and the encoded protein can be quite different depending on the individual mutation. In this article, we present an overview on the current knowledge about and impact of splicing mutations in inherited retinal diseases. We introduce the most common sub-classes of splicing mutations including examples from our own work and others and discuss current strategies for the identification and validation of splicing mutations, as well as therapeutic approaches, open questions, and future perspectives in this field of research.
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9
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Collin GB, Won J, Krebs MP, Hicks WJ, Charette JR, Naggert JK, Nishina PM. Disruption in murine Eml1 perturbs retinal lamination during early development. Sci Rep 2020; 10:5647. [PMID: 32221352 PMCID: PMC7101416 DOI: 10.1038/s41598-020-62373-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/09/2020] [Indexed: 11/23/2022] Open
Abstract
During mammalian development, establishing functional neural networks in stratified tissues of the mammalian central nervous system depends upon the proper migration and positioning of neurons, a process known as lamination. In particular, the pseudostratified neuroepithelia of the retina and cerebrocortical ventricular zones provide a platform for progenitor cell proliferation and migration. Lamination defects in these tissues lead to mispositioned neurons, disrupted neuronal connections, and abnormal function. The molecular mechanisms necessary for proper lamination in these tissues are incompletely understood. Here, we identified a nonsense mutation in the Eml1 gene in a novel murine model, tvrm360, displaying subcortical heterotopia, hydrocephalus and disorganization of retinal architecture. In the retina, Eml1 disruption caused abnormal positioning of photoreceptor cell nuclei early in development. Upon maturation, these ectopic photoreceptors possessed cilia and formed synapses but failed to produce robust outer segments, implying a late defect in photoreceptor differentiation secondary to mislocalization. In addition, abnormal positioning of Müller cell bodies and bipolar cells was evident throughout the inner neuroblastic layer. Basal displacement of mitotic nuclei in the retinal neuroepithelium was observed in tvrm360 mice at postnatal day 0. The abnormal positioning of retinal progenitor cells at birth and ectopic presence of photoreceptors and secondary neurons upon maturation suggest that EML1 functions early in eye development and is crucial for proper retinal lamination during cellular proliferation and development.
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Affiliation(s)
- G B Collin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - J Won
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - M P Krebs
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - W J Hicks
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - J R Charette
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - J K Naggert
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - P M Nishina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA.
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10
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ASCOT identifies key regulators of neuronal subtype-specific splicing. Nat Commun 2020; 11:137. [PMID: 31919425 PMCID: PMC6952364 DOI: 10.1038/s41467-019-14020-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022] Open
Abstract
Public archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize splice variants across tens of thousands of bulk and single-cell data sets in the public archive. To demonstrate the utility of ASCOT, we identify novel cell type-specific alternative exons across the nervous system and leverage ENCODE and GTEx data sets to study the unique splicing of photoreceptors. We find that PTBP1 knockdown and MSI1 and PCBP2 overexpression are sufficient to activate many photoreceptor-specific exons in HepG2 liver cancer cells. This work demonstrates how large-scale analysis of public RNA-Seq data sets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.
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11
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Mellough CB, Bauer R, Collin J, Dorgau B, Zerti D, Dolan DWP, Jones CM, Izuogu OG, Yu M, Hallam D, Steyn JS, White K, Steel DH, Santibanez-Koref M, Elliott DJ, Jackson MS, Lindsay S, Grellscheid S, Lako M. An integrated transcriptional analysis of the developing human retina. Development 2019; 146:146/2/dev169474. [PMID: 30696714 PMCID: PMC6361134 DOI: 10.1242/dev.169474] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/24/2018] [Indexed: 12/11/2022]
Abstract
The scarcity of embryonic/foetal material as a resource for direct study means that there is still limited understanding of human retina development. Here, we present an integrated transcriptome analysis combined with immunohistochemistry in human eye and retinal samples from 4 to 19 post-conception weeks. This analysis reveals three developmental windows with specific gene expression patterns that informed the sequential emergence of retinal cell types and enabled identification of stage-specific cellular and biological processes, and transcriptional regulators. Each stage is characterised by a specific set of alternatively spliced transcripts that code for proteins involved in the formation of the photoreceptor connecting cilium, pre-mRNA splicing and epigenetic modifiers. Importantly, our data show that the transition from foetal to adult retina is characterised by a large increase in the percentage of mutually exclusive exons that code for proteins involved in photoreceptor maintenance. The circular RNA population is also defined and shown to increase during retinal development. Collectively, these data increase our understanding of human retinal development and the pre-mRNA splicing process, and help to identify new candidate disease genes.
