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Kuo DH, Szczupak L, Weisblat DA, Portiansky EL, Winchell CJ, Lee JR, Tsai FY. Transgenesis enables mapping of segmental ganglia in the leech Helobdella austinensis. J Exp Biol 2024; 227:jeb247419. [PMID: 38940760 PMCID: PMC11418187 DOI: 10.1242/jeb.247419] [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: 01/26/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]
Abstract
The analysis of how neural circuits function in individuals and change during evolution is simplified by the existence of neurons identified as homologous within and across species. Invertebrates, including leeches, have been used for these purposes in part because their nervous systems comprise a high proportion of identified neurons, but technical limitations make it challenging to assess the full extent to which assumptions of stereotypy hold true. Here, we introduce Minos plasmid-mediated transgenesis as a tool for introducing transgenes into the embryos of the leech Helobdella austinensis (Spiralia; Lophotrochozoa; Annelida; Clitellata; Hirudinida; Glossiphoniidae). We identified an enhancer driving pan-neuronal expression of markers, including histone2B:mCherry, which allowed us to enumerate neurons in segmental ganglia. Unexpectedly, we found that the segmental ganglia of adult transgenic H. austinensis contain fewer and more variable numbers of neurons than in previously examined leech species.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
- Museum of Zoology, National Taiwan University, Taipei, Taiwan106
| | - Lidia Szczupak
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBYNE UBA-CONICET, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - David A. Weisblat
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Enrique L. Portiansky
- Laboratory of Image Analysis, School of Veterinary Sciences, National University of La Plata, CONICET, B1900 La Plata, Argentina
| | - Christopher J. Winchell
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Jun-Ru Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
| | - Fu-Yu Tsai
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
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Moakley DF, Campbell M, Anglada-Girotto M, Feng H, Califano A, Au E, Zhang C. Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.597128. [PMID: 38915499 PMCID: PMC11195221 DOI: 10.1101/2024.06.13.597128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cell type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a few neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron type-specific AS regulatory landscape from 133 mouse neocortical cell types defined by single-cell transcriptomes. This approach reliably inferred the regulons of 350 RBPs and their cell type-specific activities. Our analysis revealed driving factors delineating neuronal identities, among which we validated Elavl2 as a key RBP for MGE-specific splicing in GABAergic interneurons using an in vitro ESC differentiation system. We also identified a module of exons and candidate regulators specific for long- and short-projection neurons across multiple neuronal classes. This study provides a resource for elucidating splicing regulatory programs that drive neuronal molecular diversity, including those that do not align with gene expression-based classifications.
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Affiliation(s)
- Daniel F Moakley
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Melissa Campbell
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Neurosciences, University of California, San Diego, USA
| | - Miquel Anglada-Girotto
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Present address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Huijuan Feng
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Edmund Au
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
- Columbia Translational Neuroscience Initiative Scholar, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
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Ordoñez JF, Wollesen T. Unfolding the ventral nerve center of chaetognaths. Neural Dev 2024; 19:5. [PMID: 38720353 PMCID: PMC11078758 DOI: 10.1186/s13064-024-00182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Chaetognaths are a clade of marine worm-like invertebrates with a heavily debated phylogenetic position. Their nervous system superficially resembles the protostome type, however, knowledge regarding the molecular processes involved in neurogenesis is lacking. To better understand these processes, we examined the expression profiles of marker genes involved in bilaterian neurogenesis during post-embryonic stages of Spadella cephaloptera. We also investigated whether the transcription factor encoding genes involved in neural patterning are regionally expressed in a staggered fashion along the mediolateral axis of the nerve cord as it has been previously demonstrated in selected vertebrate, insect, and annelid models. METHODS The expression patterns of genes involved in neural differentiation (elav), neural patterning (foxA, nkx2.2, pax6, pax3/7, and msx), and neuronal function (ChAT and VAChT) were examined in S. cephaloptera hatchlings and early juveniles using whole-mount fluorescent in situ hybridization and confocal microscopy. RESULTS The Sce-elav + profile of S. cephaloptera hatchlings reveals that, within 24 h of post-embryonic development, the developing neural territories are not limited to the regions previously ascribed to the cerebral ganglion, the ventral nerve center (VNC), and the sensory organs, but also extend to previously unreported CNS domains that likely contribute to the ventral cephalic ganglia. In general, the neural patterning genes are expressed in distinct neural subpopulations of the cerebral ganglion and the VNC in hatchlings, eventually becoming broadly expressed with reduced intensity throughout the CNS in early juveniles. Neural patterning gene expression domains are also present outside the CNS, including the digestive tract and sensory organs. ChAT and VAChT domains within the CNS are predominantly observed in specific subpopulations of the VNC territory adjacent to the ventral longitudinal muscles in hatchlings. CONCLUSIONS The observed spatial expression domains of bilaterian neural marker gene homologs in S. cephaloptera suggest evolutionarily conserved roles in neurogenesis for these genes among bilaterians. Patterning genes expressed in distinct regions of the VNC do not show a staggered medial-to-lateral expression profile directly superimposable to other bilaterian models. Only when the VNC is conceptually laterally unfolded from the longitudinal muscle into a flat structure, an expression pattern bearing resemblance to the proposed conserved bilaterian mediolateral regionalization becomes noticeable. This finding supports the idea of an ancestral mediolateral patterning of the trunk nervous system in bilaterians.
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Affiliation(s)
- June F Ordoñez
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, 1030, Vienna, Austria
| | - Tim Wollesen
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, 1030, Vienna, Austria.
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Kim Y, You JH, Ryu Y, Park G, Lee U, Moon HE, Park HR, Song CW, Ku JL, Park SH, Paek SH. ELAVL2 loss promotes aggressive mesenchymal transition in glioblastoma. NPJ Precis Oncol 2024; 8:79. [PMID: 38548861 PMCID: PMC10978835 DOI: 10.1038/s41698-024-00566-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Glioblastoma (GBM), the most lethal primary brain cancer, exhibits intratumoral heterogeneity and molecular plasticity, posing challenges for effective treatment. Despite this, the regulatory mechanisms underlying such plasticity, particularly mesenchymal (MES) transition, remain poorly understood. In this study, we elucidate the role of the RNA-binding protein ELAVL2 in regulating aggressive MES transformation in GBM. We found that ELAVL2 is most frequently deleted in GBM compared to other cancers and associated with distinct clinical and molecular features. Transcriptomic analysis revealed that ELAVL2-mediated alterations correspond to specific GBM subtype signatures. Notably, ELAVL2 expression negatively correlated with epithelial-to-mesenchymal transition (EMT)-related genes, and its loss promoted MES process and chemo-resistance in GBM cells, whereas ELAVL2 overexpression exerted the opposite effect. Further investigation via tissue microarray analysis demonstrated that high ELAVL2 protein expression confers a favorable survival outcome in GBM patients. Mechanistically, ELAVL2 was shown to directly bind to the transcripts of EMT-inhibitory molecules, SH3GL3 and DNM3, modulating their mRNA stability, potentially through an m6A-dependent mechanism. In summary, our findings identify ELAVL2 as a critical tumor suppressor and mRNA stabilizer that regulates MES transition in GBM, underscoring its role in transcriptomic plasticity and glioma progression.
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Affiliation(s)
- Yona Kim
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Ji Hyeon You
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yeonjoo Ryu
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Gyuri Park
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Urim Lee
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Eun Moon
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Ran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Chang W Song
- Department of Radiation Oncology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Advanced Institute of Convergence Technology, Seoul National University, Suwon, Korea.
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Takada Y, Fierro L, Sato K, Sanada T, Ishii A, Yamamoto T, Kotani T. Mature mRNA processing that deletes 3' end sequences directs translational activation and embryonic development. SCIENCE ADVANCES 2023; 9:eadg6532. [PMID: 38000026 PMCID: PMC10672166 DOI: 10.1126/sciadv.adg6532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023]
Abstract
Eggs accumulate thousands of translationally repressed mRNAs that are translated into proteins after fertilization to direct diverse developmental processes. However, molecular mechanisms underlying the translation of stored mRNAs after fertilization remain unclear. Here, we report a previously unknown RNA processing of 3' end sequences of mature mRNAs that activates the translation of stored mRNAs. Specifically, 9 to 72 nucleotides at the 3' ends of zebrafish pou5f3 and mouse Pou5f1 mRNAs were deleted in the early stages of development. Reporter assays illustrated the effective translation of the truncated forms of mRNAs. Moreover, promotion and inhibition of the shortening of 3' ends accelerated and attenuated Pou5f3 accumulation, respectively, resulting in defective development. Identification of proteins binding to unprocessed and/or processed mRNAs revealed that mRNA shortening acts as molecular switches. Comprehensive analysis revealed that >250 mRNAs underwent this processing. Therefore, our results provide a molecular principle that triggers the translational activation and directs development.
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Affiliation(s)
- Yuki Takada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ludivine Fierro
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keisuke Sato
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takahiro Sanada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Anna Ishii
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomoya Kotani
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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6
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Marchesi N, Linciano P, Campagnoli LIM, Fahmideh F, Rossi D, Costa G, Ambrosio FA, Barbieri A, Collina S, Pascale A. Short- and Long-Term Regulation of HuD: A Molecular Switch Mediated by Folic Acid? Int J Mol Sci 2023; 24:12201. [PMID: 37569576 PMCID: PMC10418318 DOI: 10.3390/ijms241512201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
The RNA-binding protein HuD has been shown to play a crucial role in gene regulation in the nervous system and is involved in various neurological and psychiatric diseases. In this study, through the creation of an interaction network on HuD and its potential targets, we identified a strong association between HuD and several diseases of the nervous system. Specifically, we focused on the relationship between HuD and the brain-derived neurotrophic factor (BDNF), whose protein is implicated in several neuronal diseases and is involved in the regulation of neuronal development, survival, and function. To better investigate this relationship and given that we previously demonstrated that folic acid (FA) is able to directly bind HuD itself, we performed in vitro experiments in neuron-like human SH-SY5Y cells in the presence of FA, also known to be a pivotal environmental factor influencing the nervous system development. Our findings show that FA exposure results in a significant increase in both HuD and BDNF transcripts and proteins after 2 and 4 h of treatment, respectively. Similar data were obtained after 2 h of FA incubation followed by 2 h of washout. This increase was no longer detected upon 24 h of FA exposure, probably due to a signaling shutdown mechanism. Indeed, we observed that following 24 h of FA exposure HuD is methylated. These findings indicate that FA regulates BDNF expression via HuD and suggest that FA can behave as an epigenetic modulator of HuD in the nervous system acting via short- and long-term mechanisms. Finally, the present results also highlight the potential of BDNF as a therapeutic target for specific neurological and psychiatric diseases.
