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Jobbins AM, Yu S, Paterson HAB, Maude H, Kefala-Stavridi A, Speck C, Cebola I, Vernia S. Pre-RNA splicing in metabolic homeostasis and liver disease. Trends Endocrinol Metab 2023; 34:823-837. [PMID: 37673766 DOI: 10.1016/j.tem.2023.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
The liver plays a key role in sensing nutritional and hormonal inputs to maintain metabolic homeostasis. Recent studies into pre-mRNA splicing and alternative splicing (AS) and their effects on gene expression have revealed considerable transcriptional complexity in the liver, both in health and disease. While the contribution of these mechanisms to cell and tissue identity is widely accepted, their role in physiological and pathological contexts within tissues is just beginning to be appreciated. In this review, we showcase recent studies on the splicing and AS of key genes in metabolic pathways in the liver, the effect of metabolic signals on the spliceosome, and therapeutic intervention points based on RNA splicing.
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Affiliation(s)
- Andrew M Jobbins
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Sijia Yu
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Helen A B Paterson
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Antonia Kefala-Stavridi
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Christian Speck
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Santiago Vernia
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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2
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Hibino E, Ichiyama Y, Tsukamura A, Senju Y, Morimune T, Ohji M, Maruo Y, Nishimura M, Mori M. Bex1 is essential for ciliogenesis and harbours biomolecular condensate-forming capacity. BMC Biol 2022; 20:42. [PMID: 35144600 PMCID: PMC8830175 DOI: 10.1186/s12915-022-01246-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Primary cilia are sensory organelles crucial for organ development. The pivotal structure of the primary cilia is a microtubule that is generated via tubulin polymerization reaction that occurs in the basal body. It remains to be elucidated how molecules with distinct physicochemical properties contribute to the formation of the primary cilia. RESULTS Here we show that brain expressed X-linked 1 (Bex1) plays an essential role in tubulin polymerization and primary cilia formation. The Bex1 protein shows the physicochemical property of being an intrinsically disordered protein (IDP). Bex1 shows cell density-dependent accumulation as a condensate either in nucleoli at a low cell density or at the apical cell surface at a high cell density. The apical Bex1 localizes to the basal body. Bex1 knockout mice present ciliopathy phenotypes and exhibit ciliary defects in the retina and striatum. Bex1 recombinant protein shows binding capacity to guanosine triphosphate (GTP) and forms the condensate that facilitates tubulin polymerization in the reconstituted system. CONCLUSIONS Our data reveals that Bex1 plays an essential role for the primary cilia formation through providing the reaction field for the tubulin polymerization.
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Affiliation(s)
- Emi Hibino
- Molecular Neuroscience Research Centre (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yusuke Ichiyama
- Department of Ophthalmology, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Atsushi Tsukamura
- Molecular Neuroscience Research Centre (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan.,Department of Paediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan.,Department of Vascular Physiology, National Cerebral and Cardiovascular Centre Research Institute, 6-1 Kishibe-Shimmachi, Suita, Osaka, 564-8565, Japan
| | - Yosuke Senju
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Takao Morimune
- Molecular Neuroscience Research Centre (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan.,Department of Paediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan.,Department of Vascular Physiology, National Cerebral and Cardiovascular Centre Research Institute, 6-1 Kishibe-Shimmachi, Suita, Osaka, 564-8565, Japan
| | - Masahito Ohji
- Department of Ophthalmology, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Yoshihiro Maruo
- Department of Paediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Masaki Nishimura
- Molecular Neuroscience Research Centre (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Masaki Mori
- Molecular Neuroscience Research Centre (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan. .,Department of Vascular Physiology, National Cerebral and Cardiovascular Centre Research Institute, 6-1 Kishibe-Shimmachi, Suita, Osaka, 564-8565, Japan.
