1
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Ichinose T, Kondo S, Kanno M, Shichino Y, Mito M, Iwasaki S, Tanimoto H. Translational regulation enhances distinction of cell types in the nervous system. eLife 2024; 12:RP90713. [PMID: 39010741 PMCID: PMC11251722 DOI: 10.7554/elife.90713] [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] [Indexed: 07/17/2024] Open
Abstract
Multicellular organisms are composed of specialized cell types with distinct proteomes. While recent advances in single-cell transcriptome analyses have revealed differential expression of mRNAs, cellular diversity in translational profiles remains underinvestigated. By performing RNA-seq and Ribo-seq in genetically defined cells in the Drosophila brain, we here revealed substantial post-transcriptional regulations that augment the cell-type distinctions at the level of protein expression. Specifically, we found that translational efficiency of proteins fundamental to neuronal functions, such as ion channels and neurotransmitter receptors, was maintained low in glia, leading to their preferential translation in neurons. Notably, distribution of ribosome footprints on these mRNAs exhibited a remarkable bias toward the 5' leaders in glia. Using transgenic reporter strains, we provide evidence that the small upstream open-reading frames in the 5' leader confer selective translational suppression in glia. Overall, these findings underscore the profound impact of translational regulation in shaping the proteomics for cell-type distinction and provide new insights into the molecular mechanisms driving cell-type diversity.
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Grants
- 21K06369 Ministry of Education, Culture, Sports, Science and Technology
- 21H05713 Ministry of Education, Culture, Sports, Science and Technology
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology
- JP21K15023 Ministry of Education, Culture, Sports, Science and Technology
- 22H05481 Ministry of Education, Culture, Sports, Science and Technology
- 22KK0106 Ministry of Education, Culture, Sports, Science and Technology
- 20H00519 Ministry of Education, Culture, Sports, Science and Technology
- JP20gm1410001 Japan Agency for Medical Research and Development
- Biology of Intracellular Environments RIKEN
- Special Postdoctoral Researchers RIKEN
- Incentive Research Projects RIKEN
- Takeda Science Foundation
- Tohoku University Research Program "Frontier Research in Duo"
- The Uehara Memorial Foundation
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Affiliation(s)
- Toshiharu Ichinose
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku UniversitySendaiJapan
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Shu Kondo
- Faculty of Advanced Engineering, Tokyo University of SciencesTokyoJapan
| | - Mai Kanno
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku UniversitySendaiJapan
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoKashiwaJapan
| | - Hiromu Tanimoto
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
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2
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Sikder K, Phillips E, Zhong Z, Wang N, Saunders J, Mothy D, Kossenkov A, Schneider T, Nichtova Z, Csordas G, Margulies KB, Choi JC. Perinuclear damage from nuclear envelope deterioration elicits stress responses that contribute to LMNA cardiomyopathy. SCIENCE ADVANCES 2024; 10:eadh0798. [PMID: 38718107 PMCID: PMC11078192 DOI: 10.1126/sciadv.adh0798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/03/2024] [Indexed: 05/12/2024]
Abstract
Mutations in the LMNA gene encoding lamins A/C cause an array of tissue-selective diseases, with the heart being the most commonly affected organ. Despite progress in understanding the perturbations emanating from LMNA mutations, an integrative understanding of the pathogenesis underlying cardiac dysfunction remains elusive. Using a novel conditional deletion model capable of translatome profiling, we observed that cardiomyocyte-specific Lmna deletion in adult mice led to rapid cardiomyopathy with pathological remodeling. Before cardiac dysfunction, Lmna-deleted cardiomyocytes displayed nuclear abnormalities, Golgi dilation/fragmentation, and CREB3-mediated stress activation. Translatome profiling identified MED25 activation, a transcriptional cofactor that regulates Golgi stress. Autophagy is disrupted in the hearts of these mice, which can be recapitulated by disrupting the Golgi. Systemic administration of modulators of autophagy or ER stress significantly delayed cardiac dysfunction and prolonged survival. These studies support a hypothesis wherein stress responses emanating from the perinuclear space contribute to the LMNA cardiomyopathy development.
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Affiliation(s)
- Kunal Sikder
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Elizabeth Phillips
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Zhijiu Zhong
- Translational Research and Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nadan Wang
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Jasmine Saunders
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - David Mothy
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Andrew Kossenkov
- Bioinformatics Facility, The Wistar Institute Cancer Center, Philadelphia, PA, USA
| | - Timothy Schneider
- Mitocare, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zuzana Nichtova
- Mitocare, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gyorgy Csordas
- Mitocare, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kenneth B. Margulies
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason C. Choi
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
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3
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Wilcox NS, Yarovinsky TO, Pandya P, Ramgolam VS, Moro A, Wu Y, Nicoli S, Hirschi KK, Bender JR. Distinct hypoxia-induced translational profiles of embryonic and adult-derived macrophages. iScience 2023; 26:107985. [PMID: 38047075 PMCID: PMC10690575 DOI: 10.1016/j.isci.2023.107985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/21/2023] [Accepted: 09/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tissue resident macrophages are largely of embryonic (fetal liver) origin and long-lived, while bone marrow-derived macrophages (BMDM) are recruited following an acute perturbation, such as hypoxia in the setting of myocardial ischemia. Prior transcriptome analyses identified BMDM and fetal liver-derived macrophage (FLDM) differences at the RNA expression level. Posttranscriptional regulation determining mRNA stability and translation rate may override transcriptional signals in response to hypoxia. We profiled differentially regulated BMDM and FLDM transcripts in response to hypoxia at the level of mRNA translation. Using a translating ribosome affinity purification (TRAP) assay and RNA-seq, we identified non-overlapping transcripts with increased translation rate in BMDM (Ly6e, vimentin, PF4) and FLDM (Ccl7, Ccl2) after hypoxia. We further identified hypoxia-induced transcripts within these subsets that are regulated by the RNA-binding protein HuR. These findings define translational differences in macrophage subset gene expression programs, highlighting potential therapeutic targets in ischemic myocardium.
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Affiliation(s)
- Nicholas S. Wilcox
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Timur O. Yarovinsky
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Prakruti Pandya
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Vinod S. Ramgolam
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Albertomaria Moro
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Yinyu Wu
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Stefania Nicoli
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Karen K. Hirschi
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Jeffrey R. Bender
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
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4
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Imai H, Utsumi D, Torihara H, Takahashi K, Kuroyanagi H, Yamashita A. Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification. Nucleic Acids Res 2023; 51:e76. [PMID: 37378452 PMCID: PMC10415123 DOI: 10.1093/nar/gkad545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Regulation of gene expression in response to various biological processes, including extracellular stimulation and environmental adaptation requires nascent RNA synthesis and translation. Analysis of the coordinated regulation of dynamic RNA synthesis and translation is required to determine functional protein production. However, reliable methods for the simultaneous measurement of nascent RNA synthesis and translation at the gene level are limited. Here, we developed a novel method for the simultaneous assessment of nascent RNA synthesis and translation by combining 4-thiouridine (4sU) metabolic RNA labeling and translating ribosome affinity purification (TRAP) using a monoclonal antibody against evolutionarily conserved ribosomal P-stalk proteins. The P-stalk-mediated TRAP (P-TRAP) technique recovered endogenous translating ribosomes, allowing easy translatome analysis of various eukaryotes. We validated this method in mammalian cells by demonstrating that acute unfolded protein response (UPR) in the endoplasmic reticulum (ER) induces dynamic reprogramming of nascent RNA synthesis and translation. Our nascent P-TRAP (nP-TRAP) method may serve as a simple and powerful tool for analyzing the coordinated regulation of transcription and translation of individual genes in various eukaryotes.
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Affiliation(s)
- Hirotatsu Imai
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Daisuke Utsumi
- Department of Dermatology, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Hidetsugu Torihara
- Department of Biochemistry, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Kenzo Takahashi
- Department of Dermatology, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Hidehito Kuroyanagi
- Department of Biochemistry, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Akio Yamashita
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
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5
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Rozich E, Randolph LK, Insolera R. An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown. Front Neurosci 2023; 17:1204068. [PMID: 37457002 PMCID: PMC10339317 DOI: 10.3389/fnins.2023.1204068] [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: 04/11/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Mutations in the human gene VPS13D cause the adult-onset neurodegenerative disease ataxia. Our previous work showed that disruptions in the Vps13D gene in Drosophila neurons causes mitochondrial defects. However, developmental lethality caused by Vps13D loss limited our understanding of the long-term physiological effects of Vps13D perturbation in neurons. Here, we optimized a previously generated system to temporally knock down Vps13D expression precisely in adult Drosophila neurons using a modification to the Gal4/UAS system. Adult-onset activation of Gal4 was enacted using the chemically-inducible tool which fuses a destabilization-domain to the Gal4 repressor Gal80 (Gal80-DD). Optimization of the Gal80-DD tool shows that feeding animals the DD-stabilizing drug trimethoprim (TMP) during development and rearing at a reduced temperature maximally represses Gal4 activity. Temperature shift and removal of TMP from the food after eclosion robustly activates Gal4 expression in adult neurons. Using the optimized Gal80-DD system, we find that adult-onset Vps13D RNAi expression in neurons causes the accumulation of mitophagy intermediates, progressive deficits in locomotor activity, early lethality, and brain vacuolization characteristic of neurodegeneration. The development of this optimized system allows us to more precisely examine the degenerative phenotypes caused by Vps13D disruption, and can likely be utilized in the future for other genes associated with neurological diseases whose manipulation causes developmental lethality in Drosophila.