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Affiliation(s)
- Nicoletta Marchesi
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
| | - Pasquale Linciano
- Department of Drug Sciences, Medicinal Chemistry Section, University of Pavia, 27100 Pavia, Italy; (P.L.); (D.R.); (S.C.)
| | | | - Foroogh Fahmideh
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
| | - Daniela Rossi
- Department of Drug Sciences, Medicinal Chemistry Section, University of Pavia, 27100 Pavia, Italy; (P.L.); (D.R.); (S.C.)
| | - Giosuè Costa
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy; (G.C.); (F.A.A.)
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy
- Associazione CRISEA-Centro di Ricerca e Servizi Avanzati per l’Innovazione Rurale, 88055 Catanzaro, Italy
| | - Francesca Alessandra Ambrosio
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy; (G.C.); (F.A.A.)
| | - Annalisa Barbieri
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry Section, University of Pavia, 27100 Pavia, Italy; (P.L.); (D.R.); (S.C.)
| | - Alessia Pascale
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
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Hilgers V. Regulation of neuronal RNA signatures by ELAV/Hu proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1733. [PMID: 35429136 DOI: 10.1002/wrna.1733] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 12/30/2022]
Abstract
The RNA-binding proteins encoded by the highly conserved elav/Hu gene family, found in all metazoans, regulate the expression of a wide range of genes, at both the co-transcriptional and posttranscriptional level. Nervous-system-specific ELAV/Hu proteins are prominent for their essential role in neuron differentiation, and mutations have been associated with human neurodevelopmental and neurodegenerative diseases. Drosophila ELAV, the founding member of the protein family, mediates the synthesis of neuronal RNA signatures by promoting alternative splicing and alternative polyadenylation of hundreds of genes. The recent identification of ELAV's direct RNA targets revealed the protein's central role in shaping the neuronal transcriptome, and highlighted the importance of neuronal transcript signatures for neuron maintenance and organism survival. Animals have evolved multiple cellular mechanisms to ensure robustness of ELAV/Hu function. In Drosophila, elav autoregulates in a 3'UTR-dependent manner to maintain optimal protein levels. A complete absence of ELAV causes the activation and nuclear localization of the normally cytoplasmic paralogue FNE, in a process termed EXon-Activated functional Rescue (EXAR). Other species, including mammals, seem to utilize different strategies, such as protein redundancy, to maintain ELAV protein function and effectively safeguard the identity of the neuronal transcriptome. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Development RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
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8
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Lin WY, Liu CH, Cheng J, Liu HP. Alterations of RNA-binding protein found in neurons in Drosophila neurons and glia influence synaptic transmission and lifespan. Front Mol Neurosci 2022; 15:1006455. [DOI: 10.3389/fnmol.2022.1006455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
The found in neurons (fne), a paralog of the RNA-binding protein ELAV gene family in Drosophila, is required for post-transcriptional regulation of neuronal development and differentiation. Previous explorations into the functions of the FNE protein have been limited to neurons. The function of fne in Drosophila glia remains unclear. We induced the knockdown or overexpression of fne in Drosophila neurons and glia to determine how fne affects different types of behaviors, neuronal transmission and the lifespan. Our data indicate that changes in fne expression impair associative learning, thermal nociception, and phototransduction. Examination of synaptic transmission at presynaptic and postsynaptic terminals of the larval neuromuscular junction (NMJ) revealed that loss of fne in motor neurons and glia significantly decreased excitatory junction currents (EJCs) and quantal content, while flies with glial fne knockdown facilitated short-term synaptic plasticity. In muscle cells, overexpression of fne reduced both EJC and quantal content and increased short-term synaptic facilitation. In both genders, the lifespan could be extended by the knockdown of fne in neurons and glia; the overexpression of fne shortened the lifespan. Our results demonstrate that disturbances of fne in neurons and glia influence the function of the Drosophila nervous system. Further explorations into the physiological and molecular mechanisms underlying neuronal and glial fne and elucidation of how fne affects neuronal activity may clarify certain brain functions.
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Kieffer F, Hilal F, Gay AS, Debayle D, Pronot M, Poupon G, Lacagne I, Bardoni B, Martin S, Gwizdek C. Combining affinity purification and mass spectrometry to define the network of the nuclear proteins interacting with the N-terminal region of FMRP. Front Mol Biosci 2022; 9:954087. [PMID: 36237573 PMCID: PMC9553004 DOI: 10.3389/fmolb.2022.954087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X-Syndrome (FXS) represents the most common inherited form of intellectual disability and the leading monogenic cause of Autism Spectrum Disorders. In most cases, this disease results from the absence of expression of the protein FMRP encoded by the FMR1 gene (Fragile X messenger ribonucleoprotein 1). FMRP is mainly defined as a cytoplasmic RNA-binding protein regulating the local translation of thousands of target mRNAs. Interestingly, FMRP is also able to shuttle between the nucleus and the cytoplasm. However, to date, its roles in the nucleus of mammalian neurons are just emerging. To broaden our insight into the contribution of nuclear FMRP in mammalian neuronal physiology, we identified here a nuclear interactome of the protein by combining subcellular fractionation of rat forebrains with pull‐ down affinity purification and mass spectrometry analysis. By this approach, we listed 55 candidate nuclear partners. This interactome includes known nuclear FMRP-binding proteins as Adar or Rbm14 as well as several novel candidates, notably Ddx41, Poldip3, or Hnrnpa3 that we further validated by target‐specific approaches. Through our approach, we identified factors involved in different steps of mRNA biogenesis, as transcription, splicing, editing or nuclear export, revealing a potential central regulatory function of FMRP in the biogenesis of its target mRNAs. Therefore, our work considerably enlarges the nuclear proteins interaction network of FMRP in mammalian neurons and lays the basis for exciting future mechanistic studies deepening the roles of nuclear FMRP in neuronal physiology and the etiology of the FXS.
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Affiliation(s)
- Félicie Kieffer
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Fahd Hilal
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Anne-Sophie Gay
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Delphine Debayle
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Marie Pronot
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Gwénola Poupon
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Iliona Lacagne
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Barbara Bardoni
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Stéphane Martin
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Carole Gwizdek
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
- *Correspondence: Carole Gwizdek,
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Identification and Characterization of an RRM-Containing, RNA Binding Protein in Acinetobacter baumannii. Biomolecules 2022; 12:biom12070922. [PMID: 35883478 PMCID: PMC9313427 DOI: 10.3390/biom12070922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative pathogen, known to acquire resistance to antibiotics used in the clinic. The RNA-binding proteome of this bacterium is poorly characterized, in particular for what concerns the proteins containing RNA Recognition Motif (RRM). Here, we browsed the A. baumannii proteome for homologous proteins to the human HuR(ELAVL1), an RNA binding protein containing three RRMs. We identified a unique locus that we called AB-Elavl, coding for a protein with a single RRM with an average of 34% identity to the first HuR RRM. We also widen the research to the genomes of all the bacteria, finding 227 entries in 12 bacterial phyla. Notably we observed a partial evolutionary divergence between the RNP1 and RNP2 conserved regions present in the prokaryotes in comparison to the metazoan consensus sequence. We checked the expression at the transcript and protein level, cloned the gene and expressed the recombinant protein. The X-ray and NMR structural characterization of the recombinant AB-Elavl revealed that the protein maintained the typical β1α1β2β3α2β4 and three-dimensional organization of eukaryotic RRMs. The biochemical analyses showed that, although the RNP1 and RNP2 show differences, it can bind to AU-rich regions like the human HuR, but with less specificity and lower affinity. Therefore, we identified an RRM-containing RNA-binding protein actually expressed in A. baumannii.
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11
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Emerging Roles of RNA-Binding Proteins in Neurodevelopment. J Dev Biol 2022; 10:jdb10020023. [PMID: 35735914 PMCID: PMC9224834 DOI: 10.3390/jdb10020023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.
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12
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Cai H, Zheng D, Yao Y, Yang L, Huang X, Wang L. Roles of Embryonic Lethal Abnormal Vision-Like RNA Binding Proteins in Cancer and Beyond. Front Cell Dev Biol 2022; 10:847761. [PMID: 35465324 PMCID: PMC9019298 DOI: 10.3389/fcell.2022.847761] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/04/2022] [Indexed: 12/31/2022] Open
Abstract
Embryonic lethal abnormal vision-like (ELAVL) proteins are RNA binding proteins that were originally discovered as indispensable regulators of the development and functioning of the nervous system. Subsequent studies have shown that ELAVL proteins not only exist in the nervous system, but also have regulatory effects in other tissues. ELAVL proteins have attracted attention as potential therapeutic targets because they stabilize multiple mRNAs by binding within the 3′-untranslated region and thus promote the development of tumors, including hepatocellular carcinoma, pancreatic cancer, ovarian cancer, breast cancer, colorectal carcinoma and lung cancer. Previous studies have focused on these important relationships with downstream mRNAs, but emerging studies suggest that ELAVL proteins also interact with non-coding RNAs. In this review, we will summarize the relationship of the ELAVL protein family with mRNA and non-coding RNA and the roles of ELAVL protein family members in a variety of physiological and pathological processes.
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Affiliation(s)
| | | | | | - Lehe Yang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Xiaoying Huang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Liangxing Wang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
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13
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Abstract
RNA-binding proteins (RBPs) are of fundamental importance for post-transcriptional gene regulation and protein synthesis. They are required for pre-mRNA processing and for RNA transport, degradation and translation into protein, and can regulate every step in the life cycle of their RNA targets. In addition, RBP function can be modulated by RNA binding. RBPs also participate in the formation of ribonucleoprotein complexes that build up macromolecular machineries such as the ribosome and spliceosome. Although most research has focused on mRNA-binding proteins, non-coding RNAs are also regulated and sequestered by RBPs. Functional defects and changes in the expression levels of RBPs have been implicated in numerous diseases, including neurological disorders, muscular atrophy and cancers. RBPs also contribute to a wide spectrum of kidney disorders. For example, human antigen R has been reported to have a renoprotective function in acute kidney injury (AKI) but might also contribute to the development of glomerulosclerosis, tubulointerstitial fibrosis and diabetic kidney disease (DKD), loss of bicaudal C is associated with cystic kidney diseases and Y-box binding protein 1 has been implicated in the pathogenesis of AKI, DKD and glomerular disorders. Increasing data suggest that the modulation of RBPs and their interactions with RNA targets could be promising therapeutic strategies for kidney diseases.