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Morimune T, Tano A, Tanaka Y, Yukiue H, Yamamoto T, Tooyama I, Maruo Y, Nishimura M, Mori M. Gm14230 controls Tbc1d24 cytoophidia and neuronal cellular juvenescence. PLoS One 2021; 16:e0248517. [PMID: 33886577 PMCID: PMC8062039 DOI: 10.1371/journal.pone.0248517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/28/2021] [Indexed: 11/19/2022] Open
Abstract
It is not fully understood how enzymes are regulated in the tiny reaction field of a cell. Several enzymatic proteins form cytoophidia, a cellular macrostructure to titrate enzymatic activities. Here, we show that the epileptic encephalopathy-associated protein Tbc1d24 forms cytoophidia in neuronal cells both in vitro and in vivo. The Tbc1d24 cytoophidia are distinct from previously reported cytoophidia consisting of inosine monophosphate dehydrogenase (Impdh) or cytidine-5'-triphosphate synthase (Ctps). Tbc1d24 cytoophidia is induced by loss of cellular juvenescence caused by depletion of Gm14230, a juvenility-associated lncRNA (JALNC) and zeocin treatment. Cytoophidia formation is associated with impaired enzymatic activity of Tbc1d24. Thus, our findings reveal the property of Tbc1d24 to form cytoophidia to maintain neuronal cellular juvenescence.
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Affiliation(s)
- Takao Morimune
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
- Department of Pediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Ayami Tano
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Yuya Tanaka
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Haruka Yukiue
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
| | - Takefumi Yamamoto
- Central Research Laboratory, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
| | - Yoshihiro Maruo
- Department of Pediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
| | - Masaki Nishimura
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
| | - Masaki Mori
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga, Japan
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
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4
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Abstract
The developing heart is formed of two tissue layers separated by an extracellular matrix (ECM) that provides chemical and physical signals to cardiac cells. While deposition of specific ECM components creates matrix diversity, the cardiac ECM is also dynamic, with modification and degradation playing important roles in ECM maturation and function. In this Review, we discuss the spatiotemporal changes in ECM composition during cardiac development that support distinct aspects of heart morphogenesis. We highlight conserved requirements for specific ECM components in human cardiac development, and discuss emerging evidence of a central role for the ECM in promoting heart regeneration.
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Affiliation(s)
| | - Emily S Noël
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
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5
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Wu P, Zhang M, Webster NJG. Alternative RNA Splicing in Fatty Liver Disease. Front Endocrinol (Lausanne) 2021; 12:613213. [PMID: 33716968 PMCID: PMC7953061 DOI: 10.3389/fendo.2021.613213] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Alternative RNA splicing is a process by which introns are removed and exons are assembled to construct different RNA transcript isoforms from a single pre-mRNA. Previous studies have demonstrated an association between dysregulation of RNA splicing and a number of clinical syndromes, but the generality to common disease has not been established. Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease affecting one-third of adults worldwide, increasing the risk of cirrhosis and hepatocellular carcinoma (HCC). In this review we focus on the change in alternative RNA splicing in fatty liver disease and the role for splicing regulation in disease progression.
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Affiliation(s)
- Panyisha Wu
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
| | - Moya Zhang
- University of California Los Angeles, Los Angeles, CA, United States
| | - Nicholas J. G. Webster
- VA San Diego Healthcare System, San Diego, CA, United States
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
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6
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Neuroepithelial cell competition triggers loss of cellular juvenescence. Sci Rep 2020; 10:18044. [PMID: 33093561 PMCID: PMC7582913 DOI: 10.1038/s41598-020-74874-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/07/2020] [Indexed: 12/02/2022] Open
Abstract
Cell competition is a cell–cell interaction mechanism which maintains tissue homeostasis through selective elimination of unfit cells. During early brain development, cells are eliminated through apoptosis. How cells are selected to undergo elimination remains unclear. Here we aimed to identify a role for cell competition in the elimination of suboptimal cells using an in vitro neuroepithelial model. Cell competition was observed when neural progenitor HypoE-N1 cells expressing RASV12 were surrounded by normal cells in the co-culture. The elimination through apoptosis was observed by cellular changes of RASV12 cells with rounding/fragmented morphology, by SYTOX blue-positivity, and by expression of apoptotic markers active caspase-3 and cleaved PARP. In this model, expression of juvenility-associated genes Srsf7 and Ezh2 were suppressed under cell-competitive conditions. Srsf7 depletion led to loss of cellular juvenescence characterized by suppression of Ezh2, cell growth impairment and enhancement of senescence-associated proteins. The cell bodies of eliminated cells were engulfed by the surrounding cells through phagocytosis. Our data indicates that neuroepithelial cell competition may have an important role for maintaining homeostasis in the neuroepithelium by eliminating suboptimal cells through loss of cellular juvenescence.
