1
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Onchan W, Attakitbancha C, Uttamapinant C. An expanded molecular and systems toolbox for imaging, mapping, and controlling local translation. Curr Opin Chem Biol 2024; 82:102523. [PMID: 39226865 DOI: 10.1016/j.cbpa.2024.102523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/28/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
Localized protein translation occurs through trafficking of mRNAs and protein translation machineries to different compartments of the cell, leading to rapid on-site synthesis of proteins in response to signaling cues. The spatiotemporally precise nature of the local translation process necessitates continual developments of technologies reviewed herein to visualize and map biomolecular components and the translation process with better spatial and temporal resolution and with fewer artifacts. We also discuss approaches to control local translation, which can serve as a design paradigm for subcellular genetic devices for eukaryotic synthetic biology.
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Affiliation(s)
- Warunya Onchan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chadaporn Attakitbancha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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2
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Ren J, Luo S, Shi H, Wang X. Spatial omics advances for in situ RNA biology. Mol Cell 2024:S1097-2765(24)00656-7. [PMID: 39270643 DOI: 10.1016/j.molcel.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/07/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024]
Abstract
Spatial regulation of RNA plays a critical role in gene expression regulation and cellular function. Understanding spatially resolved RNA dynamics and translation is vital for bringing new insights into biological processes such as embryonic development, neurobiology, and disease pathology. This review explores past studies in subcellular, cellular, and tissue-level spatial RNA biology driven by diverse methodologies, ranging from cell fractionation, in situ and proximity labeling, imaging, spatially indexed next-generation sequencing (NGS) approaches, and spatially informed computational modeling. Particularly, recent advances have been made for near-genome-scale profiling of RNA and multimodal biomolecules at high spatial resolution. These methods enabled new discoveries into RNA's spatiotemporal kinetics, RNA processing, translation status, and RNA-protein interactions in cells and tissues. The evolving landscape of experimental and computational strategies reveals the complexity and heterogeneity of spatial RNA biology with subcellular resolution, heralding new avenues for RNA biology research.
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Affiliation(s)
- Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shuchen Luo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hailing Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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3
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Luo M, Luo X, Sun J, Ao X, Han H, Yang X. METTL5 enhances the mRNA stability of TPRKB through m 6A modification to facilitate the aggressive phenotypes of hepatocellular carcinoma cell. Exp Cell Res 2024; 442:114219. [PMID: 39182664 DOI: 10.1016/j.yexcr.2024.114219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/30/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
N6-methyladenosine (m6A) modification plays an important role in RNA molecular functions, therefore affecting the initiation and development of hepatocellular carcinoma (HCC). Herein, multiple datasets were applied to conduct a comprehensive analysis of DEGs within HCC and the analysis revealed significant dysregulation of numerous genes. Functional and signaling pathway enrichment analyses were performed. Further, TP53RK binding protein (TPRKB) emerged as a significant factor, exhibiting high expression level within HCC tissue samples and cells which could predict HCC patients' poor OS. Knockdown investigations of TPRKB in vitro demonstrated the effect of TPRKB knockdown on attenuating the aggressiveness of HCC cells by suppressing the viability, colony formation, invasive ability, and migratory ability, inducing cell cycle arrest, and facilitating the apoptosis of HCC cells. Investigations in vivo revealed that TPRKB knockdown significantly suppressed tumor growth in mice model. Additionally, the study identified methyltransferase 5, N6-adenosine (METTL5) as a potential regulator of TPRKB expression via m6A modification, positively regulating TPRKB expression by enhancing TPRKB mRNA stability. The dynamic effects of METTL5 and TPRKB upon the phenotypes of HCC cells further confirmed that TPRKB overexpression partially abolished the anti-cancer effects of METTL5 knockdown upon the aggressiveness of HCC cells. Conclusively, our findings uncover that TPRKB, significantly overexpressed in HCC, exerts a critical effect on promoting tumor aggressiveness, and its expression shows to be positively regulated by METTL5 via m6A methylation. These insights deepen the understanding of HCC pathogenesis and open new avenues for targeted therapies, highlighting that METTL5-TPRKB axis is an underlying new therapeutic target in HCC management.