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14
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Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022; 13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
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Affiliation(s)
- Lu Wei
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
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15
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Torres-Méndez A, Pop S, Bonnal S, Almudi I, Avola A, Roberts RJV, Paolantoni C, Alcaina-Caro A, Martín-Anduaga A, Haussmann IU, Morin V, Casares F, Soller M, Kadener S, Roignant JY, Prieto-Godino L, Irimia M. Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals. SCIENCE ADVANCES 2022; 8:eabk0445. [PMID: 35089784 PMCID: PMC8797185 DOI: 10.1126/sciadv.abk0445] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/08/2021] [Indexed: 05/08/2023]
Abstract
Alternative splicing increases neuronal transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal microexon program in Drosophila and compared it with that of mammals. In nonvertebrate bilaterians, this splicing program is restricted to neurons by the posttranscriptional processing of the enhancer of microexons (eMIC) domain in Srrm234. In Drosophila, this processing is dependent on regulation by Elav/Fne. eMIC deficiency or misexpression leads to widespread neurological alterations largely emerging from impaired neuronal activity, as revealed by a combination of neuronal imaging experiments and cell type-specific rescues. These defects are associated with the genome-wide skipping of short neural exons, which are strongly enriched in ion channels. We found no overlap of eMIC-regulated exons between flies and mice, illustrating how ancient posttranscriptional programs can evolve independently in different phyla to affect distinct cellular modules while maintaining cell-type specificity.
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Affiliation(s)
- Antonio Torres-Méndez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
- Francis Crick Institute, London, UK
| | | | - Sophie Bonnal
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Isabel Almudi
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Department of Genetics, Microbiology and Statistics and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | | | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | | | - Irmgard U. Haussmann
- Department of Life Science, School of Health Sciences, Birmingham City University, Birmingham B5 3TN, UK
| | - Violeta Morin
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Fernando Casares
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | | | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- ICREA, Barcelona, Spain
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16
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Oe S, Hayashi S, Tanaka S, Koike T, Hirahara Y, Kakizaki R, Sakamoto S, Noda Y, Yamada H, Kitada M. Cpeb1 expression is post-transcriptionally regulated by AUF1, CPEB1, and microRNAs. FEBS Open Bio 2021; 12:82-94. [PMID: 34480525 PMCID: PMC8727934 DOI: 10.1002/2211-5463.13286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/23/2021] [Accepted: 09/02/2021] [Indexed: 01/04/2023] Open
Abstract
Cytoplasmic polyadenylation element binding protein 1 (CPEB1) regulates the translation of numerous mRNAs. We previously showed that AU‐rich binding factor 1 (AUF1) regulates Cpeb1 expression through the 3’ untranslated region (3’UTR). To investigate the molecular basis of the regulatory potential of the Cpeb1 3’UTR, here we performed reporter analyses that examined expression levels of Gfp reporter mRNA containing the Cpeb1 3’UTR. Our findings indicate that CPEB1 represses the translation of Cpeb1 mRNA and that miR‐145a‐5p and let‐7b‐5p are involved in the reduction in Cpeb1 expression in the absence of AUF1. These results suggest that Cpeb1 expression is post‐transcriptionally regulated by AUF1, CPEB1, and microRNAs.
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Affiliation(s)
- Souichi Oe
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Shinichi Hayashi
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Susumu Tanaka
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Taro Koike
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Yukie Hirahara
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Rio Kakizaki
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Sumika Sakamoto
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Yasuko Noda
- Department of Anatomy, Bio-imaging and Neuro-cell Science, Jichi Medical University, Shimotsuke, Japan
| | - Hisao Yamada
- Biwako Professional University of Rehabilitation, Higashi-Ohmi, Japan
| | - Masaaki Kitada
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
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17
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Deryckere A, Styfhals R, Elagoz AM, Maes GE, Seuntjens E. Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain. eLife 2021; 10:e69161. [PMID: 34425939 PMCID: PMC8384421 DOI: 10.7554/elife.69161] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/21/2021] [Indexed: 12/28/2022] Open
Abstract
Cephalopods have evolved nervous systems that parallel the complexity of mammalian brains in terms of neuronal numbers and richness in behavioral output. How the cephalopod brain develops has only been described at the morphological level, and it remains unclear where the progenitor cells are located and what molecular factors drive neurogenesis. Using histological techniques, we located dividing cells, neural progenitors and postmitotic neurons in Octopus vulgaris embryos. Our results indicate that an important pool of progenitors, expressing the conserved bHLH transcription factors achaete-scute or neurogenin, is located outside the central brain cords in the lateral lips adjacent to the eyes, suggesting that newly formed neurons migrate into the cords. Lineage-tracing experiments then showed that progenitors, depending on their location in the lateral lips, generate neurons for the different lobes, similar to the squid Doryteuthis pealeii. The finding that octopus newborn neurons migrate over long distances is reminiscent of vertebrate neurogenesis and suggests it might be a fundamental strategy for large brain development.
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Affiliation(s)
- Astrid Deryckere
- Laboratory of Developmental Neurobiology, Department of Biology, KU LeuvenLeuvenBelgium
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU LeuvenLeuvenBelgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton DohrnNaplesItaly
| | - Ali Murat Elagoz
- Laboratory of Developmental Neurobiology, Department of Biology, KU LeuvenLeuvenBelgium
| | - Gregory E Maes
- Center for Human Genetics, Genomics Core, UZ-KU LeuvenLeuvenBelgium
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook UniversityTownsvilleAustralia
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU LeuvenLeuvenBelgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU LeuvenLeuvenBelgium
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18
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RNA-Binding Protein HuD as a Versatile Factor in Neuronal and Non-Neuronal Systems. BIOLOGY 2021; 10:biology10050361. [PMID: 33922479 PMCID: PMC8145660 DOI: 10.3390/biology10050361] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary Tight regulation of gene expression is critical for various biological processes such as proliferation, development, differentiation, and death; its dysregulation is linked to the pathogenesis of diseases. Gene expression is dynamically regulated by numerous factors at DNA, RNA, and protein levels, and RNA binding proteins (RBPs) and non–coding RNAs play important roles in the regulation of RNA metabolisms. RBPs govern a diverse spectrum of RNA metabolism by recognizing and binding to the secondary structure or the certain sequence of target mRNAs, and their malfunctions caused by aberrant expression or mutation are implicated in disease pathology. HuD, an RBP in the human antigen (Hu) family, has been studied as a pivotal regulator of gene expression in neuronal systems; however, accumulating evidence reveals the significance of HuD in non–neuronal systems including certain types of cancer cells or endocrine cells in the lung, pancreas, and adrenal gland. In addition, the abnormal function of HuD suggests its pathological association with neurological disorders, cancers, and diabetes. Thus, this review discusses HuD–mediated gene regulation in neuronal and non–neuronal systems to address how it works to orchestrate gene expression and how its expression is controlled in the stress response of pathogenesis of diseases. Abstract HuD (also known as ELAVL4) is an RNA–binding protein belonging to the human antigen (Hu) family that regulates stability, translation, splicing, and adenylation of target mRNAs. Unlike ubiquitously distributed HuR, HuD is only expressed in certain types of tissues, mainly in neuronal systems. Numerous studies have shown that HuD plays essential roles in neuronal development, differentiation, neurogenesis, dendritic maturation, neural plasticity, and synaptic transmission by regulating the metabolism of target mRNAs. However, growing evidence suggests that HuD also functions as a pivotal regulator of gene expression in non–neuronal systems and its malfunction is implicated in disease pathogenesis. Comprehensive knowledge of HuD expression, abundance, molecular targets, and regulatory mechanisms will broaden our understanding of its role as a versatile regulator of gene expression, thus enabling novel treatments for diseases with aberrant HuD expression. This review focuses on recent advances investigating the emerging role of HuD, its molecular mechanisms of target gene regulation, and its disease relevance in both neuronal and non–neuronal systems.
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19
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Hsieh MC, Ho YC, Lai CY, Wang HH, Yang PS, Cheng JK, Chen GD, Ng SC, Lee AS, Tseng KW, Lin TB, Peng HY. Blocking the Spinal Fbxo3/CARM1/K + Channel Epigenetic Silencing Pathway as a Strategy for Neuropathic Pain Relief. Neurotherapeutics 2021; 18:1295-1315. [PMID: 33415686 PMCID: PMC8423947 DOI: 10.1007/s13311-020-00977-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 11/29/2022] Open
Abstract
Many epigenetic regulators are involved in pain-associated spinal plasticity. Coactivator-associated arginine methyltransferase 1 (CARM1), an epigenetic regulator of histone arginine methylation, is a highly interesting target in neuroplasticity. However, its potential contribution to spinal plasticity-associated neuropathic pain development remains poorly explored. Here, we report that nerve injury decreased the expression of spinal CARM1 and induced allodynia. Moreover, decreasing spinal CARM1 expression by Fbxo3-mediated CARM1 ubiquitination promoted H3R17me2 decrement at the K+ channel promoter, thereby causing K+ channel epigenetic silencing and the development of neuropathic pain. Remarkably, in naïve rats, decreasing spinal CARM1 using CARM1 siRNA or a CARM1 inhibitor resulted in similar epigenetic signaling and allodynia. Furthermore, intrathecal administration of BC-1215 (a novel Fbxo3 inhibitor) prevented CARM1 ubiquitination to block K+ channel gene silencing and ameliorate allodynia after nerve injury. Collectively, the results reveal that this newly identified spinal Fbxo3-CARM1-K+ channel gene functional axis promotes neuropathic pain. These findings provide essential insights that will aid in the development of more efficient and specific therapies against neuropathic pain.
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Affiliation(s)
- Ming-Chun Hsieh
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan
| | - Yu-Cheng Ho
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung City, Taiwan
| | - Cheng-Yuan Lai
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan
| | - Hsueh-Hsiao Wang
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan
| | - Po-Sheng Yang
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan
- Department of Surgery, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jen-Kun Cheng
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan
- Department of Anesthesiology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Gin-Den Chen
- Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Chung Shan Medical University, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Soo-Cheen Ng
- Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Chung Shan Medical University, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - An-Sheng Lee
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan
| | - Kuang-Wen Tseng
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan
| | - Tzer-Bin Lin
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan
- Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, 11689, Taiwan
- Department of Biotechnology, College of Medical and Health Science, Asia University, Taichung, 41354, Taiwan
| | - Hsien-Yu Peng
- Department of Medicine, Mackay Medical College, No.46, Sec. 3, Zhongzheng Rd, Sanzhi Dist, New Taipei, 25245, Taiwan.
