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Weber AI, Parthasarathy S, Borisova E, Epifanova E, Preußner M, Rusanova A, Ambrozkiewicz MC, Bessa P, Newman A, Müller L, Schaal H, Heyd F, Tarabykin V. Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression. Nucleic Acids Res 2023; 51:10218-10237. [PMID: 37697438 PMCID: PMC10602877 DOI: 10.1093/nar/gkad703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/13/2023] Open
Abstract
The seat of higher-order cognitive abilities in mammals, the neocortex, is a complex structure, organized in several layers. The different subtypes of principal neurons are distributed in precise ratios and at specific positions in these layers and are generated by the same neural progenitor cells (NPCs), steered by a spatially and temporally specified combination of molecular cues that are incompletely understood. Recently, we discovered that an alternatively spliced isoform of the TrkC receptor lacking the kinase domain, TrkC-T1, is a determinant of the corticofugal projection neuron (CFuPN) fate. Here, we show that the finely tuned balance between TrkC-T1 and the better known, kinase domain-containing isoform, TrkC-TK+, is cell type-specific in the developing cortex and established through the antagonistic actions of two RNA-binding proteins, Srsf1 and Elavl1. Moreover, our data show that Srsf1 promotes the CFuPN fate and Elavl1 promotes the callosal projection neuron (CPN) fate in vivo via regulating the distinct ratios of TrkC-T1 to TrkC-TK+. Taken together, we connect spatio-temporal expression of Srsf1 and Elavl1 in the developing neocortex with the regulation of TrkC alternative splicing and transcript stability and neuronal fate choice, thus adding to the mechanistic and functional understanding of alternative splicing in vivo.
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Affiliation(s)
- A Ioana Weber
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Srinivas Parthasarathy
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Ekaterina Borisova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ekaterina Epifanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Alexandra Rusanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Mateusz C Ambrozkiewicz
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Paraskevi Bessa
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew G Newman
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Lisa Müller
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Victor Tarabykin
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
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2
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Identification of alternative transcripts of NSD1 gene in Sotos Syndrome patients and healthy subjects. Gene 2023; 851:146970. [DOI: 10.1016/j.gene.2022.146970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
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3
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Sarantopoulou D, Brooks TG, Nayak S, Mrčela A, Lahens NF, Grant GR. Comparative evaluation of full-length isoform quantification from RNA-Seq. BMC Bioinformatics 2021; 22:266. [PMID: 34034652 PMCID: PMC8145802 DOI: 10.1186/s12859-021-04198-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 05/16/2021] [Indexed: 11/18/2022] Open
Abstract
Background Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short. Results Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control. Conclusions Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04198-1.
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Affiliation(s)
- Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Titus MB, Wright EG, Bono JM, Poliakon AK, Goldstein BR, Super MK, Young LA, Manaj M, Litchford M, Reist NE, Killian DJ, Olesnicky EC. The conserved alternative splicing factor caper regulates neuromuscular phenotypes during development and aging. Dev Biol 2021; 473:15-32. [PMID: 33508255 PMCID: PMC7987824 DOI: 10.1016/j.ydbio.2021.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
RNA-binding proteins play an important role in the regulation of post-transcriptional gene expression throughout the nervous system. This is underscored by the prevalence of mutations in genes encoding RNA splicing factors and other RNA-binding proteins in a number of neurodegenerative and neurodevelopmental disorders. The highly conserved alternative splicing factor Caper is widely expressed throughout the developing embryo and functions in the development of various sensory neural subtypes in the Drosophila peripheral nervous system. Here we find that caper dysfunction leads to aberrant neuromuscular junction morphogenesis, as well as aberrant locomotor behavior during larval and adult stages. Despite its widespread expression, our results indicate that caper function is required to a greater extent within the nervous system, as opposed to muscle, for neuromuscular junction development and for the regulation of adult locomotor behavior. Moreover, we find that Caper interacts with the RNA-binding protein Fmrp to regulate adult locomotor behavior. Finally, we show that caper dysfunction leads to various phenotypes that have both a sex and age bias, both of which are commonly seen in neurodegenerative disorders in humans.
