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Papadimitriou E, Thomaidou D. Post-transcriptional mechanisms controlling neurogenesis and direct neuronal reprogramming. Neural Regen Res 2024; 19:1929-1939. [PMID: 38227517 DOI: 10.4103/1673-5374.390976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/08/2023] [Indexed: 01/17/2024] Open
Abstract
Neurogenesis is a tightly regulated process in time and space both in the developing embryo and in adult neurogenic niches. A drastic change in the transcriptome and proteome of radial glial cells or neural stem cells towards the neuronal state is achieved due to sophisticated mechanisms of epigenetic, transcriptional, and post-transcriptional regulation. Understanding these neurogenic mechanisms is of major importance, not only for shedding light on very complex and crucial developmental processes, but also for the identification of putative reprogramming factors, that harbor hierarchically central regulatory roles in the course of neurogenesis and bare thus the capacity to drive direct reprogramming towards the neuronal fate. The major transcriptional programs that orchestrate the neurogenic process have been the focus of research for many years and key neurogenic transcription factors, as well as repressor complexes, have been identified and employed in direct reprogramming protocols to convert non-neuronal cells, into functional neurons. The post-transcriptional regulation of gene expression during nervous system development has emerged as another important and intricate regulatory layer, strongly contributing to the complexity of the mechanisms controlling neurogenesis and neuronal function. In particular, recent advances are highlighting the importance of specific RNA binding proteins that control major steps of mRNA life cycle during neurogenesis, such as alternative splicing, polyadenylation, stability, and translation. Apart from the RNA binding proteins, microRNAs, a class of small non-coding RNAs that block the translation of their target mRNAs, have also been shown to play crucial roles in all the stages of the neurogenic process, from neural stem/progenitor cell proliferation, neuronal differentiation and migration, to functional maturation. Here, we provide an overview of the most prominent post-transcriptional mechanisms mediated by RNA binding proteins and microRNAs during the neurogenic process, giving particular emphasis on the interplay of specific RNA binding proteins with neurogenic microRNAs. Taking under consideration that the molecular mechanisms of neurogenesis exert high similarity to the ones driving direct neuronal reprogramming, we also discuss the current advances in in vitro and in vivo direct neuronal reprogramming approaches that have employed microRNAs or RNA binding proteins as reprogramming factors, highlighting the so far known mechanisms of their reprogramming action.
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Chen T, Jiang H, Shen Y, Cui T, Yang Z, Liu Y, Zhao J, Chen X. Impacts of exposure to nanopolystyrene and/or chrysene at ambient concentrations on neurotoxicity in Siniperca chuatsi. CHEMOSPHERE 2023; 340:139830. [PMID: 37597625 DOI: 10.1016/j.chemosphere.2023.139830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/01/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Health risks caused by widespread environmental pollutants such as nanopolystyrene (NP) and chrysene (CHR) in aquatic ecosystems have aroused considerable concern. The present study established juvenile Mandarin fish (Siniperca chuatsi) models of NP and/or CHR exposure at ambient concentrations for 21 days to systematically investigate the underlying neurotoxicity mechanisms. The results showed that single and combined exposure to NP and CHR not only reduced the density of small neuronal cells in the grey matter layer of the optic tectum, but also induced brain oxidative stress according to physiological parameters including CAT, GSH-Px, SOD, T-AOC, and MDA. The co-exposure alleviated the histopathological damage, compared to NP and CHR single exposure group. These results indicate that NP and/or CHR causes neurotoxicity in S. chuatsi, in accordance with decreased acetylcholinesterase activity and altered expression of several marker genes of nervous system functions and development including c-fos, shha, elavl3, and mbpa. Transcriptomics analysis was performed to further investigate the potential molecular mechanisms of neurotoxicity. We propose that single NP and co-exposure induced oxidative stress activates MMP, which degrades tight junction proteins according to decreased expression of claudin, JAM, caveolin and TJP, ultimately damaging the integrity of the blood-brain barrier in S. chuatsi. Remarkably, the co-exposure exacerbated the blood-brain barrier disruption. More importantly, single NP and co-exposure induced neuronal apoptosis mainly activates the expression of apoptosis-related genes through the death receptor apoptosis pathway, while CHR acted through both death receptor apoptosis and endoplasmic reticulum apoptosis pathways. Additionally, subchronic CHR exposure caused neuroinflammation, supported by activation of TNF/NF-κB and JAK-STAT signaling pathways via targeting-related genes, while the co-exposure greatly alleviated the neuroinflammation. Collectively, our findings illuminate the underlying neurotoxicity molecular mechanisms of NP and/or CHR exposure on aquatic organisms.