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20
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Discrepancy between Jun/Fos Proto-Oncogene mRNA and Protein Expression in the Rheumatoid Arthritis Synovial Membrane. J 2020. [DOI: 10.3390/j3020015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory and destructive joint disease characterized by overexpression of pro-inflammatory/pro-destructive mediators, whose regulation has been the focus of our previous studies. Since the expression of these proteins commonly depends on AP-1, the expression of the AP-1-forming subunits cJun, JunB, JunD, and cFos was assessed in synovial membrane (SM) samples of RA, osteoarthritis (OA), joint trauma (JT), and normal controls (NC) using ELISA and qRT-PCR. With respect to an observed discrepancy between mRNA and protein levels, the expression of the mRNA stability-modifying factors AU-rich element RNA-binding protein (AUF)-1, tristetraprolin (TTP), and human antigen R (HuR) was measured. JunB and JunD protein expression was significantly higher in RA-SM compared to OA and/or NC. By contrast, jun/fos mRNA expression was significantly (cjun) or numerically decreased (junB, junD, cfos) in RA and OA compared to JT and/or NC. Remarkably, TTP and HuR were also affected by discrepancies between their mRNA and protein levels, since they were significantly decreased at the mRNA level in RA versus NC, but significantly or numerically increased at the protein level when compared to JT and NC. Discrepancies between the mRNA and protein expression for Jun/Fos and TTP/HuR suggest broad alterations of post-transcriptional processes in the RA-SM. In this context, increased levels of mRNA-destabilizing TTP may contribute to the low levels of jun/fos and ttp/hur mRNA, whereas abundant mRNA-stabilizing HuR may augment translation of the remaining mRNA into protein with potential consequences for the composition of the resulting AP-1 complexes and the expression of AP-1-dependent genes in RA.
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21
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RNA binding protein HuD and microRNA-203a cooperatively regulate insulinoma-associated 1 mRNA. Biochem Biophys Res Commun 2019; 521:971-976. [PMID: 31722792 DOI: 10.1016/j.bbrc.2019.11.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 02/02/2023]
Abstract
RNA binding protein HuD regulates translation and turnover of target mRNAs, thereby affecting gene expression at the posttranscriptional level in mainly neuronal as well as pancreatic β-cells. Here, we identified insulinoma-associated 1 (INSM1), an essential factor governing differentiation and proliferation of neuroendocrine cells, as a novel target of HuD and demonstrated the regulatory mechanism of INSM1 expression by HuD. HuD bound to 3'untranslated region (3'UTR) of Insm1 mRNA and negatively regulated its expression; knockdown of HuD increased INSM1 expression, while HuD overexpression repressed it by destabilizing its mRNA. In addition, we further demonstrated that HuD enhanced reduction of INSM1 by miR-203a, a novel miRNA targeting Insm1 mRNA 3'UTR. These results suggest that HuD and miR-203a cooperatively regulate INSM1 expression and it provides a novel regulatory mechanism of INSM1 expression by HuD and miR-203a.
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22
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Pabis M, Popowicz GM, Stehle R, Fernández-Ramos D, Asami S, Warner L, García-Mauriño SM, Schlundt A, Martínez-Chantar ML, Díaz-Moreno I, Sattler M. HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs. Nucleic Acids Res 2019; 47:1011-1029. [PMID: 30418581 PMCID: PMC6344896 DOI: 10.1093/nar/gky1138] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/28/2018] [Indexed: 12/22/2022] Open
Abstract
HuR/ELAVL1 is an RNA-binding protein involved in differentiation and stress response that acts primarily by stabilizing messenger RNA (mRNA) targets. HuR comprises three RNA recognition motifs (RRMs) where the structure and RNA binding of RRM3 and of full-length HuR remain poorly understood. Here, we report crystal structures of RRM3 free and bound to cognate RNAs. Our structural, NMR and biochemical data show that RRM3 mediates canonical RNA interactions and reveal molecular details of a dimerization interface localized on the α-helical face of RRM3. NMR and SAXS analyses indicate that the three RRMs in full-length HuR are flexibly connected in the absence of RNA, while they adopt a more compact arrangement when bound to RNA. Based on these data and crystal structures of tandem RRM1,2-RNA and our RRM3-RNA complexes, we present a structural model of RNA recognition involving all three RRM domains of full-length HuR. Mutational analysis demonstrates that RRM3 dimerization and RNA binding is required for functional activity of full-length HuR in vitro and to regulate target mRNAs levels in human cells, thus providing a fine-tuning for HuR activity in vivo.
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Affiliation(s)
- Marta Pabis
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.,Max Planck Research Group hosted by the Malopolska Centre of Biotechnology of the Jagiellonian University, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - David Fernández-Ramos
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias. Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Sam Asami
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Lisa Warner
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Andreas Schlundt
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - María L Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias. Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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23
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Carelli S, Giallongo T, Rey F, Latorre E, Bordoni M, Mazzucchelli S, Gorio MC, Pansarasa O, Provenzani A, Cereda C, Di Giulio AM. HuR interacts with lincBRN1a and lincBRN1b during neuronal stem cells differentiation. RNA Biol 2019; 16:1471-1485. [PMID: 31345103 PMCID: PMC6779397 DOI: 10.1080/15476286.2019.1637698] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
LncRNAs play crucial roles in cellular processes and their regulatory effects in the adult brain and neural stem cells (NSCs) remain to be entirely characterized. We report that 10 lncRNAs (LincENC1, FABL, lincp21, HAUNT, PERIL, lincBRN1a, lincBRN1b, HOTTIP, TUG1 and FENDRR) are expressed during murine NSCs differentiation and interact with the RNA-binding protein ELAVL1/HuR. Furthermore, we characterize the function of two of the deregulated lncRNAs, lincBRN1a and lincBRN1b, during NSCs' differentiation. Their inhibition leads to the induction of differentiation, with a concomitant decrease in stemness and an increase in neuronal markers, indicating that they exert key functions in neuronal cells differentiation. Furthermore, we describe here that HuR regulates their half-life, suggesting their synergic role in the differentiation process. We also identify six human homologs (PANTR1, TUG1, HOTTIP, TP53COR, ELDRR and FENDRR) of the mentioned 10 lncRNAs and we report their deregulation during human iPSCs differentiation into neurons. In conclusion, our results strongly indicate a key synergic role for lncRNAs and HuR in neuronal stem cells fate.
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Affiliation(s)
- Stephana Carelli
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan , Milan , Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan , Milan , Italy
| | - Toniella Giallongo
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan , Milan , Italy
| | - Federica Rey
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan , Milan , Italy
| | - Elisa Latorre
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan , Milan , Italy
| | - Matteo Bordoni
- Center of Genomic and post-Genomic, IRCCS Mondino Foundation , Pavia , Italy
| | - Serena Mazzucchelli
- Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan , Milan , Italy
| | - Maria Carlotta Gorio
- Department of Biomedical and Clinical Sciencse L. Sacco, University of Milan , Milan , Italy
| | - Orietta Pansarasa
- Center of Genomic and post-Genomic, IRCCS Mondino Foundation , Pavia , Italy
| | - Alessandro Provenzani
- Laboratory of Genomic Screening Center for Integrative Biology, - CIBIO, University of Trento , Trento , Italy
| | - Cristina Cereda
- Center of Genomic and post-Genomic, IRCCS Mondino Foundation , Pavia , Italy
| | - Anna Maria Di Giulio
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan , Milan , Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan , Milan , Italy
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24
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Mirisis AA, Carew TJ. The ELAV family of RNA-binding proteins in synaptic plasticity and long-term memory. Neurobiol Learn Mem 2019; 161:143-148. [PMID: 30998973 DOI: 10.1016/j.nlm.2019.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/14/2019] [Accepted: 04/13/2019] [Indexed: 12/26/2022]
Abstract
The mechanisms of de novo gene expression and translation of specific gene transcripts have long been known to support long-lasting changes in synaptic plasticity and behavioral long-term memory. In recent years, it has become increasingly apparent that gene expression is heavily regulated not only on the level of transcription, but also through post-transcriptional gene regulation, which governs the subcellular localization, stability, and likelihood of translation of mRNAs. Specific families of RNA-binding proteins (RBPs) bind transcripts which contain AU-rich elements (AREs) within their 3' UTR and thereby govern their downstream fate. These post-transcriptional gene regulatory mechanisms are coordinated through the same cell signaling pathways that play critical roles in long-term memory formation. In this review, we discuss recent results that demonstrate the roles that these ARE-binding proteins play in LTM formation.
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Affiliation(s)
| | - Thomas J Carew
- Center for Neural Science, New York University, New York, NY 10003, USA.
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25
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Grassi E, Santoro R, Umbach A, Grosso A, Oliviero S, Neri F, Conti L, Ala U, Provero P, DiCunto F, Merlo GR. Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors. Front Cell Neurosci 2019; 12:518. [PMID: 30687010 PMCID: PMC6338052 DOI: 10.3389/fncel.2018.00518] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 01/09/2023] Open
Abstract
Alternative polyadenylation (APA) is a widespread mechanism involving about half of the expressed genes, resulting in varying lengths of the 3′ untranslated region (3′UTR). Variations in length and sequence of the 3′UTR may underlie changes of post-transcriptional processing, localization, miRNA targeting and stability of mRNAs. During embryonic development a large array of mRNAs exhibit APA, with a prevalence of the longer 3′UTR versions in differentiating cells. Little is known about polyA+ site usage during differentiation of mammalian neural progenitors. Here we exploit a model of adherent neural stem (ANS) cells, which homogeneously and efficiently differentiate into GABAergic neurons. RNAseq data shows a global trend towards lengthening of the 3′UTRs during differentiation. Enriched expression of the longer 3′UTR variants of Pes1 and Gng2 was detected in the mouse brain in areas of cortical and subcortical neuronal differentiation, respectively, by two-probes fluorescent in situ hybridization (FISH). Among the coding genes upregulated during differentiation of ANS cells we found Elavl3, a neural-specific RNA-binding protein homologous to Drosophila Elav. In the insect, Elav regulates polyA+ site choice while interacting with paused Pol-II promoters. We tested the role of Elavl3 in ANS cells, by silencing Elavl3 and observed consistent changes in 3′UTR length and delayed neuronal differentiation. These results indicate that choice of the polyA+ site and lengthening of 3′UTRs is a possible additional mechanism of posttranscriptional RNA modification involved in neuronal differentiation.