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Affiliation(s)
- Carla B. Mellough
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK,Lions Eye Institute, 2 Verdun Street, Nedlands, Perth, WA 6009, Australia
| | - Roman Bauer
- School of Computing, Newcastle University, Newcastle NE4 5TG, UK
| | - Joseph Collin
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Birthe Dorgau
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Darin Zerti
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - David W. P. Dolan
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Carl M. Jones
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Osagie G. Izuogu
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Min Yu
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Dean Hallam
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Jannetta S. Steyn
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Kathryn White
- EM Research Services, Newcastle University, Newcastle NE2 4HH, UK
| | - David H. Steel
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | | | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Michael S. Jackson
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Sushma Grellscheid
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
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12
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Identification of novel transcripts and peptides in developing murine lens. Sci Rep 2018; 8:11162. [PMID: 30042402 PMCID: PMC6057992 DOI: 10.1038/s41598-018-28727-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/19/2018] [Indexed: 01/09/2023] Open
Abstract
We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). Here, we extend our analyses to identify novel transcripts and peptides in developing mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. Additionally, we identified 13,281 novel alternative splicing (AS) events in mouse lens including 6,990 exon skipping (ES), 2,447 alternative 3' splice site (A3SS), 1,900 alternative 5' splice site (A5SS), 1,771 mutually exclusive exons (MXE), and 173 intron retention (IR). Finally, we integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. All 20 peptides were validated through matching MS/MS spectra of synthetic peptides. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens.
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13
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Zelinger L, Swaroop A. RNA Biology in Retinal Development and Disease. Trends Genet 2018; 34:341-351. [PMID: 29395379 DOI: 10.1016/j.tig.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 02/06/2023]
Abstract
For decades, RNA has served in a supporting role between the genetic carrier (DNA) and the functional molecules (proteins). It is finally time for RNA to take center stage in all aspects of biology. The retina provides a unique opportunity to dissect the molecular underpinnings of neuronal diversity and disease. Transcriptome profiles of the retina and its resident cell types have unraveled unique features of the RNA landscape. The discovery of distinct RNA molecules and the recognition that RNA processing is a major cause of retinal neurodegeneration have prompted the design of biomarkers and novel therapeutic paradigms. We review here RNA biology as it pertains to the retina, emphasizing new avenues for investigations in development and disease.
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Affiliation(s)
- Lina Zelinger
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Carey KT, Wickramasinghe VO. Regulatory Potential of the RNA Processing Machinery: Implications for Human Disease. Trends Genet 2018; 34:279-290. [PMID: 29329719 DOI: 10.1016/j.tig.2017.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/14/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Splicing and nuclear export of mRNA are critical steps in the gene expression pathway. While RNA processing factors can perform general, essential functions for intron removal and bulk export of mRNA, emerging evidence highlights that the core RNA splicing and export machineries also display regulatory potential. Here, we discuss recent insights into how this regulatory potential can selectively alter gene expression and regulate important biological processes. We also highlight the participation of RNA processing pathways in the cellular response to DNA damage at multiple levels. These findings have important implications for the contribution of selective mRNA processing and export to the development of human cancers and neurodegenerative disorders.
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Affiliation(s)
- Kirstyn T Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
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15
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Kim JW, Yang HJ, Brooks MJ, Zelinger L, Karakülah G, Gotoh N, Boleda A, Gieser L, Giuste F, Whitaker DT, Walton A, Villasmil R, Barb JJ, Munson PJ, Kaya KD, Chaitankar V, Cogliati T, Swaroop A. NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. Cell Rep 2017; 17:2460-2473. [PMID: 27880916 DOI: 10.1016/j.celrep.2016.10.074] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/29/2016] [Accepted: 10/20/2016] [Indexed: 01/01/2023] Open
Abstract
Gene regulatory networks (GRNs) guiding differentiation of cell types and cell assemblies in the nervous system are poorly understood because of inherent complexities and interdependence of signaling pathways. Here, we report transcriptome dynamics of differentiating rod photoreceptors in the mammalian retina. Given that the transcription factor NRL determines rod cell fate, we performed expression profiling of developing NRL-positive (rods) and NRL-negative (S-cone-like) mouse photoreceptors. We identified a large-scale, sharp transition in the transcriptome landscape between postnatal days 6 and 10 concordant with rod morphogenesis. Rod-specific temporal DNA methylation corroborated gene expression patterns. De novo assembly and alternative splicing analyses revealed previously unannotated rod-enriched transcripts and the role of NRL in transcript maturation. Furthermore, we defined the relationship of NRL with other transcriptional regulators and downstream cognate effectors. Our studies provide the framework for comprehensive system-level analysis of the GRN underlying the development of a single sensory neuron, the rod photoreceptor.
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Affiliation(s)
- Jung-Woong Kim
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA; Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun-Jin Yang
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew John Brooks
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Lina Zelinger
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Gökhan Karakülah
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Norimoto Gotoh
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA; Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Alexis Boleda
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Linn Gieser
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Felipe Giuste
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Dustin Thad Whitaker
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA; Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX 77843, USA
| | - Ashley Walton
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafael Villasmil
- Flow Cytometry Core, NEI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Joanna Barb
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Jonathan Munson
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Koray Dogan Kaya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Vijender Chaitankar
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Tiziana Cogliati
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD 20892, USA.