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Affiliation(s)
- Tiantian Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hewei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yawei Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Tingwen Cui
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Zonglin Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yufei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinliang Zhao
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
| | - Xiaowu Chen
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
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Mulligan MR, Bicknell LS. The molecular genetics of nELAVL in brain development and disease. Eur J Hum Genet 2023; 31:1209-1217. [PMID: 37697079 PMCID: PMC10620143 DOI: 10.1038/s41431-023-01456-z] [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: 07/06/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Embryonic development requires tight control of gene expression levels, activity, and localisation. This control is coordinated by multiple levels of regulation on DNA, RNA and protein. RNA-binding proteins (RBPs) are recognised as key regulators of post-transcriptional gene regulation, where their binding controls splicing, polyadenylation, nuclear export, mRNA stability, translation rate and decay. In brain development, the ELAVL family of RNA binding proteins undertake essential functions across spatiotemporal windows to help regulate and specify transcriptomic programmes for cell specialisation. Despite their recognised importance in neural tissues, their molecular roles and connections to pathology are less explored. Here we provide an overview of the neuronal ELAVL family, noting commonalities and differences amongst different species, their molecular characteristics, and roles in the cell. We bring together the available molecular genetics evidence to link different ELAVL proteins to phenotypes and disease, in both the brain and beyond, including ELAVL2, which is the least studied ELAVL family member. We find that ELAVL-related pathology shares a common neurological theme, but different ELAVL proteins are more strongly connected to different phenotypes, reflecting their specialised expression across time and space.
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Affiliation(s)
- Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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Lin X, Yang X, Chen C, Ma W, Wang Y, Li X, Zhao K, Deng Q, Feng W, Ma Y, Wang H, Zhu L, Sahu SK, Chen F, Zhang X, Dong Z, Liu C, Liu L, Liu C. Single-nucleus chromatin landscapes during zebrafish early embryogenesis. Sci Data 2023; 10:464. [PMID: 37468546 PMCID: PMC10356945 DOI: 10.1038/s41597-023-02373-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Vertebrate embryogenesis is a remarkable process, during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis-regulatory elements (CREs) and gene expression within the hierarchy of cell fate decisions. Here, we employed single-nucleus ATAC-seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis, including 3.3 hpf, 5.25 hpf, 6 hpf, 10 hpf, 12 hpf, 18 hpf and 24 hpf, obtained 51,620 high-quality nuclei and 23 clusters. Furthermore, by integrating snATAC-seq data with single-cell RNA-seq data, we described the dynamics of chromatin accessibility and gene expression across developmental time points, which validates the accuracy of the chromatin landscape data. Together, our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.
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Affiliation(s)
- Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Xueqian Yang
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | | | - Wen Ma
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Yiqi Wang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xuerong Li
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Kaichen Zhao
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Weimin Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Yuting Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
| | - Hui Wang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lveming Zhu
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | | | - Fengzhen Chen
- China National GeneBank, Shenzhen, Guangdong, 518120, China
| | | | - Zhiqiang Dong
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Chuanyu Liu
- BGI Research, Shenzhen, 518083, China.
- Shenzhen Bay Laboratory, Shenzhen, 518000, China.
| | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Hangzhou, 310030, China.
- Shenzhen Bay Laboratory, Shenzhen, 518000, China.
| | - Chang Liu
- BGI Research, Shenzhen, 518083, China.
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5
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Castellá M, Blasco-Roset A, Peyrou M, Gavaldà-Navarro A, Villarroya J, Quesada-López T, Lorente-Poch L, Sancho J, Szymczak F, Piron A, Rodríguez-Fernández S, Carobbio S, Goday A, Domingo P, Vidal-Puig A, Giralt M, Eizirik DL, Villarroya F, Cereijo R. Adipose tissue plasticity in pheochromocytoma patients suggests a role of the splicing machinery in human adipose browning. iScience 2023; 26:106847. [PMID: 37250773 PMCID: PMC10209542 DOI: 10.1016/j.isci.2023.106847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/31/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
Adipose tissue from pheochromocytoma patients acquires brown fat features, making it a valuable model for studying the mechanisms that control thermogenic adipose plasticity in humans. Transcriptomic analyses revealed a massive downregulation of splicing machinery components and splicing regulatory factors in browned adipose tissue from patients, with upregulation of a few genes encoding RNA-binding proteins potentially involved in splicing regulation. These changes were also observed in cell culture models of human brown adipocyte differentiation, confirming a potential involvement of splicing in the cell-autonomous control of adipose browning. The coordinated changes in splicing are associated with a profound modification in the expression levels of splicing-driven transcript isoforms for genes involved in the specialized metabolism of brown adipocytes and those encoding master transcriptional regulators of adipose browning. Splicing control appears to be a relevant component of the coordinated gene expression changes that allow human adipose tissue to acquire a brown phenotype.