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Affiliation(s)
- Ming Luo
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Xiong Luo
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jichun Sun
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Xiang Ao
- Department of Respiratory and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Haoyan Han
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Xin Yang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
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4
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Zare A, Salehi S, Bader J, Schneider C, Fischer U, Veh A, Arampatzi P, Mann M, Briese M, Sendtner M. hnRNP R promotes O-GlcNAcylation of eIF4G and facilitates axonal protein synthesis. Nat Commun 2024; 15:7430. [PMID: 39198412 PMCID: PMC11358521 DOI: 10.1038/s41467-024-51678-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 08/12/2024] [Indexed: 09/01/2024] Open
Abstract
Motoneurons critically depend on precise spatial and temporal control of translation for axon growth and the establishment and maintenance of neuromuscular connections. While defects in local translation have been implicated in the pathogenesis of motoneuron disorders, little is known about the mechanisms regulating axonal protein synthesis. Here, we report that motoneurons derived from Hnrnpr knockout mice show reduced axon growth accompanied by lowered synthesis of cytoskeletal and synaptic components in axons. Mutant mice display denervated neuromuscular junctions and impaired motor behavior. In axons, hnRNP R is a component of translation initiation complexes and, through interaction with O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (Ogt), modulates O-GlcNAcylation of eIF4G. Restoring axonal O-GlcNAc levels rescued local protein synthesis and axon growth defects of hnRNP R knockout motoneurons. Together, these findings demonstrate a function of hnRNP R in controlling the local production of key factors required for axon growth and formation of neuromuscular innervations.
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Affiliation(s)
- Abdolhossein Zare
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Saeede Salehi
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Jakob Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Cornelius Schneider
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Alexander Veh
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | | | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Briese
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
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5
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Lo J, Vaeth KF, Bhardwaj G, Mukherjee N, Russ HA, Moore JK, Taliaferro JM. The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609768. [PMID: 39253515 PMCID: PMC11383297 DOI: 10.1101/2024.08.26.609768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting RNA binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP as well as the impacts of that RNA localization on cell function have generally remained unknown. Here, we demonstrate that the RBP HNRNPA2B1 acts to keep specific RNAs out of neuronal projections. Using subcellular fractionation, high-throughput sequencing, and single molecule RNA FISH, we find that hundreds of RNAs demonstrate markedly increased abundance in neurites in HNRNPA2B1 knockout cells. These RNAs often encode motor proteins and are enriched for known HNRNPA2B1 binding sites and motifs in their 3' UTRs. The speed and processivity of microtubule-based transport is impaired in these cells, specifically in their neurites. HNRNPA2B1 point mutations that increase its cytoplasmic abundance relative to wildtype lead to stronger suppression of RNA mislocalization defects than seen with wildtype HNRNPA2B1. We further find that the subcellular localizations of HNRNPA2B1 target RNAs are sensitive to perturbations of RNA decay machinery, suggesting that it is HNRNPA2B1's known role in regulating RNA stability that may explain these observations. These findings establish HNRNPA2B1 as a negative regulator of neurite RNA abundance and link the subcellular activities of motor proteins with the subcellular abundance of the RNAs that encode them.
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Affiliation(s)
- Joelle Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine F Vaeth
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Holger A Russ
- Diabetes Institute, University of Florida, Gainesville, FL, USA
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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6
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Chekulaeva M. Mechanistic insights into the basis of widespread RNA localization. Nat Cell Biol 2024; 26:1037-1046. [PMID: 38956277 DOI: 10.1038/s41556-024-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/20/2024] [Indexed: 07/04/2024]
Abstract
The importance of subcellular mRNA localization is well established, but the underlying mechanisms mostly remain an enigma. Early studies suggested that specific mRNA sequences recruit RNA-binding proteins (RBPs) to regulate mRNA localization. However, despite the observation of thousands of localized mRNAs, only a handful of these sequences and RBPs have been identified. This suggests the existence of alternative, and possibly predominant, mechanisms for mRNA localization. Here I re-examine currently described mRNA localization mechanisms and explore alternative models that could account for its widespread occurrence.