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Xu M, Xie Y(A, Abouzeid H, Gordon CT, Fiorentino A, Sun Z, Lehman A, Osman IS, Dharmat R, Riveiro-Alvarez R, Bapst-Wicht L, Babino D, Arno G, Busetto V, Zhao L, Li H, Lopez-Martinez MA, Azevedo LF, Hubert L, Pontikos N, Eblimit A, Lorda-Sanchez I, Kheir V, Plagnol V, Oufadem M, Soens ZT, Yang L, Bole-Feysot C, Pfundt R, Allaman-Pillet N, Nitschké P, Cheetham ME, Lyonnet S, Agrawal SA, Li H, Pinton G, Michaelides M, Besmond C, Li Y, Yuan Z, von Lintig J, Webster AR, Le Hir H, Stoilov P, Amiel J, Hardcastle AJ, Ayuso C, Sui R, Chen R, Allikmets R, Schorderet DF, Black G, Hall G, Gillespie R, Ramsden S, Manson F, Sergouniotis P, Inglehearn C, Toomes C, Ali M, McKibbin M, Poulter J, Lord E, Nemeth A, Halford S, Downes S, Yu J. Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies. Am J Hum Genet 2017; 100:592-604. [PMID: 28285769 DOI: 10.1016/j.ajhg.2017.02.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 02/15/2017] [Indexed: 10/20/2022] Open
Abstract
Pre-mRNA splicing factors play a fundamental role in regulating transcript diversity both temporally and spatially. Genetic defects in several spliceosome components have been linked to a set of non-overlapping spliceosomopathy phenotypes in humans, among which skeletal developmental defects and non-syndromic retinitis pigmentosa (RP) are frequent findings. Here we report that defects in spliceosome-associated protein CWC27 are associated with a spectrum of disease phenotypes ranging from isolated RP to severe syndromic forms. By whole-exome sequencing, recessive protein-truncating mutations in CWC27 were found in seven unrelated families that show a range of clinical phenotypes, including retinal degeneration, brachydactyly, craniofacial abnormalities, short stature, and neurological defects. Remarkably, variable expressivity of the human phenotype can be recapitulated in Cwc27 mutant mouse models, with significant embryonic lethality and severe phenotypes in the complete knockout mice while mice with a partial loss-of-function allele mimic the isolated retinal degeneration phenotype. Our study describes a retinal dystrophy-related phenotype spectrum as well as its genetic etiology and highlights the complexity of the spliceosomal gene network.
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17
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Disparate Regulatory Mechanisms Control Fat3 and P75NTR Protein Transport through a Conserved Kif5-Interaction Domain. PLoS One 2016; 11:e0165519. [PMID: 27788242 PMCID: PMC5082931 DOI: 10.1371/journal.pone.0165519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/13/2016] [Indexed: 11/19/2022] Open
Abstract
Directed transport delivers proteins to specific cellular locations and is one mechanism by which cells establish and maintain polarized cellular architectures. The atypical cadherin Fat3 directs the polarized extension of dendrites in retinal amacrine cells by influencing the distribution of cytoskeletal regulators during retinal development, however the mechanisms regulating the distribution of Fat3 remain unclear. We report a novel Kinesin/Kif5 Interaction domain (Kif5-ID) in Fat3 that facilitates Kif5B binding, and determines the distribution of Fat3 cytosolic domain constructs in neurons and MDCK cells. The Kif5-ID sequence is conserved in the neurotrophin receptor P75NTR, which also binds Kif5B, and Kif5-ID mutations similarly result in P75NTR mislocalization. Despite these similarities, Kif5B-mediated protein transport is differentially regulated by these two cargos. For Fat3, the Kif5-ID is regulated by alternative splicing, and the timecourse of splicing suggests that the distribution of Fat3 may switch between early and later stages of retinal development. In contrast, P75NTR binding to Kif5B is enhanced by tyrosine phosphorylation and thus has the potential to be dynamically regulated on a more rapid time scale.