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Affiliation(s)
- Elena Grassi
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Roberto Santoro
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Alessandro Umbach
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Anna Grosso
- Department of Neurosciences, University of Turin, Turin, Italy
| | - Salvatore Oliviero
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Life Science and System Biology, University of Turin, Turin, Italy
| | - Francesco Neri
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Life Science and System Biology, University of Turin, Turin, Italy
| | - Luciano Conti
- Centre for Integrative Biology-CIBIO, University of Trento, Povo, Italy
| | - Ugo Ala
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Ferdinando DiCunto
- Department of Molecular Biotechnology, University of Turin, Turin, Italy.,Department of Neurosciences, University of Turin, Turin, Italy
| | - Giorgio R Merlo
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
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26
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Neuroprotective action of Eicosapentaenoic (EPA) and Docosahexaenoic (DHA) acids on Paraquat intoxication in Drosophila melanogaster. Neurotoxicology 2019; 70:154-160. [DOI: 10.1016/j.neuro.2018.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 11/19/2022]
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27
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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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28
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Smith FW, Cumming M, Goldstein B. Analyses of nervous system patterning genes in the tardigrade Hypsibius exemplaris illuminate the evolution of panarthropod brains. EvoDevo 2018; 9:19. [PMID: 30069303 PMCID: PMC6065069 DOI: 10.1186/s13227-018-0106-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Both euarthropods and vertebrates have tripartite brains. Several orthologous genes are expressed in similar regionalized patterns during brain development in both vertebrates and euarthropods. These similarities have been used to support direct homology of the tripartite brains of vertebrates and euarthropods. If the tripartite brains of vertebrates and euarthropods are homologous, then one would expect other taxa to share this structure. More generally, examination of other taxa can help in tracing the evolutionary history of brain structures. Tardigrades are an interesting lineage on which to test this hypothesis because they are closely related to euarthropods, and whether they have a tripartite brain or unipartite brain has recently been a focus of debate. RESULTS We tested this hypothesis by analyzing the expression patterns of six3, orthodenticle, pax6, unplugged, and pax2/5/8 during brain development in the tardigrade Hypsibius exemplaris-formerly misidentified as Hypsibius dujardini. These genes were expressed in a staggered anteroposterior order in H. exemplaris, similar to what has been reported for mice and flies. However, only six3, orthodenticle, and pax6 were expressed in the developing brain. Unplugged was expressed broadly throughout the trunk and posterior head, before the appearance of the nervous system. Pax2/5/8 was expressed in the developing central and peripheral nervous system in the trunk. CONCLUSION Our results buttress the conclusion of our previous study of Hox genes-that the brain of tardigrades is only homologous to the protocerebrum of euarthropods. They support a model based on fossil evidence that the last common ancestor of tardigrades and euarthropods possessed a unipartite brain. Our results are inconsistent with the hypothesis that the tripartite brain of euarthropods is directly homologous to the tripartite brain of vertebrates.
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Affiliation(s)
- Frank W. Smith
- Biology Department, University of North Florida, Jacksonville, FL USA
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Mandy Cumming
- Biology Department, University of North Florida, Jacksonville, FL USA
| | - Bob Goldstein
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
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29
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Zybura-Broda K, Wolder-Gontarek M, Ambrozek-Latecka M, Choros A, Bogusz A, Wilemska-Dziaduszycka J, Rylski M. HuR (Elavl1) and HuB (Elavl2) Stabilize Matrix Metalloproteinase-9 mRNA During Seizure-Induced Mmp-9 Expression in Neurons. Front Neurosci 2018; 12:224. [PMID: 29686606 PMCID: PMC5900018 DOI: 10.3389/fnins.2018.00224] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/22/2018] [Indexed: 01/28/2023] Open
Abstract
Matrix metalloproteinase-9 (Mmp-9) is involved in different general and cell-type–specific processes, both in neuronal and non-neuronal cells. Moreover, it is implicated in an induction or progression of various human disorders, including diseases of the central nervous system. Mechanisms regulating activity-driven Mmp-9 expression in neurons are still not fully understood. Here, we show that stabilization of Mmp-9 mRNA is one of the factors responsible for the neuronal activity-evoked upregulation of Mmp-9 mRNA expression in hippocampal neurons. Furthermore, we demonstrate that the molecular mechanism related to this stabilization is dependent on the neuronal seizure-triggered transiently increased binding of the mRNA stability-inducing protein, HuR, to ARE1 and ARE4 motifs of the 3′UTR for Mmp-9 mRNA as well as the stably augmented association of another mRNA-stabilizing protein, HuB, to the ARE1 element of the 3′UTR. Intriguingly, we demonstrate further that both HuR and HuB are crucial for an incidence of Mmp-9 mRNA stabilization after neuronal activation. This study identifies Mmp-9 mRNA as the first HuB target regulated by mRNA stabilization in neurons. Moreover, these results are the first to describe an existence of HuR-dependent mRNA stabilization in neurons of the brain.
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Affiliation(s)
- Katarzyna Zybura-Broda
- Department of Clinical Cytology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | | | | | - Artur Choros
- Department of Clinical Cytology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Bogusz
- Department of Clinical Cytology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | | | - Marcin Rylski
- Department of Clinical Cytology, Centre of Postgraduate Medical Education, Warsaw, Poland
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30
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Shaikh MN, Tejedor FJ. Mnb/Dyrk1A orchestrates a transcriptional network at the transition from self-renewing neurogenic progenitors to postmitotic neuronal precursors. J Neurogenet 2018; 32:37-50. [PMID: 29495936 DOI: 10.1080/01677063.2018.1438427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Down syndrome and microcephaly related gene Mnb/Dyrk1A encodes an evolutionary conserved protein kinase subfamily that plays important roles in neurodevelopment. minibrain (mnb) mutants of Drosophila melanogaster (Dm) exhibit reduced adult brains due to neuronal deficits generated during larval development. These deficits are the consequence of the apoptotic cell death of numerous neuronal precursors that fail to properly exit the cell cycle and differentiate. We have recently found that in both the Dm larval brain and the embryonic vertebrate central nervous system (CNS), a transient expression of Mnb/Dyrk1A promotes the cell cycle exit of newborn neuronal precursors by upregulating the expression of the cyclin-dependent kinase inhibitor p27kip1 (called Dacapo in Dm). In the larval brain, Mnb performs this action by regulating the expression of three transcription factors, Asense (Ase), Deadpan (Dpn) and Prospero (Pros), which are key regulators of the self-renewal, proliferation, and terminal differentiation of neural progenitor cells. We have here studied in detail the cellular/temporal expression pattern of Ase, Dpn, Pros and Mnb, and have analyzed possible regulatory effects among them at the transitions from neurogenic progenitors to postmitotic neuronal precursors in the Dm larval brain. The emerging picture of this analysis reveals an intricate regulatory network in which Mnb appears to play a pivotal role helping to delineate the dynamics of the expression patterns of Ase, Dpn and Pros, as well as their specific functions in the aforementioned transitions. Our results also show that Ase, Dpn and Pros perform several cross-regulatory actions and contribute to shape the precise cellular/temporal expression pattern of Mnb. We propose that Mnb/Dyrk1A plays a central role in CNS neurogenesis by integrating molecular mechanisms that regulate progenitor self-renewal, cell cycle progression and neuronal differentiation.
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Affiliation(s)
- Mirja N Shaikh
- a Instituto de Neurociencias , CSIC and Universidad Miguel Hernandez , Alicante , Spain
| | - Francisco J Tejedor
- a Instituto de Neurociencias , CSIC and Universidad Miguel Hernandez , Alicante , Spain
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31
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Autophagy Stimulus Promotes Early HuR Protein Activation and p62/SQSTM1 Protein Synthesis in ARPE-19 Cells by Triggering Erk1/2, p38 MAPK, and JNK Kinase Pathways. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4956080. [PMID: 29576851 PMCID: PMC5822911 DOI: 10.1155/2018/4956080] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 11/03/2017] [Accepted: 12/05/2017] [Indexed: 12/14/2022]
Abstract
RNA-binding protein dysregulation and altered expression of proteins involved in the autophagy/proteasome pathway play a role in many neurodegenerative disease onset/progression, including age-related macular degeneration (AMD). HuR/ELAVL1 is a master regulator of gene expression in human physiopathology. In ARPE-19 cells exposed to the proteasomal inhibitor MG132, HuR positively affects at posttranscriptional level p62 expression, a stress response gene involved in protein aggregate clearance with a role in AMD. Here, we studied the early effects of the proautophagy AICAR + MG132 cotreatment on the HuR-p62 pathway. We treated ARPE-19 cells with Erk1/2, AMPK, p38MAPK, PKC, and JNK kinase inhibitors in the presence of AICAR + MG132 and evaluated HuR localization/phosphorylation and p62 expression. Two-hour AICAR + MG132 induces both HuR cytoplasmic translocation and threonine phosphorylation via the Erk1/2 pathway. In these conditions, p62 mRNA is loaded on polysomes and its translation in de novo protein is favored. Additionally, for the first time, we report that JNK can phosphorylate HuR, however, without modulating its localization. Our study supports HuR's role as an upstream regulator of p62 expression in ARPE-19 cells, helps to understand better the early events in response to a proautophagy stimulus, and suggests that modulation of the autophagy-regulating kinases as potential therapeutic targets for AMD may be relevant.
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32
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The Structure of the ZMYND8/Drebrin Complex Suggests a Cytoplasmic Sequestering Mechanism of ZMYND8 by Drebrin. Structure 2017; 25:1657-1666.e3. [DOI: 10.1016/j.str.2017.08.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/27/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022]
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33
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Nasti R, Rossi D, Amadio M, Pascale A, Unver MY, Hirsch AKH, Collina S. Compounds Interfering with Embryonic Lethal Abnormal Vision (ELAV) Protein–RNA Complexes: An Avenue for Discovering New Drugs. J Med Chem 2017; 60:8257-8267. [DOI: 10.1021/acs.jmedchem.6b01871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rita Nasti
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Marialaura Amadio
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - Alessia Pascale
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - M. Yagiz Unver
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Simona Collina
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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34
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Rajman M, Metge F, Fiore R, Khudayberdiev S, Aksoy-Aksel A, Bicker S, Ruedell Reschke C, Raoof R, Brennan GP, Delanty N, Farrell MA, O'Brien DF, Bauer S, Norwood B, Veno MT, Krüger M, Braun T, Kjems J, Rosenow F, Henshall DC, Dieterich C, Schratt G. A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses. EMBO J 2017; 36:1770-1787. [PMID: 28487411 DOI: 10.15252/embj.201695748] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/31/2022] Open
Abstract
Synaptic downscaling is a homeostatic mechanism that allows neurons to reduce firing rates during chronically elevated network activity. Although synaptic downscaling is important in neural circuit development and epilepsy, the underlying mechanisms are poorly described. We performed small RNA profiling in picrotoxin (PTX)-treated hippocampal neurons, a model of synaptic downscaling. Thereby, we identified eight microRNAs (miRNAs) that were increased in response to PTX, including miR-129-5p, whose inhibition blocked synaptic downscaling in vitro and reduced epileptic seizure severity in vivo Using transcriptome, proteome, and bioinformatic analysis, we identified the calcium pump Atp2b4 and doublecortin (Dcx) as miR-129-5p targets. Restoring Atp2b4 and Dcx expression was sufficient to prevent synaptic downscaling in PTX-treated neurons. Furthermore, we characterized a functional crosstalk between miR-129-5p and the RNA-binding protein (RBP) Rbfox1. In the absence of PTX, Rbfox1 promoted the expression of Atp2b4 and Dcx. Upon PTX treatment, Rbfox1 expression was downregulated by miR-129-5p, thereby allowing the repression of Atp2b4 and Dcx. We therefore identified a novel activity-dependent miRNA/RBP crosstalk during synaptic scaling, with potential implications for neural network homeostasis and epileptogenesis.