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Affiliation(s)
- Emily Rozich
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
| | - Lynsey K. Randolph
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Ryan Insolera
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
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6
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Sikder K, Phillips E, Zhong Z, Wang N, Saunders J, Mothy D, Kossenkov A, Schneider T, Nichtova Z, Csordas G, Margulies KB, Choi JC. Perinuclear damage from nuclear envelope deterioration elicits stress responses that contribute to LMNA cardiomyopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528563. [PMID: 36824975 PMCID: PMC9949050 DOI: 10.1101/2023.02.14.528563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Mutations in the LMNA gene encoding nuclear lamins A/C cause a diverse array of tissue-selective diseases, with the heart being the most commonly affected organ. Despite progress in understanding the molecular perturbations emanating from LMNA mutations, an integrative understanding of the pathogenesis leading to cardiac dysfunction remains elusive. Using a novel cell-type specific Lmna deletion mouse model capable of translatome profiling, we found that cardiomyocyte-specific Lmna deletion in adult mice led to rapid cardiomyopathy with pathological remodeling. Prior to the onset of cardiac dysfunction, lamin A/C-depleted cardiomyocytes displayed nuclear envelope deterioration, golgi dilation/fragmentation, and CREB3-mediated golgi stress activation. Translatome profiling identified upregulation of Med25, a transcriptional co-factor that can selectively dampen UPR axes. Autophagy is disrupted in the hearts of these mice, which can be recapitulated by disrupting the golgi or inducing nuclear damage by increased matrix stiffness. Systemic administration of pharmacological modulators of autophagy or ER stress significantly improved the cardiac function. These studies support a hypothesis wherein stress responses emanating from the perinuclear space contribute to the development of LMNA cardiomyopathy. Teaser Interplay of stress responses underlying the development of LMNA cardiomyopathy.
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7
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Hadidi K, Steinbuch KB, Dozier LE, Patrick GN, Tor Y. Inherently Emissive Puromycin Analogues for Live Cell Labelling. Angew Chem Int Ed Engl 2023; 62:e202216784. [PMID: 36973168 PMCID: PMC10213139 DOI: 10.1002/anie.202216784] [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: 11/14/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023]
Abstract
Puromycin derivatives containing an emissive thieno[3,4-d]-pyrimidine core, modified with azetidine and 3,3-difluoroazetidine as Me2 N surrogates, exhibit translation inhibition and bactericidal activity similar to the natural antibiotic. The analogues are capable of cellular puromycylation of nascent peptides, generating emissive products without any follow-up chemistry. The 3,3-difluoroazetidine-containing analogue is shown to fluorescently label newly translated peptides and be visualized in both live and fixed HEK293T cells and rat hippocampal neurons.
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Affiliation(s)
- Kaivin Hadidi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
| | - Kfir B Steinbuch
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
| | - Lara E Dozier
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0347, USA
| | - Gentry N Patrick
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0347, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0358, USA
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8
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Wester LE, Lanjuin A, Bruckisch EH, Perez-Matos MC, Stine PG, Heintz C, Denzel MS, Mair WB. A single-copy knockin translating ribosome immunoprecipitation toolkit for tissue-specific profiling of actively translated mRNAs in C. elegans. CELL REPORTS METHODS 2023; 3:100433. [PMID: 37056370 PMCID: PMC10088236 DOI: 10.1016/j.crmeth.2023.100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 01/11/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023]
Abstract
Here, we introduce a single-copy knockin translating ribosome immunoprecipitation (SKI TRIP) toolkit, a collection of Caenorhabditis elegans strains engineered by CRISPR in which tissue-specific expression of FLAG-tagged ribosomal subunit protein RPL-22 is driven by cassettes present in single copy from defined sites in the genome. Through in-depth characterization of the effects of the FLAG tag in animals in which endogenous RPL-22 has been tagged, we show that it incorporates into actively translating ribosomes and efficiently and cleanly pulls down cell-type-specific transcripts. Importantly, the presence of the tag does not impact overall mRNA translation, create bias in transcript use, or cause changes to fitness of the animal. We propose SKI TRIP use for the study of tissue-specific differences in translation and for investigating processes that are acutely sensitive to changes in translation like development or aging.
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Affiliation(s)
- Laura E. Wester
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
| | - Anne Lanjuin
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Emanuel H.W. Bruckisch
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
| | - Maria C. Perez-Matos
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter G. Stine
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Caroline Heintz
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Martin S. Denzel
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
- Altos Labs, Cambridge, UK
| | - William B. Mair
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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9
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Bhattacharjee S, Iyer EPR, Iyer SC, Nanda S, Rubaharan M, Ascoli GA, Cox DN. The Zinc-BED transcription factor Bedwarfed promotes proportional dendritic growth and branching through transcriptional and translational regulation in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528686. [PMID: 36824896 PMCID: PMC9948997 DOI: 10.1101/2023.02.15.528686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Dendrites are the primary points of sensory or synaptic inputs to a neuron and play an essential role in synaptic integration and neural function. Despite the functional importance of dendrites, relatively less is known about the underlying mechanisms regulating cell-type specific dendritic patterning. Herein, we have dissected functional roles of a previously uncharacterized gene, CG3995 , in cell-type specific dendritic development in Drosophila melanogaster . CG3995 , which we have named bedwarfed ( bdwf ), encodes a zinc-finger BED-type protein which is required for proportional growth and branching of dendritic arbors, exhibits nucleocytoplasmic expression, and functions in both transcriptional and translational cellular pathways. At the transcriptional level, we demonstrate a reciprocal regulatory relationship between Bdwf and the homeodomain transcription factor (TF) Cut. We show that Cut positively regulates Bdwf expression and that Bdwf acts as a downstream effector of Cut-mediated dendritic development, whereas overexpression of Bdwf negatively regulates Cut expression in multidendritic sensory neurons. Proteomic analyses revealed that Bdwf interacts with ribosomal proteins and disruption of these proteins produced phenotypically similar dendritic hypotrophy defects as observed in bdwf mutant neurons. We further demonstrate that Bdwf and its ribosomal protein interactors are required for normal microtubule and F-actin cytoskeletal architecture. Finally, our findings reveal that Bdwf is required to promote protein translation and ribosome trafficking along the dendritic arbor. Taken together, these results provide new insights into the complex, combinatorial and multi-functional roles of transcription factors (TFs) in directing diversification of cell-type specific dendritic development.
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Affiliation(s)
| | | | | | - Sumit Nanda
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, 22030, USA
| | | | - Giorgio A. Ascoli
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, 22030, USA
| | - Daniel N. Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA
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10
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Palmateer CM, Artikis C, Brovero SG, Friedman B, Gresham A, Arbeitman MN. Single-cell transcriptome profiles of Drosophila fruitless-expressing neurons from both sexes. eLife 2023; 12:e78511. [PMID: 36724009 PMCID: PMC9891730 DOI: 10.7554/elife.78511] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 01/08/2023] [Indexed: 02/02/2023] Open
Abstract
Drosophila melanogaster reproductive behaviors are orchestrated by fruitless neurons. We performed single-cell RNA-sequencing on pupal neurons that produce sex-specifically spliced fru transcripts, the fru P1-expressing neurons. Uniform Manifold Approximation and Projection (UMAP) with clustering generates an atlas containing 113 clusters. While the male and female neurons overlap in UMAP space, more than half the clusters have sex differences in neuron number, and nearly all clusters display sex-differential expression. Based on an examination of enriched marker genes, we annotate clusters as circadian clock neurons, mushroom body Kenyon cell neurons, neurotransmitter- and/or neuropeptide-producing, and those that express doublesex. Marker gene analyses also show that genes that encode members of the immunoglobulin superfamily of cell adhesion molecules, transcription factors, neuropeptides, neuropeptide receptors, and Wnts have unique patterns of enriched expression across the clusters. In vivo spatial gene expression links to the clusters are examined. A functional analysis of fru P1 circadian neurons shows they have dimorphic roles in activity and period length. Given that most clusters are comprised of male and female neurons indicates that the sexes have fru P1 neurons with common gene expression programs. Sex-specific expression is overlaid on this program, to build the potential for vastly different sex-specific behaviors.