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Affiliation(s)
- M Brandon Titus
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Ethan G Wright
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Andrea K Poliakon
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Brandon R Goldstein
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Meg K Super
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Lauren A Young
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Melpomeni Manaj
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Morgan Litchford
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Noreen E Reist
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
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5
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Noureen N, Wu S, Lv Y, Yang J, Alfred Yung WK, Gelfond J, Wang X, Koul D, Ludlow A, Zheng S. Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation. Nat Commun 2021; 12:139. [PMID: 33420056 PMCID: PMC7794223 DOI: 10.1038/s41467-020-20474-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the complex. Here we show that telomerase enzymatic activity can be robustly estimated from the expression of a 13-gene signature. We demonstrate the validity of the expression-based approach, named EXTEND, using cell lines, cancer samples, and non-neoplastic samples. When applied to over 9,000 tumors and single cells, we find a strong correlation between telomerase activity and cancer stemness. This correlation is largely driven by a small population of proliferating cancer cells that exhibits both high telomerase activity and cancer stemness. This study establishes a computational framework for quantifying telomerase enzymatic activity and provides new insights into the relationships among telomerase, cancer proliferation, and stemness.
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Affiliation(s)
- Nighat Noureen
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA
| | - Shaofang Wu
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Yingli Lv
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA
| | - Juechen Yang
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA
| | - W K Alfred Yung
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan Gelfond
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA
| | - Xiaojing Wang
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA
| | - Dimpy Koul
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Ludlow
- Department of Movement Science, University of Michigan, Ann Arbor, MI, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA.
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6
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Seo YA, Choi EK, Aring L, Paschall M, Iwase S. Transcriptome Analysis of the Cerebellum of Mice Fed a Manganese-Deficient Diet. Front Genet 2020; 11:558725. [PMID: 33408735 PMCID: PMC7780674 DOI: 10.3389/fgene.2020.558725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
Manganese (Mn), primarily acquired through diet, is required for brain function and development. Epidemiological studies have found an association between both low and high levels of Mn and impaired neurodevelopment in children. Recent genetic studies have revealed that patients with congenital Mn deficiency display severe psychomotor disability and cerebral and cerebellar atrophy. Although the impact of Mn on gene expression is beginning to be appreciated, Mn-dependent gene expression remains to be explored in vertebrate animals. The goal of this study was to use a mouse model to define the impact of a low-Mn diet on brain metal levels and gene expression. We interrogated gene expression changes in the Mn-deficient mouse brain at the genome-wide scale by RNA-seq analysis of the cerebellum of mice fed low or normal Mn diets. A total of 137 genes were differentially expressed in Mn-deficient cerebellums compared with Mn-adequate cerebellums (Padj < 0.05). Mn-deficient mice displayed downregulation of key pathways involved with "focal adhesion," "neuroactive ligand-receptor interaction," and "cytokine-cytokine receptor interaction" and upregulation of "herpes simplex virus 1 infection," "spliceosome," and "FoxO signaling pathway." Reactome pathway analysis identified upregulation of the splicing-related pathways and transcription-related pathways, as well as downregulation of "metabolism of carbohydrate," and "extracellular matrix organization," and "fatty acid metabolism" reactomes. The recurrent identifications of splicing-related pathways suggest that Mn deficiency leads to upregulation of splicing machineries and downregulation of diverse biological pathways.
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Affiliation(s)
- Young Ah Seo
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Eun-Kyung Choi
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Luisa Aring
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Molly Paschall
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
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7
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Wiley CA. Emergent Viral Infections of the CNS. J Neuropathol Exp Neurol 2020; 79:823-842. [PMID: 32647884 DOI: 10.1093/jnen/nlaa054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 02/07/2023] Open
Abstract
Biological evolution of the microbiome continually drives the emergence of human viral pathogens, a subset of which attack the nervous system. The sheer number of pathogens that have appeared, along with their abundance in the environment, demand our attention. For the most part, our innate and adaptive immune systems have successfully protected us from infection; however, in the past 5 decades, through pathogen mutation and ecosystem disruption, a dozen viruses emerged to cause significant neurologic disease. Most of these pathogens have come from sylvatic reservoirs having made the energetically difficult, and fortuitously rare, jump into humans. But the human microbiome is also replete with agents already adapted to the host that need only minor mutations to create neurotropic/toxic agents. While each host/virus symbiosis is unique, this review examines virologic and immunologic principles that govern the pathogenesis of different viral CNS infections that were described in the past 50 years (Influenza, West Nile Virus, Zika, Rift Valley Fever Virus, Hendra/Nipah, Enterovirus-A71/-D68, Human parechovirus, HIV, and SARS-CoV). Knowledge of these pathogens provides us the opportunity to respond and mitigate infection while at the same time prepare for inevitable arrival of unknown agents.