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Kadota Y, Jam FA, Yukiue H, Terakado I, Morimune T, Tano A, Tanaka Y, Akahane S, Fukumura M, Tooyama I, Mori M. Srsf7 Establishes the Juvenile Transcriptome through Age-Dependent Alternative Splicing in Mice. iScience 2020; 23:100929. [PMID: 32146325 PMCID: PMC7063262 DOI: 10.1016/j.isci.2020.100929] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/26/2020] [Accepted: 02/17/2020] [Indexed: 11/25/2022] Open
Abstract
The juvenile phase is characterized by continuously progressing physiological processes such as growth and maturation, which are accompanied by transitions in gene expression. The contribution of transcriptome dynamics to the establishment of juvenile properties remains unclear. Here, we investigated alternative splicing (AS) events in postnatal growth and elucidated the landscape of age-dependent alternative splicing (ADAS) in C57BL/6 mice. Our analysis of ADAS in the cerebral cortex, cardiomyocytes, and hepatocytes revealed numerous juvenile-specific splicing isoforms that shape the juvenile transcriptome, which in turn functions as a basis for the highly anabolic status of juvenile cells. Mechanistically, the juvenile-expressed splicing factor Srsf7 mediates ADAS, as exemplified by switching from juvenile to adult forms of anabolism-associated genes Eif4a2 and Rbm7. Suppression of Srsf7 results in “fast-forwarding” of this transcriptome transition, causing impaired anabolism and growth in mice. Thus, juvenile-specific AS is indispensable for the anabolic state of juveniles and differentiates juveniles from adults. Age-dependent alternative splicing (ADAS) was determined in mice Srsf7 depletion causes loss of cellular juvenescence Srsf7 mutation causes a shift from juvenile to adult-type transcriptome Srsf7 promotes juvenile growth and anabolism through ADAS
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Affiliation(s)
- Yosuke Kadota
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Faidruz Azura Jam
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Haruka Yukiue
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Ichiro Terakado
- Research Center for Animal Life Science (RCALS), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Takao Morimune
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan; Department of Pediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Ayami Tano
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Yuya Tanaka
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Sayumi Akahane
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Mayu Fukumura
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Masaki Mori
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan.
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8
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Tano A, Kadota Y, Morimune T, Jam FA, Yukiue H, Bellier JP, Sokoda T, Maruo Y, Tooyama I, Mori M. The juvenility-associated long noncoding RNA Gm14230 maintains cellular juvenescence. J Cell Sci 2019; 132:jcs.227801. [PMID: 30872457 DOI: 10.1242/jcs.227801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/05/2019] [Indexed: 12/12/2022] Open
Abstract
Juvenile animals possess distinct properties that are missing in adults. These properties include capabilities for higher growth, faster wound healing, plasticity and regeneration. However, the molecular mechanisms underlying these juvenile physiological properties are not fully understood. To obtain insight into the distinctiveness of juveniles from adults at the molecular level, we assessed long noncoding RNAs (lncRNAs) that are highly expressed selectively in juvenile cells. The noncoding elements of the transcriptome were investigated in hepatocytes and cardiomyocytes isolated from juvenile and adult mice. Here, we identified 62 juvenility-associated lncRNAs (JAlncs), which are selectively expressed in both hepatocytes and cardiomyocytes from juvenile mice. Among these common (shared) JAlncs, Gm14230 is evolutionarily conserved and is essential for cellular juvenescence. Loss of Gm14230 impairs cell growth and causes cellular senescence. Gm14230 safeguards cellular juvenescence through recruiting the histone methyltransferase Ezh2 to Tgif2, thereby repressing the functional role of Tgif2 in cellular senescence. Thus, we identify Gm14230 as a juvenility-selective lncRNA required to maintain cellular juvenescence.
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Affiliation(s)
- Ayami Tano
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Yosuke Kadota
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Takao Morimune
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan.,Department of Pediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Faidruz Azura Jam
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Haruka Yukiue
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Jean-Pierre Bellier
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Tatsuyuki Sokoda
- Department of Pediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Yoshihiro Maruo
- Department of Pediatrics, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Masaki Mori
- Molecular Neuroscience Research Center (MNRC), Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
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