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Affiliation(s)
- Colleen M Palmateer
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Catherina Artikis
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Savannah G Brovero
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Benjamin Friedman
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Alexis Gresham
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Michelle N Arbeitman
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
- Program of Neuroscience, Florida State UniversityTallahasseeUnited States
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11
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Ishii K, Cortese M, Leng X, Shokhirev MN, Asahina K. A neurogenetic mechanism of experience-dependent suppression of aggression. SCIENCE ADVANCES 2022; 8:eabg3203. [PMID: 36070378 PMCID: PMC9451153 DOI: 10.1126/sciadv.abg3203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aggression is an ethologically important social behavior, but excessive aggression can be detrimental to fitness. Social experiences among conspecific individuals reduce aggression in many species, the mechanism of which is largely unknown. We found that loss-of-function mutation of nervy (nvy), a Drosophila homolog of vertebrate myeloid translocation genes (MTGs), increased aggressiveness only in socially experienced flies and that this could be reversed by neuronal expression of human MTGs. A subpopulation of octopaminergic/tyraminergic neurons labeled by nvy was specifically required for such social experience-dependent suppression of aggression, in both males and females. Cell type-specific transcriptomic analysis of these neurons revealed aggression-controlling genes that are likely downstream of nvy. Our results illustrate both genetic and neuronal mechanisms by which the nervous system suppresses aggression in a social experience-dependent manner, a poorly understood process that is considered important for maintaining the fitness of animals.
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Affiliation(s)
- Kenichi Ishii
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Matteo Cortese
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Xubo Leng
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Maxim N. Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kenta Asahina
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
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12
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Chen N, Zhang Y, Adel M, Kuklin EA, Reed ML, Mardovin JD, Bakthavachalu B, VijayRaghavan K, Ramaswami M, Griffith LC. Local translation provides the asymmetric distribution of CaMKII required for associative memory formation. Curr Biol 2022; 32:2730-2738.e5. [PMID: 35545085 DOI: 10.1016/j.cub.2022.04.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/18/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
Abstract
How compartment-specific local proteomes are generated and maintained is inadequately understood, particularly in neurons, which display extreme asymmetries. Here we show that local enrichment of Ca2+/calmodulin-dependent protein kinase II (CaMKII) in axons of Drosophila mushroom body neurons is necessary for cellular plasticity and associative memory formation. Enrichment is achieved via enhanced axoplasmic translation of CaMKII mRNA, through a mechanism requiring the RNA-binding protein Mub and a 23-base Mub-recognition element in the CaMKII 3' UTR. Perturbation of either dramatically reduces axonal, but not somatic, CaMKII protein without altering the distribution or amount of mRNA in vivo, and both are necessary and sufficient to enhance axonal translation of reporter mRNA. Together, these data identify elevated levels of translation of an evenly distributed mRNA as a novel strategy for generating subcellular biochemical asymmetries. They further demonstrate the importance of distributional asymmetry in the computational and biological functions of neurons.
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Affiliation(s)
- Nannan Chen
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Yunpeng Zhang
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Mohamed Adel
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Elena A Kuklin
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Martha L Reed
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Jacob D Mardovin
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Baskar Bakthavachalu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - K VijayRaghavan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - Mani Ramaswami
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology and School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - Leslie C Griffith
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA.
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13
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Certel SJ, Ruchti E, McCabe BD, Stowers RS. A conditional glutamatergic synaptic vesicle marker for Drosophila. G3 (BETHESDA, MD.) 2022; 12:6493328. [PMID: 35100385 PMCID: PMC8895992 DOI: 10.1093/g3journal/jkab453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 12/24/2021] [Indexed: 11/21/2022]
Abstract
Glutamate is a principal neurotransmitter used extensively by the nervous systems of all vertebrate and invertebrate animals. It is primarily an excitatory neurotransmitter that has been implicated in nervous system development, as well as a myriad of brain functions from the simple transmission of information between neurons to more complex aspects of nervous system function including synaptic plasticity, learning, and memory. Identification of glutamatergic neurons and their sites of glutamate release are thus essential for understanding the mechanisms of neural circuit function and how information is processed to generate behavior. Here, we describe and characterize smFLAG-vGlut, a conditional marker of glutamatergic synaptic vesicles for the Drosophila model system. smFLAG-vGlut is validated for functionality, conditional expression, and specificity for glutamatergic neurons and synaptic vesicles. The utility of smFLAG-vGlut is demonstrated by glutamatergic neurotransmitter phenotyping of 26 different central complex neuron types of which nine were established to be glutamatergic. This illumination of glutamate neurotransmitter usage will enhance the modeling of central complex neural circuitry and thereby our understanding of information processing by this region of the fly brain. The use of smFLAG for glutamatergic neurotransmitter phenotyping and identification of glutamate release sites can be extended to any Drosophila neuron(s) represented by a binary transcription system driver.
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Affiliation(s)
- Sarah J Certel
- Division of Biological Sciences, Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT 59812, USA
| | - Evelyne Ruchti
- Brain Mind Institute, Swiss Federal Institute of Technology (EPFL), Lausanne VD 1015, Switzerland
| | - Brian D McCabe
- Brain Mind Institute, Swiss Federal Institute of Technology (EPFL), Lausanne VD 1015, Switzerland
| | - R Steven Stowers
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
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14
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Pulianmackal AJ, Kanakousaki K, Flegel K, Grushko OG, Gourley E, Rozich E, Buttitta LA. Misregulation of Nucleoporins 98 and 96 leads to defects in protein synthesis that promote hallmarks of tumorigenesis. Dis Model Mech 2022; 15:dmm049234. [PMID: 35107131 PMCID: PMC8938402 DOI: 10.1242/dmm.049234] [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: 08/03/2021] [Accepted: 01/15/2022] [Indexed: 11/20/2022] Open
Abstract
Nucleoporin 98KD (Nup98) is a promiscuous translocation partner in hematological malignancies. Most disease models of Nup98 translocations involve ectopic expression of the fusion protein under study, leaving the endogenous Nup98 loci unperturbed. Overlooked in these approaches is the loss of one copy of normal Nup98 in addition to the loss of Nup96 - a second Nucleoporin encoded within the same mRNA and reading frame as Nup98 - in translocations. Nup98 and Nup96 are also mutated in a number of other cancers, suggesting that their disruption is not limited to blood cancers. We found that reducing Nup98-96 function in Drosophila melanogaster (in which the Nup98-96 shared mRNA and reading frame is conserved) de-regulates the cell cycle. We found evidence of overproliferation in tissues with reduced Nup98-96, counteracted by elevated apoptosis and aberrant signaling associated with chronic wounding. Reducing Nup98-96 function led to defects in protein synthesis that triggered JNK signaling and contributed to hallmarks of tumorigenesis when apoptosis was inhibited. We suggest that partial loss of Nup98-96 function in translocations could de-regulate protein synthesis, leading to signaling that cooperates with other mutations to promote tumorigenesis.
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Affiliation(s)
| | | | | | | | | | | | - Laura A. Buttitta
- Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Corbacho J, Sanabria-Reinoso E, Buono L, Fernández-Miñan A, Martínez-Morales JR. Trap-TRAP, a Versatile Tool for Tissue-Specific Translatomics in Zebrafish. Front Cell Dev Biol 2022; 9:817191. [PMID: 35174174 PMCID: PMC8841413 DOI: 10.3389/fcell.2021.817191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Developmental and physiological processes depend on the transcriptional and translational activity of heterogeneous cell populations. A main challenge in gene expression studies is dealing with this intrinsic complexity while keeping sequencing efficiency. Translating ribosome affinity purification (TRAP) methods have allowed cell-specific recovery of polyribosome-associated RNAs by genetic tagging of ribosomes in selected cell populations. Here we combined the TRAP approach with adapted enhancer trap methods (trap-TRAP) to systematically generate zebrafish transgenic lines suitable for tissue-specific translatome interrogation. Through the random integration of a GFP-tagged version of the large subunit ribosomal protein L10a (EGFP-Rpl10a), we have generated stable lines driving expression in a variety of tissues, including the retina, skeletal muscle, lateral line primordia, rhombomeres, or jaws. To increase the range of applications, a UAS:TRAP transgenic line compatible with available Gal4 lines was also generated and tested. The resulting collection of lines and applications constitutes a resource for the zebrafish community in developmental genetics, organ physiology and disease modelling.