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Affiliation(s)
- Clayton A Wiley
- From the Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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8
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Sulakhe D, D'Souza M, Wang S, Balasubramanian S, Athri P, Xie B, Canzar S, Agam G, Gilliam TC, Maltsev N. Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. Brief Bioinform 2020; 20:1754-1768. [PMID: 29931155 DOI: 10.1093/bib/bby047] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
In recent years, the emphasis of scientific inquiry has shifted from whole-genome analyses to an understanding of cellular responses specific to tissue, developmental stage or environmental conditions. One of the central mechanisms underlying the diversity and adaptability of the contextual responses is alternative splicing (AS). It enables a single gene to encode multiple isoforms with distinct biological functions. However, to date, the functions of the vast majority of differentially spliced protein isoforms are not known. Integration of genomic, proteomic, functional, phenotypic and contextual information is essential for supporting isoform-based modeling and analysis. Such integrative proteogenomics approaches promise to provide insights into the functions of the alternatively spliced protein isoforms and provide high-confidence hypotheses to be validated experimentally. This manuscript provides a survey of the public databases supporting isoform-based biology. It also presents an overview of the potential global impact of AS on the human canonical gene functions, molecular interactions and cellular pathways.
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Affiliation(s)
- Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
| | - Mark D'Souza
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA
| | - Sheng Wang
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, USA
| | - Sandhya Balasubramanian
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Genentech, Inc. 1 DNA Way, Mail Stop: 35-6J, South San Francisco, CA, USA
| | - Prashanth Athri
- Department of Computer Science and Engineering, Amrita School of Engineering, Bengaluru, Amrita Vishwa Vidyapeetham, Kasavanahalli, Carmelaram P.O., Bengaluru, Karnataka, India
| | - Bingqing Xie
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - Stefan Canzar
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, USA.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gady Agam
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - T Conrad Gilliam
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
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9
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Meldolesi J. Alternative Splicing by NOVA Factors: From Gene Expression to Cell Physiology and Pathology. Int J Mol Sci 2020; 21:ijms21113941. [PMID: 32486302 PMCID: PMC7312376 DOI: 10.3390/ijms21113941] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/24/2022] Open
Abstract
NOVA1 and NOVA2, the two members of the NOVA family of alternative splicing factors, bind YCAY clusters of pre-mRNAs and assemble spliceosomes to induce the maintenance/removal of introns and exons, thus governing the development of mRNAs. Members of other splicing families operate analogously. Activity of NOVAs accounts for up to 700 alternative splicing events per cell, taking place both in the nucleus (co-transcription of mRNAs) and in the cytoplasm. Brain neurons express high levels of NOVAs, with NOVA1 predominant in cerebellum and spinal cord, NOVA2 in the cortex. Among brain physiological processes NOVAs play critical roles in axon pathfinding and spreading, structure and function of synapses, as well as the regulation of surface receptors and voltage-gated channels. In pathology, NOVAs contribute to neurodegenerative diseases and epilepsy. In vessel endothelial cells, NOVA2 is essential for angiogenesis, while in adipocytes, NOVA1 contributes to regulation of thermogenesis and obesity. In many cancers NOVA1 and also NOVA2, by interacting with specific miRNAs and by additional mechanisms, activate oncogenic roles promoting cell proliferation, colony formation, migration, and invasion. In conclusion, NOVAs regulate cell functions of physiological and pathological nature. Single cell identification and distinction, and new therapies addressed to NOVA targets might be developed in the near future.