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Affiliation(s)
- Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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7
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Li Y, Yi Y, Gao X, Wang X, Zhao D, Wang R, Zhang LS, Gao B, Zhang Y, Zhang L, Cao Q, Chen K. 2'-O-methylation at internal sites on mRNA promotes mRNA stability. Mol Cell 2024; 84:2320-2336.e6. [PMID: 38906115 PMCID: PMC11196006 DOI: 10.1016/j.molcel.2024.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/23/2024]
Abstract
2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yang Yi
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rui Wang
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Yadong Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Qi Cao
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Boston, MA, USA; Prostate Cancer Program, Dana-Farber/Harvard Cancer Center, Boston, MA, USA.
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8
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Li X, Uslu VV, Chen Y, Han X, Berr A, Zhang W, Dong Y. Specific chromatin states and m6A modifications are associated with mRNA mobility in planta. HORTICULTURE RESEARCH 2024; 11:uhae101. [PMID: 38863994 PMCID: PMC11165156 DOI: 10.1093/hr/uhae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Affiliation(s)
- Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Veli Vural Uslu
- RLP AgroScience GmbH, Neustadt an der Weinstraße 67435, Germany
- MAPS, Center for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Ying Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiao Han
- College of Biology Science and Engineering, Fuzhou University, Fuzhou, China
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Yihan Dong
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
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9
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Zaninello M, Schlegel T, Nolte H, Pirzada M, Savino E, Barth E, Klein I, Wüstenberg H, Uddin T, Wolff L, Wirth B, Lehmann HC, Cioni JM, Langer T, Rugarli EI. CLUH maintains functional mitochondria and translation in motoneuronal axons and prevents peripheral neuropathy. SCIENCE ADVANCES 2024; 10:eadn2050. [PMID: 38809982 PMCID: PMC11135423 DOI: 10.1126/sciadv.adn2050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Transporting and translating mRNAs in axons is crucial for neuronal viability. Local synthesis of nuclear-encoded mitochondrial proteins protects long-lived axonal mitochondria from damage; however, the regulatory factors involved are largely unknown. We show that CLUH, which binds mRNAs encoding mitochondrial proteins, prevents peripheral neuropathy and motor deficits in the mouse. CLUH is enriched in the growth cone of developing spinal motoneurons and is required for their growth. The lack of CLUH affects the abundance of target mRNAs and the corresponding mitochondrial proteins more prominently in axons, leading to ATP deficits in the growth cone. CLUH interacts with ribosomal subunits, translation initiation, and ribosome recycling components and preserves axonal translation. Overexpression of the ribosome recycling factor ABCE1 rescues the mRNA and translation defects, as well as the growth cone size, in CLUH-deficient motoneurons. Thus, we demonstrate a role for CLUH in mitochondrial quality control and translational regulation in axons, which is essential for their development and long-term integrity and function.