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18
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Bolch SN, Dugger DR, Chong T, McDowell JH, Smith WC. A Splice Variant of Bardet-Biedl Syndrome 5 (BBS5) Protein that Is Selectively Expressed in Retina. PLoS One 2016; 11:e0148773. [PMID: 26867008 PMCID: PMC4750968 DOI: 10.1371/journal.pone.0148773] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/22/2016] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Bardet-Biedl syndrome is a complex ciliopathy that usually manifests with some form of retinal degeneration, amongst other ciliary-related deficiencies. One of the genetic causes of this syndrome results from a defect in Bardet-Biedl Syndrome 5 (BBS5) protein. BBS5 is one component of the BBSome, a complex of proteins that regulates the protein composition in cilia. In this study, we identify a smaller molecular mass form of BBS5 as a variant formed by alternative splicing and show that expression of this splice variant is restricted to the retina. METHODS Reverse transcription PCR from RNA was used to isolate and identify potential alternative transcripts of Bbs5. A peptide unique to the C-terminus of the BBS5 splice variant was synthesized and used to prepare antibodies that selectively recognized the BBS5 splice variant. These antibodies were used on immunoblots of tissue extracts to determine the extent of expression of the alternative transcript and on tissue slices to determine the localization of expressed protein. Pull-down of fluorescently labeled arrestin1 by immunoprecipitation of the BBS5 splice variant was performed to assess functional interaction between the two proteins. RESULTS PCR from mouse retinal cDNA using Bbs5-specific primers amplified a unique cDNA that was shown to be a splice variant of BBS5 resulting from the use of cryptic splicing sites in Intron 7. The resulting transcript codes for a truncated form of the BBS5 protein with a unique 24 amino acid C-terminus, and predicted 26.5 kD molecular mass. PCR screening of RNA isolated from various ciliated tissues and immunoblots of protein extracts from these same tissues showed that this splice variant was expressed in retina, but not brain, heart, kidney, or testes. Quantitative PCR showed that the splice variant transcript is 8.9-fold (+/- 1.1-fold) less abundant than the full-length transcript. In the retina, the splice variant of BBS5 appears to be most abundant in the connecting cilium of photoreceptors, where BBS5 is also localized. Like BBS5, the binding of BBS5L to arrestin1 can be modulated by phosphorylation through protein kinase C. CONCLUSIONS In this study we have identified a novel splice variant of BBS5 that appears to be expressed only in the retina. The BBS5 splice variant is expressed at approximately 10% of full-length BBS5 level. No unique functional or localization properties could be identified for the splice variant compared to BBS5.
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Affiliation(s)
- Susan N. Bolch
- Department of Ophthalmology, University of Florida, Gainesville, Florida, United States of America
| | - Donald R. Dugger
- Department of Ophthalmology, University of Florida, Gainesville, Florida, United States of America
| | - Timothy Chong
- Department of Ophthalmology, University of Florida, Gainesville, Florida, United States of America
| | - J. Hugh McDowell
- Department of Ophthalmology, University of Florida, Gainesville, Florida, United States of America
| | - W. Clay Smith
- Department of Ophthalmology, University of Florida, Gainesville, Florida, United States of America
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19
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Schweizer RM, vonHoldt BM, Harrigan R, Knowles JC, Musiani M, Coltman D, Novembre J, Wayne RK. Genetic subdivision and candidate genes under selection in North American grey wolves. Mol Ecol 2015; 25:380-402. [PMID: 26333947 DOI: 10.1111/mec.13364] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/05/2015] [Accepted: 08/25/2015] [Indexed: 12/12/2022]
Abstract
Previous genetic studies of the highly mobile grey wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat colour and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42 036 single-nucleotide polymorphisms (SNPs) in 111 North American grey wolves. Using these SNP data and individual-level measurements of 12 environmental variables, we identified six ecotypes: West Forest, Boreal Forest, Arctic, High Arctic, British Columbia and Atlantic Forest. Next, we explored signals of selection across these wolf ecotypes through the use of three complementary methods to detect selection: FST /haplotype homozygosity bivariate percentilae, bayescan, and environmentally correlated directional selection with bayenv. Across all methods, we found consistent signals of selection on genes related to morphology, coat coloration, metabolism, as predicted, as well as vision and hearing. In several high-ranking candidate genes, including LEPR, TYR and SLC14A2, we found variation in allele frequencies that follow environmental changes in temperature and precipitation, a result that is consistent with local adaptation rather than genetic drift. Our findings show that local adaptation can occur despite gene flow in a highly mobile species and can be detected through a moderately dense genomic scan. These patterns of local adaptation revealed by SNP genotyping likely reflect high fidelity to natal habitats of dispersing wolves, strong ecological divergence among habitats, and moderate levels of linkage in the wolf genome.
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Affiliation(s)
- Rena M Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Ryan Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - James C Knowles
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
| | - Marco Musiani
- Faculties of Environmental Design and Veterinary Medicine (Joint Appointment), EVDS, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
| | - David Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
| | - John Novembre
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
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20
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Alternative Splicing Shapes the Phenotype of a Mutation in BBS8 To Cause Nonsyndromic Retinitis Pigmentosa. Mol Cell Biol 2015; 35:1860-70. [PMID: 25776555 DOI: 10.1128/mcb.00040-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/10/2015] [Indexed: 01/27/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a genetic disorder affecting multiple systems and organs in the body. Several mutations in genes associated with BBS affect only photoreceptor cells and cause nonsyndromic retinitis pigmentosa (RP), raising the issue of why certain mutations manifest as a systemic disorder whereas other changes in the same gene affect only a specific cell type. Here, we show that cell-type-specific alternative splicing is responsible for confining the phenotype of the A-to-G substitution in the 3' splice site of BBS8 exon 2A (IVS1-2A>G mutation) in the BBS8 gene to photoreceptor cells. The IVS1-2A>G mutation leads to missplicing of BBS8 exon 2A, producing a frameshift in the BBS8 reading frame and thus eliminating the protein specifically in photoreceptor cells. Cell types other than photoreceptors skip exon 2A from the mature BBS8 transcript, which renders them immune to the mutation. We also show that the splicing of Bbs8 exon 2A in photoreceptors is directed exclusively by redundant splicing enhancers located in the adjacent introns. These intronic sequences are sufficient for photoreceptor-cell-specific splicing of heterologous exons, including an exon with a randomized sequence.