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Affiliation(s)
- Jacopo Meldolesi
- Department of Neuroscience, San Raffaele Institute and San Raffaele University, via Olgettina 58, 20132 Milan, Italy
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10
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Olesnicky EC, Bono JM, Bell L, Schachtner LT, Lybecker MC. The RNA-binding protein caper is required for sensory neuron development in Drosophila melanogaster. Dev Dyn 2017; 246:610-624. [PMID: 28543982 DOI: 10.1002/dvdy.24523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/18/2017] [Accepted: 05/16/2017] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Alternative splicing mediated by RNA-binding proteins (RBPs) is emerging as a fundamental mechanism for the regulation of gene expression. Alternative splicing has been shown to be a widespread phenomenon that facilitates the diversification of gene products in a tissue-specific manner. Although defects in alternative splicing are rooted in many neurological disorders, only a small fraction of splicing factors have been investigated in detail. RESULTS We find that the splicing factor Caper is required for the development of multiple different mechanosensory neuron subtypes at multiple life stages in Drosophila melanogaster. Disruption of Caper function causes defects in dendrite morphogenesis of larval dendrite arborization neurons and neuronal positioning of embryonic proprioceptors, as well as the development and maintenance of adult mechanosensory bristles. Additionally, we find that Caper dysfunction results in aberrant locomotor behavior in adult flies. Transcriptome-wide analyses further support a role for Caper in alternative isoform regulation of genes that function in neurogenesis. CONCLUSIONS Our results provide the first evidence for a fundamental and broad requirement for the highly conserved splicing factor Caper in the development and maintenance of the nervous system and provide a framework for future studies on the detailed mechanism of Caper-mediated RNA regulation. Developmental Dynamics 246:610-624, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Laura Bell
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Logan T Schachtner
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Meghan C Lybecker
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
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11
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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12
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Shimada MK, Sanbonmatsu R, Yamaguchi-Kabata Y, Yamasaki C, Suzuki Y, Chakraborty R, Gojobori T, Imanishi T. Selection pressure on human STR loci and its relevance in repeat expansion disease. Mol Genet Genomics 2016; 291:1851-69. [PMID: 27290643 DOI: 10.1007/s00438-016-1219-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 05/21/2016] [Indexed: 12/30/2022]
Abstract
Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases.
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Affiliation(s)
- Makoto K Shimada
- Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan. .,National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan. .,Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan.
| | - Ryoko Sanbonmatsu
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Yumi Yamaguchi-Kabata
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Chisato Yamasaki
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Ranajit Chakraborty
- Health Science Center, University of North Texas, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | - Takashi Gojobori
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Computational Bioscience Research Center, King Abdullah University of Science and Technology, Ibn Al-Haytham Building (West), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tadashi Imanishi
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
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13
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Wiley CA, Bhardwaj N, Ross TM, Bissel SJ. Emerging Infections of CNS: Avian Influenza A Virus, Rift Valley Fever Virus and Human Parechovirus. Brain Pathol 2015; 25:634-50. [PMID: 26276027 PMCID: PMC4538697 DOI: 10.1111/bpa.12281] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 06/22/2015] [Indexed: 11/28/2022] Open
Abstract
History is replete with emergent pandemic infections that have decimated the human population. Given the shear mass of humans that now crowd the earth, there is every reason to suspect history will repeat itself. We describe three RNA viruses that have recently emerged in the human population to mediate severe neurological disease. These new diseases are results of new mutations in the infectious agents or new exposure pathways to the agents or both. To appreciate their pathogenesis, we summarize the essential virology and immune response to each agent. Infection is described in the context of known host defenses. Once the viruses evade immune defenses and enter central nervous system (CNS) cells, they rapidly co-opt host RNA processing to a cataclysmic extent. It is not clear why the brain is particularly susceptible to RNA viruses; but perhaps because of its tremendous dependence on RNA processing for physiological functioning, classical mechanisms of host defense (eg, interferon disruption of viral replication) are diminished or not available. Effectiveness of immunity, immunization and pharmacological therapies is reviewed to contextualize the scope of the public health challenge. Unfortunately, vaccines that confer protection from systemic disease do not necessarily confer protection for the brain after exposure through unconventional routes.
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Affiliation(s)
| | - Nitin Bhardwaj
- Department of Infectious Diseases and MicrobiologyUniversity of PittsburghPittsburghPA
- Present address:
Sanofi Pasteur1755 Steeles Avenue WestTorontoOntarioCanadaM2R 3T4
| | - Ted M. Ross
- Center for Vaccine DevelopmentUniversity of GeorgiaAthensGA
- Department of Infectious DiseasesUniversity of GeorgiaAthensGA
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14
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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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