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Affiliation(s)
- Marta Zaninello
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Tim Schlegel
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Mujeeb Pirzada
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Elisa Savino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Esther Barth
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Ines Klein
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Hauke Wüstenberg
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Tesmin Uddin
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Lisa Wolff
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
| | - Brunhilde Wirth
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne 50931, Germany
- Center for Rare Diseases Cologne (CESEK), University Hospital of Cologne, Cologne 50937, Germany
| | - Helmar C. Lehmann
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Thomas Langer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Elena I. Rugarli
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne 50931, Germany
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10
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Tegowski M, Meyer KD. Studying m 6A in the brain: a perspective on current methods, challenges, and future directions. Front Mol Neurosci 2024; 17:1393973. [PMID: 38711483 PMCID: PMC11070500 DOI: 10.3389/fnmol.2024.1393973] [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: 02/29/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024] Open
Abstract
A major mechanism of post-transcriptional RNA regulation in cells is the addition of chemical modifications to RNA nucleosides, which contributes to nearly every aspect of the RNA life cycle. N6-methyladenosine (m6A) is a highly prevalent modification in cellular mRNAs and non-coding RNAs, and it plays important roles in the control of gene expression and cellular function. Within the brain, proper regulation of m6A is critical for neurodevelopment, learning and memory, and the response to injury, and m6A dysregulation has been implicated in a variety of neurological disorders. Thus, understanding m6A and how it is regulated in the brain is important for uncovering its roles in brain function and potentially identifying novel therapeutic pathways for human disease. Much of our knowledge of m6A has been driven by technical advances in the ability to map and quantify m6A sites. Here, we review current technologies for characterizing m6A and highlight emerging methods. We discuss the advantages and limitations of current tools as well as major challenges going forward, and we provide our perspective on how continued developments in this area can propel our understanding of m6A in the brain and its role in brain disease.
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Affiliation(s)
- Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Kate D. Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, United States
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11
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Perlegos AE, Byrns CN, Bonini NM. Cell type-specific regulation of m 6 A modified RNAs in the aging Drosophila brain. Aging Cell 2024; 23:e14076. [PMID: 38205931 PMCID: PMC10928574 DOI: 10.1111/acel.14076] [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: 08/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The aging brain is highly vulnerable to cellular stress, and neurons employ numerous mechanisms to combat neurotoxic proteins and promote healthy brain aging. The RNA modification m6 A is highly enriched in the Drosophila brain and is critical for the acute heat stress response of the brain. Here we examine m6 A in the fly brain with the chronic stresses of aging and degenerative disease. m6 A levels dynamically increased with both age and disease in the brain, marking integral neuronal identity and signaling pathway transcripts that decline in level with age and disease. Unexpectedly, there is opposing impact of m6 A transcripts in neurons versus glia, which conferred different outcomes on animal health span upon Mettl3 knockdown to reduce m6 A: whereas Mettl3 function is normally beneficial to neurons, it is deleterious to glia. Moreover, knockdown of Mettl3 in glial tauopathy reduced tau pathology and increased animal survival. These findings provide mechanistic insight into regulation of m6 A modified transcripts with age and disease, highlighting an overall beneficial function of Mettl3 in neurons in response to chronic stresses, versus a deleterious impact in glia.
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Affiliation(s)
- Alexandra E. Perlegos
- Neuroscience Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - China N. Byrns
- Neuroscience Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Medical Scientist Training Program, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Nancy M. Bonini
- Neuroscience Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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12
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Brüll M, Geese N, Celardo I, Laumann M, Leist M. Preparation of Viable Human Neurites for Neurobiological and Neurodegeneration Studies. Cells 2024; 13:242. [PMID: 38334634 PMCID: PMC10854604 DOI: 10.3390/cells13030242] [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: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
Few models allow the study of neurite damage in the human central nervous system. We used here dopaminergic LUHMES neurons to establish a culture system that allows for (i) the observation of highly enriched neurites, (ii) the preparation of the neurite fraction for biochemical studies, and (iii) the measurement of neurite markers and metabolites after axotomy. LUHMES-based spheroids, plated in culture dishes, extended neurites of several thousand µm length, while all somata remained aggregated. These cultures allowed an easy microscopic observation of live or fixed neurites. Neurite-only cultures (NOC) were produced by cutting out the still-aggregated somata. The potential application of such cultures was exemplified by determinations of their protein and RNA contents. For instance, the mitochondrial TOM20 protein was highly abundant, while nuclear histone H3 was absent. Similarly, mitochondrial-encoded RNAs were found at relatively high levels, while the mRNA for a histone or the neuronal nuclear marker NeuN (RBFOX3) were relatively depleted in NOC. Another potential use of NOC is the study of neurite degeneration. For this purpose, an algorithm to quantify neurite integrity was developed. Using this tool, we found that the addition of nicotinamide drastically reduced neurite degeneration. Also, the chelation of Ca2+ in NOC delayed the degeneration, while inhibitors of calpains had no effect. Thus, NOC proved to be suitable for biochemical analysis and for studying degeneration processes after a defined cut injury.