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21
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Whitney IE, Kautzman AG, Reese BE. Alternative splicing of the LIM-homeodomain transcription factor Isl1 in the mouse retina. Mol Cell Neurosci 2015; 65:102-13. [PMID: 25752730 DOI: 10.1016/j.mcn.2015.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 02/12/2015] [Accepted: 03/05/2015] [Indexed: 11/25/2022] Open
Abstract
Islet-1 (Isl1) is a LIM-homeodomain (LIM-HD) transcription factor that functions in a combinatorial manner with other LIM-HD proteins to direct the differentiation of distinct cell types within the central nervous system and many other tissues. A study of pancreatic cell lines showed that Isl1 is alternatively spliced generating a second isoform, Isl1β, which is missing 23 amino acids within the C-terminal region. This study examines the expression of the canonical and alternative Isl1 transcripts across other tissues, in particular, within the retina, where Isl1 is required for the differentiation of multiple neuronal cell types. The alternative splicing of Isl1 is shown to occur in multiple tissues, but the relative abundance of Isl1α and Isl1β expression varies greatly across them. In most tissues, Isl1α is the more abundant transcript, but in others the transcripts are expressed equally, or the alternative splice variant is dominant. Within the retina, differential expression of the two Isl1 transcripts increases as a function of development, with dynamic changes in expression peaking at E16.5 and again at P10. At the cellular level, individual retinal ganglion cells vary in their expression, with a subset of small-to-medium sized cells expressing only the alternative isoform. The functional significance of the difference in protein sequence between the two Isl1 isoforms was also assessed using a luciferase assay, demonstrating that the alternative isoform forms a less effective transcriptional complex for activating gene expression. These results demonstrate the differential presence of the canonical and alternative isoforms of Isl1 amongst retinal ganglion cell classes. As Isl1 participates in the differentiation of multiple cell types within the CNS, the present results support a role for alternative splicing in the establishment of cellular diversity in the developing nervous system.
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Affiliation(s)
- Irene E Whitney
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, United States; Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106-9625, United States.
| | - Amanda G Kautzman
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, United States; Department of Psychological & Brain Sciences, University of California at Santa Barbara, Santa Barbara, CA 93106-9660, United States.
| | - Benjamin E Reese
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, United States; Department of Psychological & Brain Sciences, University of California at Santa Barbara, Santa Barbara, CA 93106-9660, United States.
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22
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Wan J, Oliver VF, Wang G, Zhu H, Zack DJ, Merbs SL, Qian J. Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC Genomics 2015; 16:49. [PMID: 25652663 PMCID: PMC4331481 DOI: 10.1186/s12864-015-1271-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/22/2015] [Indexed: 01/20/2023] Open
Abstract
Background DNA methylation plays an important role in regulating gene expression during many biological processes. However, the mechanism of DNA-methylation-dependent gene regulation is not fully understood. Here, we explore two possible DNA methylation regulatory mechanisms with opposite modes of gene expression regulation. Results By comparing the genome-wide methylation and expression patterns in different tissues, we find that majority of tissue-specific differentially methylated regions (T-DMRs) are negatively correlated with expression of their associated genes (negative T-DMRs), consistent with the classical dogma that DNA methylation suppresses gene expression; however, a significant portion of T-DMRs are positively correlated with gene expression (positive T-DMRs). We observe that the positive T-DMRs have similar genomic location as negative T-DMRs, except that the positive T-DMRs are more enriched in the promoter regions. Both positive and negative T-DMRs are enriched in DNase I hypersensitivity sites (DHSs), suggesting that both are likely to be functional. The CpG sites of both positive and negative T-DMRs are also more evolutionarily conserved than the genomic background. Interestingly, the putative target genes of the positive T-DMR are enriched for negative regulators such as transcriptional repressors, suggesting a novel mode of indirect DNA methylation inhibition of expression through transcriptional repressors. Likewise, two distinct sets of DNA sequence motifs exist for positive and negative T-DMRs, suggesting that two distinct sets of transcription factors (TFs) are involved in positive and negative regulation mediated by DNA methylation. Conclusions We find both negative and positive association between T-DMRs and gene expression, which implies the existence of two different mechanisms of DNA methylation-dependent gene regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1271-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wan
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MA, USA.
| | - Verity F Oliver
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MA, USA.
| | - Guohua Wang
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MA, USA.
| | - Heng Zhu
- Department of Pharmacology and Molecular Science, Johns Hopkins University School of Medicine, Baltimore, MA, USA.
| | - Donald J Zack
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MA, USA. .,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MA, USA. .,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA, USA. .,Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA. .,Institut de la Vision, Université Pierre et Marie Curie, 17 rue Moreau, Paris, France.
| | - Shannath L Merbs
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MA, USA.