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16
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Di Bartolomei G, Scheiffele P. An Optimized Protocol for the Mapping of Cell Type-Specific Ribosome-Associated Transcript Isoforms from Small Mouse Brain Regions. Methods Mol Biol 2022; 2537:37-49. [PMID: 35895257 DOI: 10.1007/978-1-0716-2521-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the past years, technological advances in transcriptomics provided deep insights into gene expression programs and their role in tissue organization and cellular functions. The isolation of ribosome-associated transcripts is a powerful approach for deep profiling of cell type-specific transcripts, and particularly well-suited for quantitative analysis of transcript isoforms. This method employs conditional ribosome epitope-tagging in genetically defined cell types, followed by affinity-isolation of ribosome-associated mRNAs. Advantages of this approach are twofold: first, the method enables rapid retrieval of mRNAs without tissue dissociation and cell sorting steps. Second, capturing of ribosome-associated mRNAs, enriches for transcripts recruited for active translation, therefore providing an approximation to the cellular translatome. Here, we describe one application of this method for the identification of the transcriptome of excitatory neuronal cells (mitral and tufted cells) of the mouse olfactory bulb, through RiboTag isolation from the vGlut2-IRES-cre mouse line as genetic driver of endogenously tagged ribosome expression.
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17
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Juarez-Carreño S, Vallejo DM, Carranza-Valencia J, Palomino-Schätzlein M, Ramon-Cañellas P, Santoro R, de Hartog E, Ferres-Marco D, Romero A, Peterson HP, Ballesta-Illan E, Pineda-Lucena A, Dominguez M, Morante J. Body-fat sensor triggers ribosome maturation in the steroidogenic gland to initiate sexual maturation in Drosophila. Cell Rep 2021; 37:109830. [PMID: 34644570 DOI: 10.1016/j.celrep.2021.109830] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 06/25/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022] Open
Abstract
Fat stores are critical for reproductive success and may govern maturation initiation. Here, we report that signaling and sensing fat sufficiency for sexual maturation commitment requires the lipid carrier apolipophorin in fat cells and Sema1a in the neuroendocrine prothoracic gland (PG). Larvae lacking apolpp or Sema1a fail to initiate maturation despite accruing sufficient fat stores, and they continue gaining weight until death. Mechanistically, sensing peripheral body-fat levels via the apolipophorin/Sema1a axis regulates endocytosis, endoplasmic reticulum remodeling, and ribosomal maturation for the acquisition of the PG cells' high biosynthetic and secretory capacity. Downstream of apolipophorin/Sema1a, leptin-like upd2 triggers the cessation of feeding and initiates sexual maturation. Human Leptin in the insect PG substitutes for upd2, preventing obesity and triggering maturation downstream of Sema1a. These data show how peripheral fat levels regulate the control of the maturation decision-making process via remodeling of endomembranes and ribosomal biogenesis in gland cells.
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Affiliation(s)
- Sergio Juarez-Carreño
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Diana Marcela Vallejo
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Juan Carranza-Valencia
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | | | - Pol Ramon-Cañellas
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Roberto Santoro
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Emily de Hartog
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Dolors Ferres-Marco
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Aitana Romero
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Hannah Payette Peterson
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Esther Ballesta-Illan
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Antonio Pineda-Lucena
- Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Avenida Fernando Abril Martorell, 106, 46026 Valencia, Spain; Programa de Terapias Moleculares, Centro de Investigación Médica Aplicada, Universidad de Navarra, Avenida Pío XII, 55, 31008 Pamplona, Spain
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain.
| | - Javier Morante
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas (CSIC), and Universidad Miguel Hernández (UMH), Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain.
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18
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Hopes T, Norris K, Agapiou M, McCarthy CGP, Lewis PA, O'Connell MJ, Fontana J, Aspden JL. Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Nucleic Acids Res 2021; 50:2240-2257. [PMID: 34283226 PMCID: PMC8887423 DOI: 10.1093/nar/gkab606] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/23/2021] [Accepted: 07/02/2021] [Indexed: 12/02/2022] Open
Abstract
Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.
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Affiliation(s)
- Tayah Hopes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK
| | - Karl Norris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michaela Agapiou
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Charley G P McCarthy
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Philip A Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Mary J O'Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Juan Fontana
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK
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19
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Bertin B, Renaud Y, Jagla T, Lavergne G, Dondi C, Da Ponte JP, Junion G, Jagla K. Gelsolin and dCryAB act downstream of muscle identity genes and contribute to preventing muscle splitting and branching in Drosophila. Sci Rep 2021; 11:13197. [PMID: 34162956 PMCID: PMC8222376 DOI: 10.1038/s41598-021-92506-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/03/2021] [Indexed: 11/30/2022] Open
Abstract
A combinatorial code of identity transcription factors (iTFs) specifies the diversity of muscle types in Drosophila. We previously showed that two iTFs, Lms and Ap, play critical role in the identity of a subset of larval body wall muscles, the lateral transverse (LT) muscles. Intriguingly, a small portion of ap and lms mutants displays an increased number of LT muscles, a phenotype that recalls pathological split muscle fibers in human. However, genes acting downstream of Ap and Lms to prevent these aberrant muscle feature are not known. Here, we applied a cell type specific translational profiling (TRAP) to identify gene expression signatures underlying identity of muscle subsets including the LT muscles. We found that Gelsolin (Gel) and dCryAB, both encoding actin-interacting proteins, displayed LT muscle prevailing expression positively regulated by, the LT iTFs. Loss of dCryAB function resulted in LTs with irregular shape and occasional branched ends also observed in ap and lms mutant contexts. In contrast, enlarged and then split LTs with a greater number of myonuclei formed in Gel mutants while Gel gain of function resulted in unfused myoblasts, collectively indicating that Gel regulates LTs size and prevents splitting by limiting myoblast fusion. Thus, dCryAB and Gel act downstream of Lms and Ap and contribute to preventing LT muscle branching and splitting. Our findings offer first clues to still unknown mechanisms of pathological muscle splitting commonly detected in human dystrophic muscles and causing muscle weakness.
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Affiliation(s)
- Benjamin Bertin
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Yoan Renaud
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Teresa Jagla
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Guillaume Lavergne
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Cristiana Dondi
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Jean-Philippe Da Ponte
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Guillaume Junion
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France.
| | - Krzysztof Jagla
- GReD Institute - INSERM U1103, CNRS UMR6293, Université Clermont Auvergne, 28, place Henri-Dunant, 63000, Clermont-Ferrand, France.
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20
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Pallos J, Jeng S, McWeeney S, Martin I. Dopamine neuron-specific LRRK2 G2019S effects on gene expression revealed by translatome profiling. Neurobiol Dis 2021; 155:105390. [PMID: 33984508 DOI: 10.1016/j.nbd.2021.105390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) mutations are the most common genetic cause of late-onset Parkinson's disease. The pathogenic G2019S mutation enhances LRRK2 kinase activity and induces neurodegeneration in C. elegans, Drosophila and rodent models through unclear mechanisms. Gene expression profiling has the potential to provide detailed insight into the biological pathways modulated by LRRK2 kinase activity. Prior in vivo studies have surveyed the effects of LRRK2 G2019S on genome-wide mRNA expression in complex brain tissues with high cellular heterogeneity, limiting their power to detect more restricted gene expression changes occurring in a cell type-specific manner. Here, we used translating ribosome affinity purification (TRAP) coupled to RNA-seq to profile dopamine neuron-specific gene expression changes caused by LRRK2 G2019S in the Drosophila CNS. A number of genes were differentially expressed in the presence of mutant LRRK2 that represent a broad range of molecular functions including DNA repair (RfC3), mRNA metabolism and translation (Ddx1 and lin-28), calcium homeostasis (MCU), and other categories (Ugt37c1, disp, l(1)G0196, CG6602, CG1126 and CG11068). Further analysis on a subset of these genes revealed that LRRK2 G2019S did not alter their expression across the whole brain, consistent with dopamine neuron-specific effects uncovered by the TRAP approach that may yield insight into the neurodegenerative process. To our knowledge, this is the first study to profile the effects of LRRK2 G2019S specifically on DA neuron gene expression in vivo. Beyond providing a set of differentially expressed gene candidates relevant to LRRK2, we demonstrate the effective use of TRAP to perform high-resolution assessment of dopamine neuron gene expression for the study of PD.
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Affiliation(s)
- Judit Pallos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Shannon McWeeney
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR, USA.
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21
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Palmateer CM, Moseley SC, Ray S, Brovero SG, Arbeitman MN. Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior. PLoS Genet 2021; 17:e1009240. [PMID: 33901168 PMCID: PMC8102012 DOI: 10.1371/journal.pgen.1009240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/06/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
Examining the role of chromatin modifications and gene expression in neurons is critical for understanding how the potential for behaviors are established and maintained. We investigate this question by examining Drosophila melanogaster fru P1 neurons that underlie reproductive behaviors in both sexes. We developed a method to purify cell-type-specific chromatin (Chromatag), using a tagged histone H2B variant that is expressed using the versatile Gal4/UAS gene expression system. Here, we use Chromatag to evaluate five chromatin modifications, at three life stages in both sexes. We find substantial changes in chromatin modification profiles across development and fewer differences between males and females. Additionally, we find chromatin modifications that persist in different sets of genes from pupal to adult stages, which may point to genes important for cell fate determination in fru P1 neurons. We generated cell-type-specific RNA-seq data sets, using translating ribosome affinity purification (TRAP). We identify actively translated genes in fru P1 neurons, revealing novel stage- and sex-differences in gene expression. We also find chromatin modification enrichment patterns that are associated with gene expression. Next, we use the chromatin modification data to identify cell-type-specific super-enhancer-containing genes. We show that genes with super-enhancers in fru P1 neurons differ across development and between the sexes. We validated that a set of genes are expressed in fru P1 neurons, which were chosen based on having a super-enhancer and TRAP-enriched expression in fru P1 neurons.