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Affiliation(s)
- Markus Brüll
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
| | - Nils Geese
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
| | - Ivana Celardo
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
| | - Michael Laumann
- Electron Microscopy Centre, University of Konstanz, 78457 Konstanz, Germany;
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
- Center for Alternatives to Animal Testing in Europe (CAAT-Europe), University of Konstanz, 78457 Konstanz, Germany
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13
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Ugalde MV, Alecki C, Rizwan J, Le P, Jacob-Tomas S, Xu JM, Minotti S, Wu T, Durham H, Yeo G. Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis. RESEARCH SQUARE 2023:rs.3.rs-3673702. [PMID: 38168440 PMCID: PMC10760236 DOI: 10.21203/rs.3.rs-3673702/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. However, this is challenging in neuronal projections because of their polarized morphology and constant synaptic proteome remodeling. Using high-resolution fluorescence microscopy, we discovered that neurons localize a subset of chaperone mRNAs to their dendrites and use microtubule-based transport to increase this asymmetric localization following proteotoxic stress. The most abundant dendritic chaperone mRNA encodes a constitutive heat shock protein 70 family member (HSPA8). Proteotoxic stress also enhanced HSPA8 mRNA translation efficiency in dendrites. Stress-mediated HSPA8 mRNA localization to the dendrites was impaired by depleting fused in sarcoma-an amyotrophic lateral sclerosis-related protein-in cultured mouse motor neurons and expressing a pathogenic variant of heterogenous nuclear ribonucleoprotein A2/B1 in neurons derived from human induced pluripotent stem cells. These results reveal a crucial and unexpected neuronal stress response in which RNA-binding proteins increase the dendritic localization of HSPA8 mRNA to maintain proteostasis and prevent neurodegeneration.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Gene Yeo
- University of California, San Diego
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14
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Zhang H, Yin M, Huang H, Zhao G, Lu M. METTL16 in human diseases: What should we do next? Open Med (Wars) 2023; 18:20230856. [PMID: 38045858 PMCID: PMC10693013 DOI: 10.1515/med-2023-0856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
METTL16 is a class-I methyltransferase that is responsible for depositing a vertebrate-conserved S-adenosylmethionine site. Since 2017, there has been a growing body of research focused on METTL16, particularly in the field of structural studies. However, the role of METTL16 in cell biogenesis and human diseases has not been extensively studied, with limited understanding of its function in disease pathology. Recent studies have highlighted the complex and sometimes contradictory role that METTL16 plays in various diseases. In this work, we aim to provide a comprehensive summary of the current research on METTL16 in human diseases.