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Affiliation(s)
- Moisés Castellá
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Albert Blasco-Roset
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Marion Peyrou
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Aleix Gavaldà-Navarro
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Joan Villarroya
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Tania Quesada-López
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
| | | | - Juan Sancho
- Endocrine Surgery Unit, Hospital del Mar, 08003 Barcelona, Spain
| | - Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Anthony Piron
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sonia Rodríguez-Fernández
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge 289, UK
| | - Stefania Carobbio
- Bases Moleculares de Patologías Humanas, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
| | - Albert Goday
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Endocrinology Service, Hospital del Mar, IMIM, 08003 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Pere Domingo
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge 289, UK
| | - Marta Giralt
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Décio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
| | - Francesc Villarroya
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Rubén Cereijo
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
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6
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
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8
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Diaz-Garcia S, Ko VI, Vazquez-Sanchez S, Chia R, Arogundade OA, Rodriguez MJ, Traynor BJ, Cleveland D, Ravits J. Nuclear depletion of RNA-binding protein ELAVL3 (HuC) in sporadic and familial amyotrophic lateral sclerosis. Acta Neuropathol 2021; 142:985-1001. [PMID: 34618203 PMCID: PMC8568872 DOI: 10.1007/s00401-021-02374-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/07/2022]
Abstract
Amyotrophic lateral sclerosis is a progressive fatal neurodegenerative disease caused by loss of motor neurons and characterized neuropathologically in almost all cases by nuclear depletion and cytoplasmic aggregation of TDP-43, a nuclear RNA-binding protein (RBP). We identified ELAVL3 as one of the most downregulated genes in our transcriptome profiles of laser captured microdissection of motor neurons from sporadic ALS nervous systems and the most dysregulated of all RBPs. Neuropathological characterizations showed ELAVL3 nuclear depletion in a great percentage of remnant motor neurons, sometimes accompanied by cytoplasmic accumulations. These abnormalities were common in sporadic cases with and without intermediate expansions in ATXN2 and familial cases carrying mutations in C9orf72 and SOD1. Depletion of ELAVL3 occurred at both the RNA and protein levels and a short protein isoform was identified, but it is not related to a TDP-43-dependent cryptic exon in intron 3. Strikingly, ELAVL3 abnormalities were more frequent than TDP-43 abnormalities and occurred in motor neurons still with normal nuclear TDP-43 present, but all neurons with abnormal TDP-43 also had abnormal ELAVL3. In a neuron-like cell culture model using SH-SY5Y cells, ELAVL3 mislocalization occurred weeks before TDP-43 abnormalities were seen. We interrogated genetic databases, but did not identify association of ELAVL3 genetic structure with ALS. Taken together, these findings suggest that ELAVL3 is an important RBP in ALS pathogenesis acquired early and the neuropathological data suggest that it is involved by loss of function rather than cytoplasmic toxicity.
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Affiliation(s)
- Sandra Diaz-Garcia
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
| | - Vivian I. Ko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
| | - Sonia Vazquez-Sanchez
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0670 USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA USA
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3707 USA
| | | | - Maria J. Rodriguez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
| | - Bryan J. Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3707 USA
| | - Don Cleveland
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0670 USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA USA
| | - John Ravits
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
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9
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Wilson C, Cáceres A. New insights on epigenetic mechanisms supporting axonal development: histone marks and miRNAs. FEBS J 2020; 288:6353-6364. [PMID: 33332753 DOI: 10.1111/febs.15673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/21/2020] [Accepted: 12/15/2020] [Indexed: 11/27/2022]
Abstract
Mechanisms supporting axon growth and the establishment of neuronal polarity have remained largely disconnected from their genetic and epigenetic fundamentals. Recently, post-transcriptional modifications of histones involved in chromatin folding and transcription, and microRNAs controlling translation have emerged as regulators of axonal specification, growth, and guidance. In this article, we review novel evidence supporting the concept that epigenetic mechanisms work at both transcriptional and post-transcriptional levels to shape axons. We also discuss the role of splicing on axonal growth, as one of the most (if not the most) powerful post-transcriptional mechanism to diversify genetic information. Overall, we think exploring the gap between epigenetics and axonal growth raises new questions and perspectives to the development of axons in physiological and pathological contexts.