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Affiliation(s)
- Colleen M. Palmateer
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Shawn C. Moseley
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Surjyendu Ray
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Savannah G. Brovero
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Michelle N. Arbeitman
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
- Program of Neuroscience, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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22
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Immarigeon C, Frei Y, Delbare SYN, Gligorov D, Machado Almeida P, Grey J, Fabbro L, Nagoshi E, Billeter JC, Wolfner MF, Karch F, Maeda RK. Identification of a micropeptide and multiple secondary cell genes that modulate Drosophila male reproductive success. Proc Natl Acad Sci U S A 2021; 118:e2001897118. [PMID: 33876742 PMCID: PMC8053986 DOI: 10.1073/pnas.2001897118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Even in well-characterized genomes, many transcripts are considered noncoding RNAs (ncRNAs) simply due to the absence of large open reading frames (ORFs). However, it is now becoming clear that many small ORFs (smORFs) produce peptides with important biological functions. In the process of characterizing the ribosome-bound transcriptome of an important cell type of the seminal fluid-producing accessory gland of Drosophila melanogaster, we detected an RNA, previously thought to be noncoding, called male-specific abdominal (msa). Notably, msa is nested in the HOX gene cluster of the Bithorax complex and is known to contain a micro-RNA within one of its introns. We find that this RNA encodes a "micropeptide" (9 or 20 amino acids, MSAmiP) that is expressed exclusively in the secondary cells of the male accessory gland, where it seems to accumulate in nuclei. Importantly, loss of function of this micropeptide causes defects in sperm competition. In addition to bringing insights into the biology of a rare cell type, this work underlines the importance of small peptides, a class of molecules that is now emerging as important actors in complex biological processes.
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Affiliation(s)
- Clément Immarigeon
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland;
| | - Yohan Frei
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Sofie Y N Delbare
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - Dragan Gligorov
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Pedro Machado Almeida
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jasmine Grey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - Léa Fabbro
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Emi Nagoshi
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jean-Christophe Billeter
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9700 CC, The Netherlands
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - François Karch
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Robert K Maeda
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland;
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23
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Lehmkuhl EM, Loganathan S, Alsop E, Blythe AD, Kovalik T, Mortimore NP, Barrameda D, Kueth C, Eck RJ, Siddegowda BB, Joardar A, Ball H, Macias ME, Bowser R, Van Keuren-Jensen K, Zarnescu DC. TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6. Acta Neuropathol Commun 2021; 9:52. [PMID: 33762006 PMCID: PMC7992842 DOI: 10.1186/s40478-021-01148-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/06/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease in which 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP-43. Using tagged ribosome affinity purifications in Drosophila models of TDP-43 proteinopathy, we identified TDP-43 dependent translational alterations in motor neurons impacting the spliceosome, pentose phosphate and oxidative phosphorylation pathways. A subset of the mRNAs with altered ribosome association are also enriched in TDP-43 complexes suggesting that they may be direct targets. Among these, dlp mRNA, which encodes the glypican Dally like protein (Dlp)/GPC6, a wingless (Wg/Wnt) signaling regulator is insolubilized both in flies and patient tissues with TDP-43 pathology. While Dlp/GPC6 forms puncta in the Drosophila neuropil and ALS spinal cords, it is reduced at the neuromuscular synapse in flies suggesting compartment specific effects of TDP-43 proteinopathy. These findings together with genetic interaction data show that Dlp/GPC6 is a novel, physiologically relevant target of TDP-43 proteinopathy.
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Affiliation(s)
- Erik M. Lehmkuhl
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Suvithanandhini Loganathan
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Eric Alsop
- Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ 85004 USA
| | - Alexander D. Blythe
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Tina Kovalik
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Rd, Phoenix, AZ 85013 USA
| | - Nicholas P. Mortimore
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Dianne Barrameda
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Chuol Kueth
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Randall J. Eck
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Bhavani B. Siddegowda
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Archi Joardar
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Hannah Ball
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Maria E. Macias
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Rd, Phoenix, AZ 85013 USA
| | | | - Daniela C. Zarnescu
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
- Department of Neuroscience, University of Arizona, 1040 4th St, Tucson, AZ 85721 USA
- Department of Neurology, University of Arizona, 1501 N Campbell Ave, Tucson, AZ 85724 USA
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24
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Mohr SE, Tattikota SG, Xu J, Zirin J, Hu Y, Perrimon N. Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila. Genetics 2021; 217:6156631. [PMID: 33713129 DOI: 10.1093/genetics/iyab019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 01/26/2023] Open
Abstract
Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify clusters of cells that share common gene expression signatures. A major challenge in scRNAseq studies is to map the clusters to specific anatomical regions along the body and within tissues. Existing data, such as information obtained from large-scale in situ RNA hybridization studies, cell type specific transcriptomics, gene expression reporters, antibody stainings, and fluorescent tagged proteins, can help to map clusters to anatomy. However, in many cases, additional validation is needed to precisely map the spatial location of cells in clusters. Several approaches are available for spatial resolution in Drosophila, including mining of existing datasets, and use of existing or new tools for direct or indirect detection of RNA, or direct detection of proteins. Here, we review available resources and emerging technologies that will facilitate spatial mapping of scRNAseq clusters at high resolution in Drosophila. Importantly, we discuss the need, available approaches, and reagents for multiplexing gene expression detection in situ, as in most cases scRNAseq clusters are defined by the unique coexpression of sets of genes.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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25
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Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A, Soldano A, Roignant JY. Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J 2021; 40:e104975. [PMID: 33428246 PMCID: PMC7883056 DOI: 10.15252/embj.2020104975] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
N6‐methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. This modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior, albeit the underlying molecular mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6A reader in the nervous system, being required to limit axonal growth. Mechanistically, we show that the m6A reader Ythdf directly interacts with Fmr1, the fly homolog of Fragile X mental retardation RNA binding protein (FMRP), to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system and modulates Fmr1 target transcript selection.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Tina Lence
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Hans-Hermann Wessels
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department CIBIO, University of Trento, Trento, Italy
| | - Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anke Busch
- Bioinformatics Core Facility, IMB, Mainz, Germany
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Michela Notarangelo
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Heidelberg-Mannheim, Heidelberg, Germany
| | - Alessandro Quattrone
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessia Soldano
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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26
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RPL-4 and RPL-9 ̶Mediated Ribosome Purifications Facilitate the Efficient Analysis of Gene Expression in Caenorhabditis elegans Germ Cells. G3-GENES GENOMES GENETICS 2020; 10:4063-4069. [PMID: 32883755 PMCID: PMC7642943 DOI: 10.1534/g3.120.401644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In many organisms, tissue complexity and cellular diversity create a barrier that can hinder our understanding of gene expression programs. To address this problem, methods have been developed that allow for easy isolation of translated mRNAs from genetically defined cell populations. A prominent example is the Translating Ribosome Affinity Purification method also called TRAP. Here, ribosome associated mRNAs are isolated via purification of the ribosomal protein RPL10A/uL1, which is expressed under the control of a tissue specific promoter. Originally developed to investigate gene expression in mouse neurons, it has by now been adopted to many different organisms and tissues. Interestingly, TRAP has never been used successfully to analyze mRNA translation in germ cells. Employing a combination of genetic and biochemical approaches, I assessed several ribosomal proteins for their suitability for TRAP using the Caenorhabditis elegans germline as a target tissue. Surprisingly, I found that RPL10A/uL1 is not the ideal ribosomal component to perform such an analysis in germ cells. Instead other proteins such as RPL4/uL4 or RPL9/eL6 are much better suited for this task. Tagged variants of these proteins are well expressed in germ cells, integrated into translating ribosomes and do not influence germ cell functions. Furthermore, germ cell-specific mRNAs are much more efficiently co-purified with RPL4/uL4 and RPL9/uL6 compared to RPL10A/uL1. This study provides a solid basis upon which future germ cell TRAP experiments can be built, and it highlights the need for rigorous testing when adopting such methods to a new biological system.