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Affiliation(s)
- Hui Zhang
- Department of Gastroenterology, Wuhan Tongji Aerospace City Hospital, Wuhan, Hubei Province, 430000, China
| | - Mengqi Yin
- Department of Neurology, Wuhan No. 1 Hospital, Wuhan, Hubei Province, 430000, China
| | - Hua Huang
- Department of Gastroenterology, The Second Affiliated Hospital, Kunming Medical University, Kunming, 665000, Yunnan Province, China
| | - Gongfang Zhao
- Department of Gastroenterology, The Second Affiliated Hospital, Kunming Medical University, Kunming, 665000, Yunnan Province, China
| | - Mingliang Lu
- Department of Gastroenterology, Beijing Luhe Hospital, Capital Medical University, Beijing, 101149, PR China
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15
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Alecki C, Rizwan J, Le P, Jacob-Tomas S, Xu S, Minotti S, Wu T, Durham H, Yeo GW, Vera M. Localized synthesis of molecular chaperones sustains neuronal proteostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560761. [PMID: 37873158 PMCID: PMC10592939 DOI: 10.1101/2023.10.03.560761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Neurons are challenged to maintain proteostasis in neuronal projections, particularly with the physiological stress at synapses to support intercellular communication underlying important functions such as memory and movement control. Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. Using high-resolution fluorescent microscopy, we discovered that neurons localize a subset of chaperone mRNAs to their dendrites, particularly more proximal regions, and increase this asymmetric localization following proteotoxic stress through microtubule-based transport from the soma. The most abundant chaperone mRNA in dendrites encodes the constitutive heat shock protein 70, HSPA8. Proteotoxic stress in cultured neurons, induced by inhibiting proteasome activity or inducing oxidative stress, enhanced transport of Hspa8 mRNAs to dendrites and the percentage of mRNAs engaged in translation on mono and polyribosomes. Knocking down the ALS-related protein Fused in Sarcoma (FUS) and a dominant mutation in the heterogenous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1) impaired stress-mediated localization of Hspa8 mRNA to dendrites in cultured murine motor neurons and human iPSC-derived neurons, respectively, revealing the importance of these RNA-binding proteins in maintaining proteostasis. These results reveal the increased dendritic localization and translation of the constitutive HSP70 Hspa8 mRNA as a crucial neuronal stress response to uphold proteostasis and prevent neurodegeneration.
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Affiliation(s)
- Celia Alecki
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Javeria Rizwan
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Phuong Le
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Suleima Jacob-Tomas
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Stella Xu
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Sandra Minotti
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Tad Wu
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Heather Durham
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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16
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Luisier R, Andreassi C, Fournier L, Riccio A. The predicted RNA-binding protein regulome of axonal mRNAs. Genome Res 2023; 33:1497-1512. [PMID: 37582635 PMCID: PMC10620043 DOI: 10.1101/gr.277804.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023]
Abstract
Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their cytoarchitecture. The targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3' Untranslated regions (UTRs) of mRNA are noncoding sequences that play a critical role in determining transcript localization and translation by interacting with specific RNA-binding proteins (RBPs). However, how 3' UTRs contribute to mRNA metabolism and the nature of RBP complexes responsible for these functions remains elusive. We performed 3' end sequencing of RNA isolated from cell bodies and axons of sympathetic neurons exposed to either nerve growth factor (NGF) or neurotrophin 3 (NTF3, also known as NT-3). NGF and NTF3 are growth factors essential for sympathetic neuron development through distinct signaling mechanisms. Whereas NTF3 acts mostly locally, NGF signal is retrogradely transported from axons to cell bodies. We discovered that both NGF and NTF3 affect transcription and alternative polyadenylation in the nucleus and induce the localization of specific 3' UTR isoforms to axons, including short 3' UTR isoforms found exclusively in axons. The integration of our data with CLIP sequencing data supports a model whereby long 3' UTR isoforms associate with RBP complexes in the nucleus and, upon reaching the axons, are remodeled locally into shorter isoforms. Our findings shed new light into the complex relationship between nuclear polyadenylation, mRNA localization, and local 3' UTR remodeling in developing neurons.
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Affiliation(s)
- Raphaëlle Luisier
- Idiap Research Institute, Martigny 1920, Switzerland;
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Catia Andreassi
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Lisa Fournier
- Idiap Research Institute, Martigny 1920, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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17
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Briney CA, Rissland OS. Planes, trains, and automobiles: How cells localize their molecules. Mol Cell 2023; 83:2618-2620. [PMID: 37541217 DOI: 10.1016/j.molcel.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
In this issue of Molecular Cell, Gasparski et al.1 and Loedige et al.2 reshape our understanding of subcellular gene product localization by highlighting the importance of messenger RNA (mRNA) stability and co-translational mechanisms in mRNA and protein localization.
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Affiliation(s)
- Chloe A Briney
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Olivia S Rissland
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.
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