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MA, USA.
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Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength. Genome Biol 2015; 16:201. [PMID: 26392272 PMCID: PMC4578845 DOI: 10.1186/s13059-015-0749-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/27/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. The core spliceosome component PRPF8 is essential for spliceosome assembly through its participation in ribonucleoprotein (RNP) complexes for splice-site recognition, branch-point formation and catalysis. PRPF8 deficiency is linked to human diseases like retinitis pigmentosa or myeloid neoplasia, but its genome-wide effects on constitutive and alternative splicing remain unclear. RESULTS Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5' splice sites. iCLIP of spliceosome components reveals that PRPF8 depletion decreases RNP complex formation at most splice sites in exon-intron junctions throughout the genome. However, impaired splicing affects only a subset of human transcripts, enriched for mitotic cell cycle factors, leading to mitotic arrest. Preferentially retained introns and differentially used exons in the affected genes contain weak 5' splice sites, but are otherwise indistinguishable from adjacent spliced introns. Experimental enhancement of splice-site strength in mini-gene constructs overcomes the effects of PRPF8 depletion on the kinetics and fidelity of splicing during transcription. CONCLUSIONS Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5' splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. Our findings exemplify the regulatory potential of changes in the core spliceosome machinery, which may be relevant to slow-onset human genetic diseases linked to PRPF8 deficiency.
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Affiliation(s)
- Vihandha O. Wickramasinghe
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Mar Gonzàlez-Porta
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - David Perera
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Arthur R. Bartolozzi
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Christopher R. Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Martina Hallegger
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - John C. Marioni
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ashok R. Venkitaraman
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
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Li HD, Menon R, Omenn GS, Guan Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Proteomics 2014; 14:2709-18. [PMID: 25265570 DOI: 10.1002/pmic.201400170] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/11/2014] [Accepted: 09/23/2014] [Indexed: 01/08/2023]
Abstract
Canonical isoforms in different databases have been defined as the most prevalent, most conserved, most expressed, longest, or the one with the clearest description of domains or posttranslational modifications. In this article, we revisit these definitions of canonical isoforms based on functional genomics and proteomics evidence, focusing on mouse data. We report a novel functional relationship network-based approach for identifying the highest connected isoforms (HCIs). We show that 46% of these HCIs are not the longest transcripts. In addition, this approach revealed many genes that have more than one highly connected isoforms. Averaged across 175 RNA-seq datasets covering diverse tissues and conditions, 65% of the HCIs show higher expression levels than nonhighest connected isoforms at the transcript level. At the protein level, these HCIs highly overlap with the expressed splice variants, based on proteomic data from eight different normal tissues. These results suggest that a more confident definition of canonical isoforms can be made through integration of multiple lines of evidence, including HCIs defined by biological processes and pathways, expression prevalence at the transcript level, and relative or absolute abundance at the protein level. This integrative proteogenomics approach can successfully identify principal isoforms that are responsible for the canonical functions of genes.
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Affiliation(s)
- Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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Hao H, Veleri S, Sun B, Kim DS, Keeley PW, Kim JW, Yang HJ, Yadav SP, Manjunath SH, Sood R, Liu P, Reese BE, Swaroop A. Regulation of a novel isoform of Receptor Expression Enhancing Protein REEP6 in rod photoreceptors by bZIP transcription factor NRL. Hum Mol Genet 2014; 23:4260-71. [PMID: 24691551 DOI: 10.1093/hmg/ddu143] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Maf-family leucine zipper transcription factor NRL is essential for rod photoreceptor development and functional maintenance in the mammalian retina. Mutations in NRL are associated with human retinopathies, and loss of Nrl in mice leads to a cone-only retina with the complete absence of rods. Among the highly down-regulated genes in the Nrl(-/-) retina, we identified receptor expression enhancing protein 6 (Reep6), which encodes a member of a family of proteins involved in shaping of membrane tubules and transport of G-protein coupled receptors. Here, we demonstrate the expression of a novel Reep6 isoform (termed Reep6.1) in the retina by exon-specific Taqman assay and rapid analysis of complementary deoxyribonucleic acid (cDNA) ends (5'-RACE). The REEP6.1 protein includes 27 additional amino acids encoded by exon 5 and is specifically expressed in rod photoreceptors of developing and mature retina. Chromatin immunoprecipitation assay identified NRL binding within the Reep6 intron 1. Reporter assays in cultured cells and transfections in retinal explants mapped an intronic enhancer sequence that mediated NRL-directed Reep6.1 expression. We also demonstrate that knockdown of Reep6 in mouse and zebrafish resulted in death of retinal cells. Our studies implicate REEP6.1 as a key functional target of NRL-centered transcriptional regulatory network in rod photoreceptors.