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27
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Lathen DR, Merrill CB, Rothenfluh A. Flying Together: Drosophila as a Tool to Understand the Genetics of Human Alcoholism. Int J Mol Sci 2020; 21:E6649. [PMID: 32932795 PMCID: PMC7555299 DOI: 10.3390/ijms21186649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
Alcohol use disorder (AUD) exacts an immense toll on individuals, families, and society. Genetic factors determine up to 60% of an individual's risk of developing problematic alcohol habits. Effective AUD prevention and treatment requires knowledge of the genes that predispose people to alcoholism, play a role in alcohol responses, and/or contribute to the development of addiction. As a highly tractable and translatable genetic and behavioral model organism, Drosophila melanogaster has proven valuable to uncover important genes and mechanistic pathways that have obvious orthologs in humans and that help explain the complexities of addiction. Vinegar flies exhibit remarkably strong face and mechanistic validity as a model for AUDs, permitting many advancements in the quest to understand human genetic involvement in this disease. These advancements occur via approaches that essentially fall into one of two categories: (1) discovering candidate genes via human genome-wide association studies (GWAS), transcriptomics on post-mortem tissue from AUD patients, or relevant physiological connections, then using reverse genetics in flies to validate candidate genes' roles and investigate their molecular function in the context of alcohol. (2) Utilizing flies to discover candidate genes through unbiased screens, GWAS, quantitative trait locus analyses, transcriptomics, or single-gene studies, then validating their translational role in human genetic surveys. In this review, we highlight the utility of Drosophila as a model for alcoholism by surveying recent advances in our understanding of human AUDs that resulted from these various approaches. We summarize the genes that are conserved in alcohol-related function between humans and flies. We also provide insight into some advantages and limitations of these approaches. Overall, this review demonstrates how Drosophila have and can be used to answer important genetic questions about alcohol addiction.
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Affiliation(s)
- Daniel R. Lathen
- Department of Psychiatry and Neuroscience Ph.D. Program, University of Utah, Salt Lake City, UT 84108, USA;
| | - Collin B. Merrill
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA;
| | - Adrian Rothenfluh
- Department of Psychiatry and Neuroscience Ph.D. Program, University of Utah, Salt Lake City, UT 84108, USA;
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA;
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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28
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Mukherjee C, Kling T, Russo B, Miebach K, Kess E, Schifferer M, Pedro LD, Weikert U, Fard MK, Kannaiyan N, Rossner M, Aicher ML, Goebbels S, Nave KA, Krämer-Albers EM, Schneider A, Simons M. Oligodendrocytes Provide Antioxidant Defense Function for Neurons by Secreting Ferritin Heavy Chain. Cell Metab 2020; 32:259-272.e10. [PMID: 32531201 PMCID: PMC7116799 DOI: 10.1016/j.cmet.2020.05.019] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/25/2020] [Accepted: 05/26/2020] [Indexed: 12/28/2022]
Abstract
An evolutionarily conserved function of glia is to provide metabolic and structural support for neurons. To identify molecules generated by glia and with vital functions for neurons, we used Drosophila melanogaster as a screening tool, and subsequently translated the findings to mice. We found that a cargo receptor operating in the secretory pathway of glia was essential to maintain axonal integrity by regulating iron buffering. Ferritin heavy chain was identified as the critical secretory cargo, required for the protection against iron-mediated ferroptotic axonal damage. In mice, ferritin heavy chain is highly expressed by oligodendrocytes and secreted by employing an unconventional secretion pathway involving extracellular vesicles. Disrupting the release of extracellular vesicles or the expression of ferritin heavy chain in oligodendrocytes causes neuronal loss and oxidative damage in mice. Our data point to a role of oligodendrocytes in providing an antioxidant defense system to support neurons against iron-mediated cytotoxicity.
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Affiliation(s)
- Chaitali Mukherjee
- Institute of Neuronal Cell Biology, Technical University Munich, 80802 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Tina Kling
- Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Belisa Russo
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Kerstin Miebach
- Institute of Developmental Biology and Neurobiology (IDN), University of Mainz, 55128 Mainz, Germany
| | - Eva Kess
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Liliana D Pedro
- Institute of Neuronal Cell Biology, Technical University Munich, 80802 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Ulrich Weikert
- Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Maryam K Fard
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Nirmal Kannaiyan
- Department of Psychiatry, Ludwig-Maximillian University, 80336 Munich, Germany
| | - Moritz Rossner
- Department of Psychiatry, Ludwig-Maximillian University, 80336 Munich, Germany
| | - Marie-Louise Aicher
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Sandra Goebbels
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Eva-Maria Krämer-Albers
- Institute of Developmental Biology and Neurobiology (IDN), University of Mainz, 55128 Mainz, Germany
| | - Anja Schneider
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Bonn, 53127 Bonn, Germany.
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, 80802 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany; Munich Cluster of Systems Neurology (SyNergy), 81377 Munich, Germany.
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29
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Traubenik S, Blanco F, Zanetti ME, Reynoso MA. TRAP-SEQ of Eukaryotic Translatomes Applied to the Detection of Polysome-Associated Long Noncoding RNAs. Methods Mol Biol 2020; 2166:451-472. [PMID: 32710425 DOI: 10.1007/978-1-0716-0712-1_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Translating ribosome affinity purification (TRAP) technology allows the isolation of polysomal complexes and the RNAs associated with at least one 80S ribosome. TRAP consists of the stabilization and affinity purification of polysomes containing a tagged version of a ribosomal protein. Quantitative assessment of the TRAP RNA is achieved by direct sequencing (TRAP-SEQ), which provides accurate quantitation of ribosome-associated RNAs, including long noncoding RNAs (lncRNAs). Here we present an updated procedure for TRAP-SEQ, as well as a primary analysis guide for identification of ribosome-associated lncRNAs. This methodology enables the study of dynamic association of lncRNAs by assessing rapid changes in their transcript levels in polysomes at organ or cell-type level, during development, or in response to endogenous or exogenous stimuli.
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Affiliation(s)
- Soledad Traubenik
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Mauricio A Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.
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30
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Sharma R, Rahi S, Mehan S. Neuroprotective potential of solanesol in intracerebroventricular propionic acid induced experimental model of autism: Insights from behavioral and biochemical evidence. Toxicol Rep 2019; 6:1164-1175. [PMID: 31763180 PMCID: PMC6861559 DOI: 10.1016/j.toxrep.2019.10.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/17/2022] Open
Abstract
Autism is the category used within the newest edition of the diagnostic and statistical manual of neurodevelopmental disorders. Autism is a spectrum of disorder where a variety of behavioural patterns observed in autistic patients, such as stereotypes and repetitive behavior, hyperexcitability, depression-like symptoms, and memory and cognitive dysfunctions. Neuropathological hallmarks that associated with autism are mitochondrial dysfunction, oxidative stress, neuroinflammation, Neuro-excitation, abnormal synapse formation, overexpression of glial cells in specific brain regions like cerebellum, cerebral cortex, amygdala, and hippocampus. ICV injection of propionic acid (PPA) (4 μl/0.26 M) mimics autistic-like behavioral and biochemical alterations in rats. Literature findings reveal that there is a link between autism neuronal mitochondrial coenzyme-Q10 (CoQ10) and ETC-complexes dysfunctions are the keys pathogenic events for autism. Therefore, in the current study, we explore the neuroprotective interventions of Solanesol (SNL) 40 and 60 mg/kg alone and in combination with standard drugs Aripiprazole (ARP) 5 mg/kg, Citalopram (CTP) 10 mg/kg, Memantine (MEM) 5 mg/kg and Donepezil (DNP) 3 mg/kg to overcome behavioral and biochemical alterations in PPA induced experimental model of Autism. Chronic treatment with SNL 60 mg/kg in combination with standard drug shows a marked improvement in locomotion, muscle coordination, long-term memory and the decrease in depressive behavior. While, chronic treatment of SNL alone and in combination with standard drug aripiprazole, citalopram, donepezil, and memantine shows the Neuroprotective potential by enhancing the cognitive deficits, biochemical alterations along with reducing the level of inflammatory mediators and oxidative stress.