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Affiliation(s)
- Marek Rajman
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Franziska Metge
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, German Center for Cardiovascular Research (DZHK), University Hospital Heidelberg, Heidelberg, Germany
| | - Roberto Fiore
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Sharof Khudayberdiev
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ayla Aksoy-Aksel
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Silvia Bicker
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Rana Raoof
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gary P Brennan
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | | | | - Sebastian Bauer
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Braxton Norwood
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Morten T Veno
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Marcus Krüger
- Institute for Genetics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Felix Rosenow
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - David C Henshall
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, German Center for Cardiovascular Research (DZHK), University Hospital Heidelberg, Heidelberg, Germany
| | - Gerhard Schratt
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
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35
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Moschall R, Gaik M, Medenbach J. Promiscuity in post-transcriptional control of gene expression: Drosophila sex-lethal and its regulatory partnerships. FEBS Lett 2017; 591:1471-1488. [PMID: 28391641 PMCID: PMC5488161 DOI: 10.1002/1873-3468.12652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/08/2017] [Accepted: 04/04/2017] [Indexed: 12/28/2022]
Abstract
The Drosophila RNA‐binding protein Sex‐lethal (Sxl) is a potent post‐transcriptional regulator of gene expression that controls female development. It regulates the expression of key factors involved in sex‐specific differences in morphology, behavior, and dosage compensation. Functional Sxl protein is only expressed in female flies, where it binds to U‐rich RNA motifs present in its target mRNAs to regulate their fate. Sxl is a very versatile regulator that, by shuttling between the nucleus and the cytoplasm, can regulate almost all aspects of post‐transcriptional gene expression including RNA processing, nuclear export, and translation. For these functions, Sxl employs multiple interactions to either antagonize RNA‐processing factors or to recruit various coregulators, thus allowing it to establish a female‐specific gene expression pattern. Here, we summarize the current knowledge about Sxl function and review recent mechanistic and structural studies that further our understanding of how such a seemingly ‘simple’ RNA‐binding protein can exert this plethora of different functions.
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Affiliation(s)
| | - Monika Gaik
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Germany
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Fragkouli A, Koukouraki P, Vlachos IS, Paraskevopoulou MD, Hatzigeorgiou AG, Doxakis E. Neuronal ELAVL proteins utilize AUF-1 as a co-partner to induce neuron-specific alternative splicing of APP. Sci Rep 2017; 7:44507. [PMID: 28291226 PMCID: PMC5349543 DOI: 10.1038/srep44507] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/08/2017] [Indexed: 12/18/2022] Open
Abstract
Aβ peptide that accumulates in Alzheimer’s disease brain, derives from proteolytic processing of the amyloid precursor protein (APP) that exists in three main isoforms derived by alternative splicing. The isoform APP695, lacking exons 7 and 8, is predominately expressed in neurons and abnormal neuronal splicing of APP has been observed in the brain of patients with Alzheimer’s disease. Herein, we demonstrate that expression of the neuronal members of the ELAVL protein family (nELAVLs) correlate with APP695 levels in vitro and in vivo. Moreover, we provide evidence that nELAVLs regulate the production of APP695; by using a series of reporters we show that concurrent binding of nELAVLs to sequences located both upstream and downstream of exon 7 is required for its skipping, whereas nELAVL-binding to a highly conserved U-rich sequence upstream of exon 8, is sufficient for its exclusion. Finally, we report that nELAVLs block APP exon 7 or 8 definition by reducing the binding of the essential splicing factor U2AF65, an effect facilitated by the concurrent binding of AUF-1. Our study provides new insights into the regulation of APP pre-mRNA processing, supports the role for nELAVLs as neuron-specific splicing regulators and reveals a novel function of AUF1 in alternative splicing.
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Affiliation(s)
- Apostolia Fragkouli
- Center for Basic Research, Biomedical Research Foundation Academy of Athens, 4 Soranou Efesiou str, 11527, Athens Greece
| | - Pelagia Koukouraki
- Center for Basic Research, Biomedical Research Foundation Academy of Athens, 4 Soranou Efesiou str, 11527, Athens Greece
| | - Ioannis S Vlachos
- Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece.,DIANA-Lab, Department of Electrical &Computer Engineering, University of Thessaly, 38221 Volos, Greece
| | - Maria D Paraskevopoulou
- Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece.,DIANA-Lab, Department of Electrical &Computer Engineering, University of Thessaly, 38221 Volos, Greece
| | - Artemis G Hatzigeorgiou
- Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece.,DIANA-Lab, Department of Electrical &Computer Engineering, University of Thessaly, 38221 Volos, Greece
| | - Epaminondas Doxakis
- Center for Basic Research, Biomedical Research Foundation Academy of Athens, 4 Soranou Efesiou str, 11527, Athens Greece
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Lim CS, Alkon DL. Inhibition of coactivator-associated arginine methyltransferase 1 modulates dendritic arborization and spine maturation of cultured hippocampal neurons. J Biol Chem 2017; 292:6402-6413. [PMID: 28264928 DOI: 10.1074/jbc.m117.775619] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/24/2017] [Indexed: 01/11/2023] Open
Abstract
An improved understanding of the molecular mechanisms in synapse formation provides insight into both learning and memory and the etiology of neurodegenerative disorders. Coactivator-associated arginine methyltransferase 1 (CARM1) is a protein methyltransferase that negatively regulates synaptic gene expression and inhibits neuronal differentiation. Despite its regulatory function in neurons, little is known about the CARM1 cellular location and its role in dendritic maturation and synapse formation. Here, we examined the effects of CARM1 inhibition on dendritic spine and synapse morphology in the rat hippocampus. CARM1 was localized in hippocampal post-synapses, with immunocytochemistry and electron microscopy revealing co-localization of CARM1 with post-synaptic density (PSD)-95 protein, a post-synaptic marker. Specific siRNA-mediated suppression of CARM1 expression resulted in precocious dendritic maturation, with increased spine width and density at sites along dendrites and induction of mushroom-type spines. These changes were accompanied by a striking increase in the cluster size and number of key synaptic proteins, including N-methyl-d-aspartate receptor subunit 2B (NR2B) and PSD-95. Similarly, pharmacological inhibition of CARM1 activity with the CARM1-specific inhibitor AMI-1 significantly increased spine width and mushroom-type spines and also increased the cluster size and number of NR2B and cluster size of PSD-95. These results suggest that CARM1 is a post-synaptic protein that plays roles in dendritic maturation and synaptic formation and that spatiotemporal regulation of CARM1 activity modulates neuronal connectivity and improves synaptic dysfunction.
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Affiliation(s)
- Chol Seung Lim
- From the Blanchette Rockefeller Neurosciences Institute, West Virginia University, Morgantown, West Virginia 26505
| | - Daniel L Alkon
- From the Blanchette Rockefeller Neurosciences Institute, West Virginia University, Morgantown, West Virginia 26505
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Bryant CD, Yazdani N. RNA-binding proteins, neural development and the addictions. GENES BRAIN AND BEHAVIOR 2016; 15:169-86. [PMID: 26643147 DOI: 10.1111/gbb.12273] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022]
Abstract
Transcriptional and post-transcriptional regulation of gene expression defines the neurobiological mechanisms that bridge genetic and environmental risk factors with neurobehavioral dysfunction underlying the addictions. More than 1000 genes in the eukaryotic genome code for multifunctional RNA-binding proteins (RBPs) that can regulate all levels of RNA biogenesis. More than 50% of these RBPs are expressed in the brain where they regulate alternative splicing, transport, localization, stability and translation of RNAs during development and adulthood. Dysfunction of RBPs can exert global effects on their targetomes that underlie neurodegenerative disorders such as Alzheimer's and Parkinson's diseases as well as neurodevelopmental disorders, including autism and schizophrenia. Here, we consider the evidence that RBPs influence key molecular targets, neurodevelopment, synaptic plasticity and neurobehavioral dysfunction underlying the addictions. Increasingly well-powered genome-wide association studies in humans and mammalian model organisms combined with ever more precise transcriptomic and proteomic approaches will continue to uncover novel and possibly selective roles for RBPs in the addictions. Key challenges include identifying the biological functions of the dynamic RBP targetomes from specific cell types throughout subcellular space (e.g. the nuclear spliceome vs. the synaptic translatome) and time and manipulating RBP programs through post-transcriptional modifications to prevent or reverse aberrant neurodevelopment and plasticity underlying the addictions.
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Affiliation(s)
- C D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - N Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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Marchesi N, Amadio M, Colombrita C, Govoni S, Ratti A, Pascale A. PKC Activation Counteracts ADAM10 Deficit in HuD-Silenced Neuroblastoma Cells. J Alzheimers Dis 2016; 54:535-47. [DOI: 10.3233/jad-160299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nicoletta Marchesi
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Pavia, Italy
| | - Marialaura Amadio
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Pavia, Italy
| | - Claudia Colombrita
- Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, ‘Dino Ferrari’ Center, University of Milan, Milan, Italy
| | - Stefano Govoni
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Pavia, Italy
| | - Antonia Ratti
- Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, ‘Dino Ferrari’ Center, University of Milan, Milan, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Pavia, Italy
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Kanost MR, Arrese EL, Cao X, Chen YR, Chellapilla S, Goldsmith MR, Grosse-Wilde E, Heckel DG, Herndon N, Jiang H, Papanicolaou A, Qu J, Soulages JL, Vogel H, Walters J, Waterhouse RM, Ahn SJ, Almeida FC, An C, Aqrawi P, Bretschneider A, Bryant WB, Bucks S, Chao H, Chevignon G, Christen JM, Clarke DF, Dittmer NT, Ferguson LCF, Garavelou S, Gordon KHJ, Gunaratna RT, Han Y, Hauser F, He Y, Heidel-Fischer H, Hirsh A, Hu Y, Jiang H, Kalra D, Klinner C, König C, Kovar C, Kroll AR, Kuwar SS, Lee SL, Lehman R, Li K, Li Z, Liang H, Lovelace S, Lu Z, Mansfield JH, McCulloch KJ, Mathew T, Morton B, Muzny DM, Neunemann D, Ongeri F, Pauchet Y, Pu LL, Pyrousis I, Rao XJ, Redding A, Roesel C, Sanchez-Gracia A, Schaack S, Shukla A, Tetreau G, Wang Y, Xiong GH, Traut W, Walsh TK, Worley KC, Wu D, Wu W, Wu YQ, Zhang X, Zou Z, Zucker H, Briscoe AD, Burmester T, Clem RJ, Feyereisen R, Grimmelikhuijzen CJP, Hamodrakas SJ, Hansson BS, Huguet E, Jermiin LS, Lan Q, Lehman HK, Lorenzen M, Merzendorfer H, Michalopoulos I, Morton DB, Muthukrishnan S, Oakeshott JG, Palmer W, Park Y, Passarelli AL, Rozas J, Schwartz LM, Smith W, Southgate A, Vilcinskas A, Vogt R, Wang P, Werren J, Yu XQ, Zhou JJ, Brown SJ, Scherer SE, Richards S, Blissard GW. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 76:118-147. [PMID: 27522922 PMCID: PMC5010457 DOI: 10.1016/j.ibmb.2016.07.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/27/2016] [Accepted: 07/14/2016] [Indexed: 05/19/2023]
Abstract
Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.