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Affiliation(s)
- Hong Hao
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shobi Veleri
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bo Sun
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Douglas S Kim
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA, USA
| | - Patrick W Keeley
- Neuroscience Research Institute Department of Molecular, Cellular and Developmental Biology and
| | - Jung-Woong Kim
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hyun-Jin Yang
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharda P Yadav
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souparnika H Manjunath
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raman Sood
- Oncogenesis and Development Section and Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Liu
- Oncogenesis and Development Section and Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin E Reese
- Neuroscience Research Institute Department of Psychological and Brain Sciences, University of California at Santa Barbara, CA, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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26
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Cano M, Wang L, Wan J, Barnett BP, Ebrahimi K, Qian J, Handa JT. Oxidative stress induces mitochondrial dysfunction and a protective unfolded protein response in RPE cells. Free Radic Biol Med 2014; 69:1-14. [PMID: 24434119 PMCID: PMC3960355 DOI: 10.1016/j.freeradbiomed.2014.01.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/06/2013] [Accepted: 01/03/2014] [Indexed: 01/18/2023]
Abstract
How cells degenerate from oxidative stress in aging-related disease is incompletely understood. This study's intent was to identify key cytoprotective pathways activated by oxidative stress and determine the extent of their protection. Using an unbiased strategy with microarray analysis, we found that retinal pigmented epithelial (RPE) cells treated with cigarette smoke extract (CSE) had overrepresented genes involved in the antioxidant and unfolded protein response (UPR). Differentially expressed antioxidant genes were predominantly located in the cytoplasm, with no induction of genes that neutralize superoxide and H2O2 in the mitochondria, resulting in accumulation of superoxide and decreased ATP production. Simultaneously, CSE induced the UPR sensors IRE1α, p-PERK, and ATP6, including CHOP, which was cytoprotective because CHOP knockdown decreased cell viability. In mice given intravitreal CSE, the RPE had increased IRE1α and decreased ATP and developed epithelial-mesenchymal transition, as suggested by decreased LRAT abundance, altered ZO-1 immunolabeling, and dysmorphic cell shape. Mildly degenerated RPE from early age-related macular degeneration (AMD) samples had prominent IRE1α, but minimal mitochondrial TOM20 immunolabeling. Although oxidative stress is thought to induce an antioxidant response with cooperation between the mitochondria and the ER, herein we show that mitochondria become impaired sufficiently to induce epithelial-mesenchymal transition despite a protective UPR. With similar responses in early AMD samples, these results suggest that mitochondria are vulnerable to oxidative stress despite a protective UPR during the early phases of aging-related disease.
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Affiliation(s)
- Marisol Cano
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Lei Wang
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Jun Wan
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Bradley P Barnett
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Katayoon Ebrahimi
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Jiang Qian
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - James T Handa
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
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Eksi R, Li HD, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PLoS Comput Biol 2013; 9:e1003314. [PMID: 24244129 PMCID: PMC3820534 DOI: 10.1371/journal.pcbi.1003314] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 09/19/2013] [Indexed: 12/13/2022] Open
Abstract
Integrating large-scale functional genomic data has significantly accelerated our understanding of gene functions. However, no algorithm has been developed to differentiate functions for isoforms of the same gene using high-throughput genomic data. This is because standard supervised learning requires ‘ground-truth’ functional annotations, which are lacking at the isoform level. To address this challenge, we developed a generic framework that interrogates public RNA-seq data at the transcript level to differentiate functions for alternatively spliced isoforms. For a specific function, our algorithm identifies the ‘responsible’ isoform(s) of a gene and generates classifying models at the isoform level instead of at the gene level. Through cross-validation, we demonstrated that our algorithm is effective in assigning functions to genes, especially the ones with multiple isoforms, and robust to gene expression levels and removal of homologous gene pairs. We identified genes in the mouse whose isoforms are predicted to have disparate functionalities and experimentally validated the ‘responsible’ isoforms using data from mammary tissue. With protein structure modeling and experimental evidence, we further validated the predicted isoform functional differences for the genes Cdkn2a and Anxa6. Our generic framework is the first to predict and differentiate functions for alternatively spliced isoforms, instead of genes, using genomic data. It is extendable to any base machine learner and other species with alternatively spliced isoforms, and shifts the current gene-centered function prediction to isoform-level predictions. In mammalian genomes, a single gene can be alternatively spliced into multiple isoforms which greatly increase the functional diversity of the genome. In the human, more than 95% of multi-exon genes undergo alternative splicing. It is hard to computationally differentiate the functions for the splice isoforms of the same gene, because they are almost always annotated with the same functions and share similar sequences. In this paper, we developed a generic framework to identify the ‘responsible’ isoform(s) for each function that the gene carries out, and therefore predict functional assignment on the isoform level instead of on the gene level. Within this generic framework, we implemented and evaluated several related algorithms for isoform function prediction. We tested these algorithms through both computational evaluation and experimental validation of the predicted ‘responsible’ isoform(s) and the predicted disparate functions of the isoforms of Cdkn2a and of Anxa6. Our algorithm represents the first effort to predict and differentiate isoforms through large-scale genomic data integration.