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Key Words
- AChE, acetylcholinesterase acetylcholinesterase
- ARP, Aripiprazole
- ATP
- Aripiprazole
- Autism
- BBB, blood-brain barrier
- CNS, center nerves system
- CTP, Citalopram
- Citalopram
- CoQ10, coenzyme-Q10
- Coenzyme-Q10
- DNP, Donepezil
- Donepezil
- ELT, escape latency
- ETC, electron-transport chain
- ICV, Intracerebroventricular
- LDH, lactate dehydrogenase
- MAPK3, mitogen-activated protein kinase 3
- MDA, malondialdehyde
- MEM, Memantine
- Memantine
- NO, nitric oxide
- PPA, propionic acid
- Propionic acid
- SNL, Solanesol
- SOD, superoxide dismutase
- UBE3A, Ubiquitin-protein ligase E3A
- i.p., Intraperitoneal route
- mitochondrial dysfunction
- p.o., Oral
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Affiliation(s)
| | | | - Sidharth Mehan
- Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, India
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Sengupta S, Crowe LB, You S, Roberts MA, Jackson FR. A Secreted Ig-Domain Protein Required in Both Astrocytes and Neurons for Regulation of Drosophila Night Sleep. Curr Biol 2019; 29:2547-2554.e2. [PMID: 31353186 DOI: 10.1016/j.cub.2019.06.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/20/2019] [Accepted: 06/19/2019] [Indexed: 12/29/2022]
Abstract
Endogenous rhythmic behaviors are evolutionarily conserved and essential for life. In mammalian and invertebrate models, well-characterized neuronal circuits and evolutionarily conserved mechanisms regulate circadian behavior and sleep [1-4]. In Drosophila, neuronal populations located in multiple brain regions mediate arousal, sleep drive, and homeostasis (reviewed in [3, 5-7]). Similar to mammals [8], there is also evidence that fly glial cells modulate the neuronal circuits controlling rhythmic behaviors, including sleep [1]. Here, we describe a novel gene (CG14141; aka Nkt) that is required for normal sleep. NKT is a 162-amino-acid protein with a single IgC2 immunoglobulin (Ig) domain and a high-quality signal peptide [9], and we show evidence that it is secreted, similar to its C. elegans ortholog (OIG-4) [10]. We demonstrate that Nkt-null flies or those with selective knockdown in either neurons or glia have decreased and fragmented night sleep, indicative of a non-redundant requirement in both cell types. We show that Nkt is required in fly astrocytes and in a specific set of wake-promoting neurons-the mushroom body (MB) α'β' cells that link sleep to memory consolidation [11]. Importantly, Nkt gene expression is required in the adult nervous system for normal sleep, consistent with a physiological rather than developmental function for the Ig-domain protein.
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Affiliation(s)
- Sukanya Sengupta
- Department of Neuroscience, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Lauren B Crowe
- Department of Neuroscience, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Samantha You
- Department of Neuroscience, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Mary A Roberts
- Department of Neuroscience, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - F Rob Jackson
- Department of Neuroscience, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA.
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Liang XH, Nichols JG, Sun H, Crooke ST. Translation can affect the antisense activity of RNase H1-dependent oligonucleotides targeting mRNAs. Nucleic Acids Res 2019; 46:293-313. [PMID: 29165591 PMCID: PMC5758896 DOI: 10.1093/nar/gkx1174] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
RNase H1-dependent antisense oligonucleotides (ASOs) can degrade complementary RNAs in both the nucleus and the cytoplasm. Since cytoplasmic mRNAs are actively engaged in translation, ASO activity may thus be affected by translating ribosomes that scan the mRNAs. Here we show that mRNAs associated with ribosomes can be cleaved using ASOs and that translation can alter ASO activity. Translation inhibition tends to increase ASO activity when targeting the coding regions of efficiently translated mRNAs, but not nuclear non-coding RNAs or less efficiently translated mRNAs. Increasing the level of RNase H1 protein eliminated the enhancing effects of translation inhibition on ASO activity, suggesting that RNase H1 recruitment to ASO/mRNA heteroduplexes is a rate limiting step and that translating ribosomes can inhibit RNase H1 recruitment. Consistently, ASO activity was not increased by translation inhibition when targeting the 3′ UTRs, independent of the translation efficiency of the mRNAs. Contrarily, the activity of 3′ UTR-targeting ASOs tended to be reduced upon translation inhibition, likely due to decreased accessibility. These results indicate that ASO activity can be affected by the translation process, and the findings also provide important information toward helping better ASO drug design.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceutics, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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Engel GL, Taber K, Vinton E, Crocker AJ. Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2019; 15:7. [PMID: 30992041 PMCID: PMC6469124 DOI: 10.1186/s12993-019-0159-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/04/2019] [Indexed: 02/08/2023]
Abstract
Our understanding of the networks of genes and protein functions involved in Alcohol Use Disorder (AUD) remains incomplete, as do the mechanisms by which these networks lead to AUD phenotypes. The fruit fly (Drosophila melanogaster) is an efficient model for functional and mechanistic characterization of the genes involved in alcohol behavior. The fly offers many advantages as a model organism for investigating the molecular and cellular mechanisms of alcohol-related behaviors, and for understanding the underlying neural circuitry driving behaviors, such as locomotor stimulation, sedation, tolerance, and appetitive (reward) learning and memory. Fly researchers are able to use an extensive variety of tools for functional characterization of gene products. To understand how the fly can guide our understanding of AUD in the era of Big Data we will explore these tools, and review some of the gene networks identified in the fly through their use, including chromatin-remodeling, glial, cellular stress, and innate immunity genes. These networks hold great potential as translational drug targets, making it prudent to conduct further research into how these gene mechanisms are involved in alcohol behavior.
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Affiliation(s)
- Gregory L. Engel
- Department of Psychological Sciences, Castleton University, Castleton, VT 05735 USA
| | - Kreager Taber
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
| | - Elizabeth Vinton
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
| | - Amanda J. Crocker
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
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Bates AS, Janssens J, Jefferis GS, Aerts S. Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics. Curr Opin Neurobiol 2019; 56:125-134. [PMID: 30703584 DOI: 10.1016/j.conb.2018.12.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/21/2022]
Abstract
At around 150 000 neurons, the adult Drosophila melanogaster central nervous system is one of the largest species, for which a complete cellular catalogue is imminent. While numerically much simpler than mammalian brains, its complexity is still difficult to parse without grouping neurons into consistent types, which can number 1-1000 cells per hemisphere. We review how neuroanatomical and gene expression data are being used to discover neuronal types at scale. The correlation among multiple co-varying neuronal properties, including lineage, gene expression, morphology, connectivity, response properties and shared behavioral significance is essential to the definition of neuronal cell type. Initial studies comparing morphological and transcriptomic definitions of neuronal type suggest that these are highly consistent, but there is much to do to match these approaches brain-wide. Matched single-cell transcriptomic and morphological data provide an effective reference point to integrate other data types, including connectomics data. This will significantly enhance our ability to make functional predictions from brain wiring diagrams as well facilitating molecular genetic manipulation of neuronal types.
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Affiliation(s)
| | - Jasper Janssens
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Gregory Sxe Jefferis
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Stein Aerts
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium.
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Xu C, Tang HW, Hung RJ, Hu Y, Ni X, Housden BE, Perrimon N. The Septate Junction Protein Tsp2A Restricts Intestinal Stem Cell Activity via Endocytic Regulation of aPKC and Hippo Signaling. Cell Rep 2019; 26:670-688.e6. [PMID: 30650359 PMCID: PMC6394833 DOI: 10.1016/j.celrep.2018.12.079] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/24/2018] [Accepted: 12/17/2018] [Indexed: 01/23/2023] Open
Abstract
Hippo signaling and the activity of its transcriptional coactivator, Yorkie (Yki), are conserved and crucial regulators of tissue homeostasis. In the Drosophila midgut, after tissue damage, Yki activity increases to stimulate stem cell proliferation, but how Yki activity is turned off once the tissue is repaired is unknown. From an RNAi screen, we identified the septate junction (SJ) protein tetraspanin 2A (Tsp2A) as a tumor suppressor. Tsp2A undergoes internalization to facilitate the endocytic degradation of atypical protein kinase C (aPKC), a negative regulator of Hippo signaling. In the Drosophila midgut epithelium, adherens junctions (AJs) and SJs are prominent in intestinal stem cells or enteroblasts (ISCs or EBs) and enterocytes (ECs), respectively. We show that when ISCs differentiate toward ECs, Tsp2A is produced, participates in SJ assembly, and turns off aPKC and Yki-JAK-Stat activity. Altogether, our study uncovers a mechanism allowing the midgut to restore Hippo signaling and restrict proliferation once tissue repair is accomplished.
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Affiliation(s)
- Chiwei Xu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hong-Wen Tang
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ruei-Jiun Hung
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xiaochun Ni
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Benjamin E Housden
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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Dermit M, Dodel M, Mardakheh FK. Methods for monitoring and measurement of protein translation in time and space. MOLECULAR BIOSYSTEMS 2018; 13:2477-2488. [PMID: 29051942 PMCID: PMC5795484 DOI: 10.1039/c7mb00476a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Regulation of protein translation constitutes a crucial step in control of gene expression. Here we review recent methods for system-wide monitoring and measurement of protein translation.
Regulation of protein translation constitutes a crucial step in control of gene expression. In comparison to transcriptional regulation, however, translational control has remained a significantly under-studied layer of gene expression. This trend is now beginning to shift thanks to recent advances in next-generation sequencing, proteomics, and microscopy based methodologies which allow accurate monitoring of protein translation rates, from single target messenger RNA molecules to genome-wide scale studies. In this review, we summarize these recent advances, and discuss how they are enabling researchers to study translational regulation in a wide variety of in vitro and in vivo biological systems, with unprecedented depth and spatiotemporal resolution.
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Affiliation(s)
- Maria Dermit
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
| | - Martin Dodel
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
| | - Faraz K Mardakheh
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.