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Affiliation(s)
- Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Estela L Arrese
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yun-Ru Chen
- Boyce Thompson Institute at Cornell University, Tower Road, Ithaca, NY, 14853, USA
| | - Sanjay Chellapilla
- KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Marian R Goldsmith
- Biological Sciences Department, University of Rhode Island, Kingston, RI, 02881, USA
| | - Ewald Grosse-Wilde
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Nicolae Herndon
- KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jiaxin Qu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Jose L Soulages
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - James Walters
- Department of Ecology and Evolutionary Biology, Univ. Kansas, Lawrence, KS, 66045, USA
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA, 02139, USA; The Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, MA, 02142, USA
| | - Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Francisca C Almeida
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Chunju An
- Department of Entomology, China Agricultural University, Beijing, China
| | - Peshtewani Aqrawi
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Anne Bretschneider
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - William B Bryant
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sascha Bucks
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Germain Chevignon
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR Sciences et Techniques, Université François-Rabelais, Tours, France
| | - Jayne M Christen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - David F Clarke
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Neal T Dittmer
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Spyridoula Garavelou
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Karl H J Gordon
- CSIRO Health and Biosecurity, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Ramesh T Gunaratna
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-21oo, Copenhagen, Denmark
| | - Yan He
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Hanna Heidel-Fischer
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Ariana Hirsh
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Yingxia Hu
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Hongbo Jiang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Christian Klinner
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Christopher König
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ashley R Kroll
- Department of Biology, Reed College, Portland, OR, 97202, USA
| | - Suyog S Kuwar
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Sandy L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Rüdiger Lehman
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Bioresources Project Group, Winchesterstrasse 2, 35394, Gießen, Germany
| | - Kai Li
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Zhaofei Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hanquan Liang
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Shanna Lovelace
- Department of Biological Sciences, University of Southern Maine, Portland, ME, 04104, USA
| | - Zhiqiang Lu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jennifer H Mansfield
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Kyle J McCulloch
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Tittu Mathew
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Brian Morton
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - David Neunemann
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Fiona Ongeri
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Ling-Ling Pu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ioannis Pyrousis
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Xiang-Jun Rao
- School of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
| | - Amanda Redding
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Charles Roesel
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Alejandro Sanchez-Gracia
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, 97202, USA
| | - Aditi Shukla
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Guillaume Tetreau
- Department of Entomology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Yang Wang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Guang-Hua Xiong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Walther Traut
- Institut fuer Biologie, Universitaet Luebeck, D-23538, Luebeck, Germany
| | - Tom K Walsh
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Di Wu
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Wenbi Wu
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yuan-Qing Wu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Xiufeng Zhang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hannah Zucker
- Neuroscience Program, Hamilton College, Clinton, NY, 13323, USA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | | | - Rollie J Clem
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - René Feyereisen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Cornelis J P Grimmelikhuijzen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-21oo, Copenhagen, Denmark
| | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens, Greece
| | - Bill S Hansson
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR Sciences et Techniques, Université François-Rabelais, Tours, France
| | - Lars S Jermiin
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Que Lan
- Department of Entomology, University of Wisconsin, Madison, USA
| | - Herman K Lehman
- Biology Department and Neuroscience Program, Hamilton College, Clinton, NY, 13323, USA
| | - Marce Lorenzen
- Dept. Entomology, North Carolina State Univ., Raleigh, NC, 27695, USA
| | - Hans Merzendorfer
- University of Siegen, School of Natural Sciences and Engineering, Institute of Biology - Molecular Biology, Adolf-Reichwein-Strasse. 2, AR-C3010, 57076 Siegen, Germany
| | - Ioannis Michalopoulos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - David B Morton
- Department of Integrative Biosciences, School of Dentistry, BRB421, L595, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR, 97239, USA
| | - Subbaratnam Muthukrishnan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - John G Oakeshott
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Will Palmer
- Department of Genetics, University of Cambridge, Downing St, Cambridge, CB2 3EH, UK
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Wendy Smith
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Agnes Southgate
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Richard Vogt
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29205, USA
| | - Ping Wang
- Department of Entomology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - John Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Xiao-Qiang Yu
- University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO, 64110, USA
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Susan J Brown
- KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Gary W Blissard
- Boyce Thompson Institute at Cornell University, Tower Road, Ithaca, NY, 14853, USA
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Carbone SE, Jovanovska V, Brookes SJH, Nurgali K. Electrophysiological and morphological changes in colonic myenteric neurons from chemotherapy-treated patients: a pilot study. Neurogastroenterol Motil 2016; 28:975-84. [PMID: 26909894 PMCID: PMC5215581 DOI: 10.1111/nmo.12795] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/14/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Patients receiving anticancer chemotherapy experience a multitude of gastrointestinal side-effects. However, the causes of these symptoms are uncertain and whether these therapeutics directly affect the enteric nervous system is unknown. Our aim was to determine whether the function and morphology of myenteric neurons are altered in specimens of the colon from chemotherapy-treated patients. METHODS Colon specimens were compared from chemotherapy-treated and non-treated patients following colorectal resections for removal of carcinoma. Intracellular electrophysiological recordings from myenteric neurons and immunohistochemistry were performed in whole mount preparations. KEY RESULTS Myenteric S neurons from chemotherapy-treated patients were hyperexcitable; more action potentials (11.4 ± 9.4, p < 0.05) were fired in response to depolarising current pulses than in non-treated patients (1.4 ± 0.5). The rheobase and the threshold to evoke action potentials were significantly lower for neurons from chemotherapy-treated patients compared to neurons from non-treated patients (p < 0.01). Fast excitatory postsynaptic potential reversal potential was more positive in neurons from chemotherapy-treated patients (p < 0.05). An increase in the number of neurons with translocation of Hu protein from the cytoplasm to the nucleus was observed in specimens from chemotherapy-treated patients (103 ± 25 neurons/mm(2) , 37.2 ± 7.0%, n = 8) compared to non-treated (26 ± 5 neurons/mm(2) , 11.9 ± 2.7%, n = 12, p < 0.01). An increase in the soma size of neuronal nitric oxide synthase-immunoreactive neurons was also observed in these specimens. CONCLUSIONS & INFERENCES This is the first study suggesting functional and structural changes in human myenteric neurons in specimens of colon from patients receiving anticancer chemotherapy. These changes may contribute to the causation of gastrointestinal symptoms experienced by chemotherapy-treated patients.
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Affiliation(s)
- S. E. Carbone
- Centre for Chronic DiseaseCollege of Health and BiomedicineVictoria UniversityMelbourneVICAustralia
| | - V. Jovanovska
- Centre for Chronic DiseaseCollege of Health and BiomedicineVictoria UniversityMelbourneVICAustralia
| | - S. J. H. Brookes
- Discipline of Human Physiology and Centre for NeuroscienceFlinders UniversityAdelaideSAAustralia
| | - K. Nurgali
- Centre for Chronic DiseaseCollege of Health and BiomedicineVictoria UniversityMelbourneVICAustralia
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Talman V, Pascale A, Jäntti M, Amadio M, Tuominen RK. Protein Kinase C Activation as a Potential Therapeutic Strategy in Alzheimer's Disease: Is there a Role for Embryonic Lethal Abnormal Vision-like Proteins? Basic Clin Pharmacol Toxicol 2016; 119:149-60. [PMID: 27001133 DOI: 10.1111/bcpt.12581] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/04/2016] [Indexed: 12/28/2022]
Abstract
Alzheimer's disease (AD), the most common cause of dementia, is an irreversible and progressive neurodegenerative disorder. It affects predominantly brain areas that are critical for memory and learning and is characterized by two main pathological hallmarks: extracellular amyloid plaques and intracellular neurofibrillary tangles. Protein kinase C (PKC) has been classified as one of the cognitive kinases controlling memory and learning. By regulating several signalling pathways involved in amyloid and tau pathologies, it also plays an inhibitory role in AD pathophysiology. Among downstream targets of PKC are the embryonic lethal abnormal vision (ELAV)-like RNA-binding proteins that modulate the stability and the translation of specific target mRNAs involved in synaptic remodelling linked to cognitive processes. This MiniReview summarizes the current evidence on the role of PKC and ELAV-like proteins in learning and memory, highlighting how their derangement can contribute to AD pathophysiology. This last aspect emphasizes the potential of pharmacological activation of PKC as a promising therapeutic strategy for the treatment of AD.
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Affiliation(s)
- Virpi Talman
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Alessia Pascale
- Section of Pharmacology, Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Maria Jäntti
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Marialaura Amadio
- Section of Pharmacology, Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Raimo K Tuominen
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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Regulation of Stem Cell Self-Renewal and Oncogenesis by RNA-Binding Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:153-88. [PMID: 27256386 DOI: 10.1007/978-3-319-29073-7_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Throughout their life span, multicellular organisms rely on stem cell systems. During development pluripotent embryonic stem cells give rise to all cell types that make up the organism. After birth, tissue stem cells maintain properly functioning tissues and organs under homeostasis as well as promote regeneration after tissue damage or injury. Stem cells are capable of self-renewal, which is the ability to divide indefinitely while retaining the potential of differentiation into multiple cell types. The ability to self-renew, however, is a double-edged sword; the molecular mechanisms of self-renewal can be a target of malignant transformation driving tumor development and progression. Growing lines of evidence have shown that RNA-binding proteins (RBPs) play pivotal roles in the regulation of self-renewal by modulating metabolism of coding and non-coding RNAs both in normal tissues and in cancers. In this review, we discuss our current understanding of tissue stem cell systems and how RBPs regulate stem cell fates as well as how the regulatory functions of RBPs contribute to oncogenesis.
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44
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Global translation variations in host cells upon attack of lytic and sublytic Staphylococcus aureus α-haemolysin1. Biochem J 2015; 472:83-95. [DOI: 10.1042/bj20150284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 09/11/2015] [Indexed: 02/07/2023]
Abstract
Staphylococcal alpha-hemolysin (AHL) is a clinically relevant toxin, whose effects on host translation are poorly understood. We characterized genome-wide alterations induced at transcriptional and transational levels by lytic and sublytic AHL, pinpointing the importance of translational control during host-pathogen interaction.