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Affiliation(s)
- Ridvan Eksi
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yuchen Wen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (GSO); (MK); (YG)
| | - Matthias Kretzler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (GSO); (MK); (YG)
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (GSO); (MK); (YG)
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28
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Wan J, Oliver VF, Zhu H, Zack DJ, Qian J, Merbs SL. Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs. Nucleic Acids Res 2013; 41:8503-14. [PMID: 23887936 PMCID: PMC3794605 DOI: 10.1093/nar/gkt652] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The exact role of intragenic DNA methylation in regulating tissue-specific gene regulation is unclear. Recently, the DNA-binding protein CTCF has been shown to participate in the regulation of alternative splicing in a DNA methylation-dependent manner. To globally evaluate the relationship between DNA methylation and tissue-specific alternative splicing, we performed genome-wide DNA methylation profiling of mouse retina and brain. In protein-coding genes, tissue-specific differentially methylated regions (T-DMRs) were preferentially located in exons and introns. Gene ontology and evolutionary conservation analysis suggest that these T-DMRs are likely to be biologically relevant. More than 14% of alternatively spliced genes were associated with a T-DMR. T-DMR-associated genes were enriched for developmental genes, suggesting that a specific set of alternatively spliced genes may be regulated through DNA methylation. Novel DNA sequences motifs overrepresented in T-DMRs were identified as being associated with positive and/or negative regulation of alternative splicing in a position-dependent context. The majority of these evolutionarily conserved motifs contain a CpG dinucleotide. Some transcription factors, which recognize these motifs, are known to be involved in splicing. Our results suggest that DNA methylation-dependent alternative splicing is widespread and lay the foundation for further mechanistic studies of the role of DNA methylation in tissue-specific splicing regulation.
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Affiliation(s)
- Jun Wan
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Pharmacology and Molecular Science, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Neuroscience, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA and Institut de la Vision, 17 rue Moreau, 75012 Paris, France
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29
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Oliver VF, Wan J, Agarwal S, Zack DJ, Qian J, Merbs SL. A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples. Epigenetics Chromatin 2013; 6:17. [PMID: 23759032 PMCID: PMC3680319 DOI: 10.1186/1756-8935-6-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/13/2013] [Indexed: 02/08/2023] Open
Abstract
Background Growing evidence suggests that DNA methylation plays a role in tissue-specific differentiation. Current approaches to methylome analysis using enrichment with the methyl-binding domain protein (MBD) are restricted to large (≥1 μg) DNA samples, limiting the analysis of small tissue samples. Here we present a technique that enables characterization of genome-wide tissue-specific methylation patterns from nanogram quantities of DNA. Results We have developed a methodology utilizing MBD2b/MBD3L1 enrichment for methylated DNA, kinase pre-treated ligation-mediated PCR amplification (MeKL) and hybridization to the comprehensive high-throughput array for relative methylation (CHARM) customized tiling arrays, which we termed MeKL-chip. Kinase modification in combination with the addition of PEG has increased ligation-mediated PCR amplification over 20-fold, enabling >400-fold amplification of starting DNA. We have shown that MeKL-chip can be applied to as little as 20 ng of DNA, enabling comprehensive analysis of small DNA samples. Applying MeKL-chip to the mouse retina (a limited tissue source) and brain, 2,498 tissue-specific differentially methylated regions (T-DMRs) were characterized. The top five T-DMRs (Rgs20, Hes2, Nfic, Cckbr and Six3os1) were validated by pyrosequencing. Conclusions MeKL-chip enables genome-wide methylation analysis of nanogram quantities of DNA with a wide range of observed-to-expected CpG ratios due to the binding properties of the MBD2b/MBD3L1 protein complex. This methodology enabled the first analysis of genome-wide methylation in the mouse retina, characterizing novel T-DMRs.
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Affiliation(s)
- Verity F Oliver
- Department of Ophthalmology, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA.
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Dynamics of regulatory networks in the developing mouse retina. PLoS One 2012; 7:e46521. [PMID: 23056331 PMCID: PMC3463606 DOI: 10.1371/journal.pone.0046521] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 09/04/2012] [Indexed: 12/14/2022] Open
Abstract
Understanding gene regulation is crucial to dissect the molecular basis of human development and disease. Previous studies on transcription regulatory networks often focused on their static properties. Here we used retinal development as a model system to investigate the dynamics of regulatory networks that are comprised of transcription factors, microRNAs and other protein-coding genes. We found that the active sub-networks are topologically different at early and late stages of retinal development. At early stages, the active sub-networks tend to be highly connected, while at late stages, the active sub-networks are more organized in modular structures. Interestingly, network motif usage at early and late stages is also distinct. For example, network motifs containing reciprocal feedback regulatory relationships between two regulators are overrepresented in early developmental stages. Additionally, our analysis of regulatory network dynamics revealed a natural turning point at which the regulatory network undergoes drastic topological changes. Taken together, this work demonstrates that adding a dynamic dimension to network analysis can provide new insights into retinal development, and we suggest the same approach would likely be useful for the analysis of other developing tissues.
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