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Affiliation(s)
- Carlos Wilson
- Centro de Investigación en Medicina Traslacional "Severo R Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Córdoba, Argentina.,Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC-CONICET-UNC), Córdoba, Argentina.,Universidad Nacional de Córdoba (UNC), Argentina
| | - Alfredo Cáceres
- Centro de Investigación en Medicina Traslacional "Severo R Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Córdoba, Argentina
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10
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Li J, Chen K, Zhu R, Zhang M. Structural Basis Underlying Strong Interactions between Ankyrins and Spectrins. J Mol Biol 2020; 432:3838-3850. [DOI: 10.1016/j.jmb.2020.04.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023]
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Iijima T, Yoshimura T. A Perspective on the Role of Dynamic Alternative RNA Splicing in the Development, Specification, and Function of Axon Initial Segment. Front Mol Neurosci 2019; 12:295. [PMID: 31866821 PMCID: PMC6906172 DOI: 10.3389/fnmol.2019.00295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is a powerful mechanism for molecular and functional diversification. In neurons, alternative splicing extensively controls various developmental steps as well as the plasticity and remodeling of neuronal activity in the adult brain. The axon initial segment (AIS) is the specialized compartment of proximal axons that initiates action potential (AP). At the AIS, the ion channels and cell adhesion molecules (CAMs) required for AP initiation are densely clustered via the scaffolding and cytoskeletal proteins. Notably, recent studies have elucidated that multiple AIS proteins are controlled by extensive alternative splicing in developing and adult brains. Here, we argue the potential role of dynamic regulation of alternative splicing in the development, specification, and functions of the AIS. In particular, we propose the novel concept that alternative splicing potentially modulates the structural and functional plasticity at the AIS.
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Affiliation(s)
- Takatoshi Iijima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Takeshi Yoshimura
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, Japan
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Li SS, Zhao XB, Tian JM, Wang HR, Wei TH. Prediction of seed gene function in progressive diabetic neuropathy by a network-based inference method. Exp Ther Med 2019; 17:4176-4182. [PMID: 31007748 PMCID: PMC6468912 DOI: 10.3892/etm.2019.7441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 03/07/2019] [Indexed: 11/07/2022] Open
Abstract
Guilt by association (GBA) algorithm has been widely used to statistically predict gene functions, and network-based approach increases the confidence and veracity of identifying molecular signatures for diseases. This work proposed a network-based GBA method by integrating the GBA algorithm and network, to identify seed gene functions for progressive diabetic neuropathy (PDN). The inference of predicting seed gene functions comprised of three steps: i) Preparing gene lists and sets; ii) constructing a co-expression matrix (CEM) on gene lists by Spearman correlation coefficient (SCC) method and iii) predicting gene functions by GBA algorithm. Ultimately, seed gene functions were selected according to the area under the receiver operating characteristics curve (AUC) index. A total of 79 differentially expressed genes (DEGs) and 40 background gene ontology (GO) terms were regarded as gene lists and sets for the subsequent analyses, respectively. The predicted results obtained from the network-based GBA approach showed that 27.5% of all gene sets had a good classified performance with AUC >0.5. Most significantly, 3 gene sets with AUC >0.6 were denoted as seed gene functions for PDN, including binding, molecular function and regulation of the metabolic process. In summary, we predicted 3 seed gene functions for PDN compared with non-progressors utilizing network-based GBA algorithm. The findings provide insights to reveal pathological and molecular mechanism underlying PDN.
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Affiliation(s)
- Shan-Shan Li
- Department of Endocrinology, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Xin-Bo Zhao
- Department of Endocrinology, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Jia-Mei Tian
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Hao-Ren Wang
- Department of Medicine, Linyi Luozhuang Central Hospital, Linyi, Shandong 276000, P.R. China
| | - Tong-Huan Wei
- Department of Medicine, People's Hospital of Linyi High-Tech Industrial Development Zone, Linyi, Shandong 276000, P.R. China
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Chen YC, Chang YW, Huang YS. Dysregulated Translation in Neurodevelopmental Disorders: An Overview of Autism-Risk Genes Involved in Translation. Dev Neurobiol 2018; 79:60-74. [PMID: 30430754 DOI: 10.1002/dneu.22653] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/17/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Abstract
Regulated local translation-whereby specific mRNAs are transported and localized in subcellular domains where they are translated in response to regional signals-allows for remote control of gene expression to concentrate proteins in subcellular compartments. Neurons are highly polarized cells with unique features favoring local control for axonal pathfinding and synaptic plasticity, which are key processes involved in constructing functional circuits in the developing brain. Neurodevelopmental disorders are caused by genetic or environmental factors that disturb the nervous system's development during prenatal and early childhood periods. The growing list of genetic mutations that affect mRNA translation raises the question of whether aberrant translatomes in individuals with neurodevelopmental disorders share common molecular features underlying their stereotypical phenotypes and, vice versa, cause a certain degree of phenotypic heterogeneity. Here, we briefly give an overview of the role of local translation during neuronal development. We take the autism-risk gene list and discuss the molecules that (perhaps) are involved in mRNA transport and translation. Both exaggerated and suppressed translation caused by mutations in those genes have been identified or suggested. Finally, we discuss some proof-of-principle regimens for use in autism mouse models to correct dysregulated translation.
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Affiliation(s)
- Yan-Chu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Wei Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
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