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Colombrita C, Onesto E, Buratti E, de la Grange P, Gumina V, Baralle FE, Silani V, Ratti A. From transcriptomic to protein level changes in TDP-43 and FUS loss-of-function cell models. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1398-410. [PMID: 26514432 DOI: 10.1016/j.bbagrm.2015.10.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/08/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022]
Abstract
The full definition of the physiological RNA targets regulated by TDP-43 and FUS RNA-binding proteins (RBPs) represents an important issue in understanding the pathogenic mechanisms associated to these two proteins in amyotrophic lateral sclerosis and frontotemporal dementia. In the last few years several high-throughput screenings have generated a plethora of data, which are difficult to compare due to the different experimental designs and models explored. In this study by using the Affymetrix Exon Arrays, we were able to assess and compare the effects of both TDP-43 and FUS loss-of-function on the whole transcriptome using the same human neuronal SK-N-BE cell model. We showed that TDP-43 and FUS depletion induces splicing and gene expression changes mainly distinct for the two RBPs, although they may regulate common pathways, including neuron differentiation and cytoskeleton organization as evidenced by functional annotation analysis. In particular, TDP-43 and FUS were found to regulate splicing and expression of genes related to neuronal (SEPT6, SULT4A1, TNIK) and RNA metabolism (DICER, ELAVL3/HuC, POLDIP3). Our extended analysis at protein level revealed that these changes have also impact on the protein isoform ratio and content, not always in a direct correlation with transcriptomic data. Contrarily to a loss-of-function mechanism, we showed that mutant TDP-43 proteins maintained their splicing activity in human ALS fibroblasts and experimental cell lines. Our findings further contribute to define the biological functions of these two RBPs in physiological and disease state, strongly encouraging the evaluation of the identified transcriptomic changes at protein level in neuronal experimental models.
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Affiliation(s)
- Claudia Colombrita
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, Milan 20122, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy
| | - Elisa Onesto
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Trieste 34149, Italy
| | | | - Valentina Gumina
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Trieste 34149, Italy
| | - Vincenzo Silani
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, Milan 20122, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy
| | - Antonia Ratti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, Milan 20122, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy.
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46
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Mashanov VS, Zueva OR, García-Arrarás JE. Heterogeneous generation of new cells in the adult echinoderm nervous system. Front Neuroanat 2015; 9:123. [PMID: 26441553 PMCID: PMC4585025 DOI: 10.3389/fnana.2015.00123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/29/2015] [Indexed: 11/13/2022] Open
Abstract
Adult neurogenesis, generation of new functional cells in the mature central nervous system (CNS), has been documented in a number of diverse organisms, ranging from humans to invertebrates. However, the origin and evolution of this phenomenon is still poorly understood for many of the key phylogenetic groups. Echinoderms are one such phylum, positioned as a sister group to chordates within the monophyletic clade Deuterostomia. They are well known for the ability of their adult organs, including the CNS, to completely regenerate after injury. Nothing is known, however, about production of new cells in the nervous tissue under normal physiological conditions in these animals. In this study, we show that new cells are continuously generated in the mature radial nerve cord (RNC) of the sea cucumber Holothuria glaberrima. Importantly, this neurogenic activity is not evenly distributed, but is significantly more extensive in the lateral regions of the RNC than along the midline. Some of the new cells generated in the apical region of the ectoneural neuroepithelium leave their place of origin and migrate basally to populate the neural parenchyma. Gene expression analysis showed that generation of new cells in the adult sea cucumber CNS is associated with transcriptional activity of genes known to be involved in regulation of various aspects of neurogenesis in other animals. Further analysis of one of those genes, the transcription factor Myc, showed that it is expressed, in some, but not all radial glial cells, suggesting heterogeneity of this CNS progenitor cell population in echinoderms.
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Affiliation(s)
| | - Olga R Zueva
- Department of Biology, University of Puerto Rico Rio Piedras, PR, USA
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Piñeiro D, Fernandez-Chamorro J, Francisco-Velilla R, Martinez-Salas E. Gemin5: A Multitasking RNA-Binding Protein Involved in Translation Control. Biomolecules 2015; 5:528-44. [PMID: 25898402 PMCID: PMC4496684 DOI: 10.3390/biom5020528] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/01/2015] [Accepted: 04/09/2015] [Indexed: 12/31/2022] Open
Abstract
Gemin5 is a RNA-binding protein (RBP) that was first identified as a peripheral component of the survival of motor neurons (SMN) complex. This predominantly cytoplasmic protein recognises the small nuclear RNAs (snRNAs) through its WD repeat domains, allowing assembly of the SMN complex into small nuclear ribonucleoproteins (snRNPs). Additionally, the amino-terminal end of the protein has been reported to possess cap-binding capacity and to interact with the eukaryotic initiation factor 4E (eIF4E). Gemin5 was also shown to downregulate translation, to be a substrate of the picornavirus L protease and to interact with viral internal ribosome entry site (IRES) elements via a bipartite non-canonical RNA-binding site located at its carboxy-terminal end. These features link Gemin5 with translation control events. Thus, beyond its role in snRNPs biogenesis, Gemin5 appears to be a multitasking protein cooperating in various RNA-guided processes. In this review, we will summarise current knowledge of Gemin5 functions. We will discuss the involvement of the protein on translation control and propose a model to explain how the proteolysis fragments of this RBP in picornavirus-infected cells could modulate protein synthesis.
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Affiliation(s)
- David Piñeiro
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, UK.
| | - Javier Fernandez-Chamorro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Encarna Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
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Amadio M, Scapagnini G, Davinelli S, Calabrese V, Govoni S, Pascale A. Involvement of ELAV RNA-binding proteins in the post-transcriptional regulation of HO-1. Front Cell Neurosci 2015; 8:459. [PMID: 25642166 PMCID: PMC4295526 DOI: 10.3389/fncel.2014.00459] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 12/17/2014] [Indexed: 12/14/2022] Open
Abstract
Heme oxygenase-1 (HO-1) is an inducible rate-controlling enzyme of heme catabolism. The cytoprotective function of HO-1 activity has been verified in multiple studies, and together with its by-products is considered a key component of the cellular stress response. The transcriptional induction of HO-1 has been largely studied in response to multiple forms of stressful stimuli but our understanding of HO-1 post-transcriptional control mechanisms in neuronal cells is currently lacking. In the present report we show the involvement of the RNA-binding proteins (RBPs) embryonic lethal abnormal vision (ELAV) in the regulation of HO-1 gene expression. Our study demonstrates a specific binding between HO-1 messenger RNA (mRNA) and ELAV proteins, accompanied by an increased expression of HO-1 at protein level, in a human neuroblastoma cell line treated with hemin. Clarifying the induction of HO-1 expression at post-transcriptional level may open therapeutic perspectives for treatments associated with the modulation of HO-1 expression.
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Affiliation(s)
- Marialaura Amadio
- Department of Drug Sciences, Section of Pharmacology, University of Pavia Pavia, Italy
| | - Giovanni Scapagnini
- Department of Medicine and Health Sciences, University of Molise Campobasso, Italy ; Inter-University Consortium "SannioTech" Benevento, Italy
| | - Sergio Davinelli
- Department of Medicine and Health Sciences, University of Molise Campobasso, Italy
| | - Vittorio Calabrese
- Inter-University Consortium "SannioTech" Benevento, Italy ; Department of Biomedical Sciences, University of Catania Catania, Italy
| | - Stefano Govoni
- Department of Drug Sciences, Section of Pharmacology, University of Pavia Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia Pavia, Italy
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Sharifnia P, Jin Y. Regulatory roles of RNA binding proteins in the nervous system of C. elegans. Front Mol Neurosci 2015; 7:100. [PMID: 25628531 PMCID: PMC4290612 DOI: 10.3389/fnmol.2014.00100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 12/11/2014] [Indexed: 11/24/2022] Open
Abstract
Neurons have evolved to employ many factors involved in the regulation of RNA processing due to their complex cellular compartments. RNA binding proteins (RBPs) are key regulators in transcription, translation, and RNA degradation. Increasing studies have shown that regulatory RNA processing is critical for the establishment, functionality, and maintenance of neural circuits. Recent advances in high-throughput transcriptomics have rapidly expanded our knowledge of the landscape of RNA regulation, but also raised the challenge for mechanistic dissection of the specific roles of RBPs in complex tissues such as the nervous system. The C. elegans genome encodes many RBPs conserved throughout evolution. The rich analytic tools in molecular genetics and simple neural anatomy of C. elegans offer advantages to define functions of genes in vivo at the level of a single cell. Notably, the discovery of microRNAs has had transformative effects to the understanding of neuronal development, circuit plasticity, and neurological diseases. Here we review recent studies unraveling diverse roles of RBPs in the development, function, and plasticity of C. elegans nervous system. We first summarize the general technologies for studying RBPs in C. elegans. We then focus on the roles of several RBPs that control gene- and cell-type specific production of neuronal transcripts.
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Affiliation(s)
- Panid Sharifnia
- Division of Biological Sciences, Neurobiology Section, University of CaliforniaSan Diego, La Jolla, CA, USA
- Neurosciences Graduate Program, University of CaliforniaSan Diego, La Jolla, CA, USA
| | - Yishi Jin
- Division of Biological Sciences, Neurobiology Section, University of CaliforniaSan Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, University of CaliforniaSan Diego, La Jolla, CA, USA
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50
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Hayashi S, Yano M, Igarashi M, Okano HJ, Okano H. Alternative role of HuD splicing variants in neuronal differentiation. J Neurosci Res 2014; 93:399-409. [PMID: 25332105 DOI: 10.1002/jnr.23496] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/26/2014] [Accepted: 09/18/2014] [Indexed: 12/18/2022]
Abstract
HuD is a neuronal RNA-binding protein that plays an important role in neuronal differentiation of the nervous system. HuD has been reported to have three RNA recognition motifs (RRMs) and three splice variants (SVs) that differ in their amino acid sequences between RRM2 and RRM3. This study investigates whether these SVs have specific roles in neuronal differentiation. In primary neural epithelial cells under differentiating conditions, HuD splice variant 1 (HuD-sv1), which is a general form, and HuD-sv2 were expressed at all tested times, whereas HuD-sv4 was transiently expressed at the beginning of differentiation, indicating that HuD-sv4 might play a role compared different from that of HuD-sv1. Indeed, HuD-sv4 did not promote neuronal differentiation in epithelial cells, whereas HuD-sv1 did promote neuronal differentiation. HuD-sv4 overexpression showed less neurite-inducing activity than HuD-sv1 in mouse neuroblastoma N1E-115 cells; however, HuD-sv4 showed stronger growth-arresting activity. HuD-sv1 was localized only in the cytoplasm, whereas HuD-sv4 was localized in both the cytoplasm and the nuclei. The Hu protein has been reported to be involved in translation and alternative splicing in the cytoplasm and nuclei, respectively. Consistent with this observation, HuD-sv1 showed translational activity on p21, which plays a role in growth arrest and neuronal differentiation, whereas HuD-sv4 did not. By contrast, HuD-sv4 showed stronger pre-mRNA splicing activity than did HuD-sv1 on Clasp2, which participates in cell division. Therefore, HuD SVs might play a role in controlling the timing of proliferation/differentiation switching by controlling the translation and alternative splicing of target genes.
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Affiliation(s)
- Satoru Hayashi
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan; CNS Drug Discovery Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
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