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37
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Roy S, Jagus R, Morse D. Translation and Translational Control in Dinoflagellates. Microorganisms 2018; 6:microorganisms6020030. [PMID: 29642465 PMCID: PMC6027434 DOI: 10.3390/microorganisms6020030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/24/2022] Open
Abstract
Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here.
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Affiliation(s)
- Sougata Roy
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada.
| | - Rosemary Jagus
- Institute of Marine & Environmental Technology, University of Maryland Center for Environmental Science701 E. Pratt St., Baltimore, MD 21202, USA.
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada.
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38
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Mora N, Oliva C, Fiers M, Ejsmont R, Soldano A, Zhang TT, Yan J, Claeys A, De Geest N, Hassan BA. A Temporal Transcriptional Switch Governs Stem Cell Division, Neuronal Numbers, and Maintenance of Differentiation. Dev Cell 2018; 45:53-66.e5. [DOI: 10.1016/j.devcel.2018.02.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 02/12/2018] [Accepted: 02/26/2018] [Indexed: 01/06/2023]
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39
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Delgado MG, Oliva C, López E, Ibacache A, Galaz A, Delgado R, Barros LF, Sierralta J. Chaski, a novel Drosophila lactate/pyruvate transporter required in glia cells for survival under nutritional stress. Sci Rep 2018; 8:1186. [PMID: 29352169 PMCID: PMC5775259 DOI: 10.1038/s41598-018-19595-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/04/2018] [Indexed: 11/08/2022] Open
Abstract
The intercellular transport of lactate is crucial for the astrocyte-to-neuron lactate shuttle (ANLS), a model of brain energetics according to which neurons are fueled by astrocytic lactate. In this study we show that the Drosophila chaski gene encodes a monocarboxylate transporter protein (MCT/SLC16A) which functions as a lactate/pyruvate transporter, as demonstrated by heterologous expression in mammalian cell culture using a genetically encoded FRET nanosensor. chaski expression is prominent in the Drosophila central nervous system and it is particularly enriched in glia over neurons. chaski mutants exhibit defects in a high energy demanding process such as synaptic transmission, as well as in locomotion and survival under nutritional stress. Remarkably, locomotion and survival under nutritional stress defects are restored by chaski expression in glia cells. Our findings are consistent with a major role for intercellular lactate shuttling in the brain metabolism of Drosophila.
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Affiliation(s)
- María Graciela Delgado
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Carlos Oliva
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Estefanía López
- Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRIDANS), Universidad de Chile, Santiago, Chile
| | - Andrés Ibacache
- Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Alex Galaz
- Centro de Estudios Científicos, Valdivia, Chile
| | - Ricardo Delgado
- Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | | | - Jimena Sierralta
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRIDANS), Universidad de Chile, Santiago, Chile.
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40
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The Expanding Toolkit of Translating Ribosome Affinity Purification. J Neurosci 2018; 37:12079-12087. [PMID: 29237735 DOI: 10.1523/jneurosci.1929-17.2017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/16/2017] [Accepted: 11/03/2017] [Indexed: 01/23/2023] Open
Abstract
Translating ribosome affinity purification is a method initially developed for profiling mRNA from genetically defined cell types in complex tissues. It has been applied both to identify target molecules in cell types that are important for controlling a variety of behaviors in the brain, and to understand the molecular consequences on those cells due to experimental manipulations, ranging from drugs of abuse to disease-causing mutations. Since its inception, a variety of methodological advances are opening new avenues of investigation. These advances include a variety of new methods for targeting cells for translating ribosome affinity purification by features such as their projections or activity, additional tags and mouse reagents increasing the flexibility of the system, and new modifications of the method specifically focused on studying the regulation of translation. The latter includes methods to assess cell type-specific regulation of translation in specific subcellular compartments. Here, I provide a summary of these recent advances and resources, highlighting both new experimental opportunities and areas for future technical development.
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41
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Roh HC, Tsai LTY, Lyubetskaya A, Tenen D, Kumari M, Rosen ED. Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo. Cell Rep 2017; 18:1048-1061. [PMID: 28122230 DOI: 10.1016/j.celrep.2016.12.087] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/28/2016] [Accepted: 12/27/2016] [Indexed: 12/31/2022] Open
Abstract
Epigenomic mechanisms direct distinct gene expression programs for different cell types. Various in vivo tissues have been subjected to epigenomic analysis; however, these studies have been limited by cellular heterogeneity, resulting in composite gene expression and epigenomic profiles. Here, we introduce "NuTRAP," a transgenic mouse that allows simultaneous isolation of cell-type-specific translating mRNA and chromatin from complex tissues. Using NuTRAP, we successfully characterize gene expression and epigenomic states of various adipocyte populations in vivo, revealing significant differences compared to either whole adipose tissue or in vitro adipocyte cell lines. We find that chromatin immunoprecipitation sequencing (ChIP-seq) using NuTRAP is highly efficient, scalable, and robust with even limited cell input. We further demonstrate the general utility of NuTRAP by analyzing hepatocyte-specific epigenomic states. The NuTRAP mouse is a resource that provides a powerful system for cell-type-specific gene expression and epigenomic profiling.
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Affiliation(s)
- Hyun Cheol Roh
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Linus T-Y Tsai
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Anna Lyubetskaya
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Danielle Tenen
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Manju Kumari
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Evan D Rosen
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02142, USA.
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42
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Chen X, Dickman D. Development of a tissue-specific ribosome profiling approach in Drosophila enables genome-wide evaluation of translational adaptations. PLoS Genet 2017; 13:e1007117. [PMID: 29194454 PMCID: PMC5728580 DOI: 10.1371/journal.pgen.1007117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/13/2017] [Accepted: 11/16/2017] [Indexed: 01/19/2023] Open
Abstract
Recent advances in next-generation sequencing approaches have revolutionized our understanding of transcriptional expression in diverse systems. However, measurements of transcription do not necessarily reflect gene translation, the process of ultimate importance in understanding cellular function. To circumvent this limitation, biochemical tagging of ribosome subunits to isolate ribosome-associated mRNA has been developed. However, this approach, called TRAP, lacks quantitative resolution compared to a superior technology, ribosome profiling. Here, we report the development of an optimized ribosome profiling approach in Drosophila. We first demonstrate successful ribosome profiling from a specific tissue, larval muscle, with enhanced resolution compared to conventional TRAP approaches. We next validate the ability of this technology to define genome-wide translational regulation. This technology is leveraged to test the relative contributions of transcriptional and translational mechanisms in the postsynaptic muscle that orchestrate the retrograde control of presynaptic function at the neuromuscular junction. Surprisingly, we find no evidence that significant changes in the transcription or translation of specific genes are necessary to enable retrograde homeostatic signaling, implying that post-translational mechanisms ultimately gate instructive retrograde communication. Finally, we show that a global increase in translation induces adaptive responses in both transcription and translation of protein chaperones and degradation factors to promote cellular proteostasis. Together, this development and validation of tissue-specific ribosome profiling enables sensitive and specific analysis of translation in Drosophila. Recent advances in next-generation sequencing approaches have revolutionized our understanding of transcriptional expression in diverse systems. However, transcriptional expression alone does not necessarily report gene translation, the process of ultimate importance in understanding cellular function. Ribosome profiling is a powerful approach to quantify the number of ribosomes associated with each mRNA to determine rates of gene translation. However, ribosome profiling requires large quantities of starting material, limiting progress in developing tissue-specific approaches. Here, we have developed the first tissue-specific ribosome profiling system in Drosophila to reveal genome-wide changes in translation. We first demonstrate successful ribosome profiling from muscle cells that exhibit superior resolution compared to other translational profiling methods. We then use transcriptional and ribosome profiling to define whether transcriptional or translational mechanisms are necessary for synaptic signaling at the neuromuscular junction. Finally, we utilize ribosome profiling to reveal adaptive changes in cellular translation following cellular stress to muscle tissue. Together, this now enables the power of Drosophila genetics to be leveraged with ribosome profiling in specific tissues.
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Affiliation(s)
- Xun Chen
- Department of Neurobiology, University of Southern California, Los Angeles, California, United States of America
- USC Neuroscience Graduate Program, University of Southern California, Los Angeles, California, United States of America
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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43
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Luis NM, Wang L, Ortega M, Deng H, Katewa SD, Li PWL, Karpac J, Jasper H, Kapahi P. Intestinal IRE1 Is Required for Increased Triglyceride Metabolism and Longer Lifespan under Dietary Restriction. Cell Rep 2017; 17:1207-1216. [PMID: 27783936 DOI: 10.1016/j.celrep.2016.10.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/18/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022] Open
Abstract
Dietary restriction (DR) is one of the most robust lifespan-extending interventions in animals. The beneficial effects of DR involve a metabolic adaptation toward increased triglyceride usage. The regulatory mechanism and the tissue specificity of this metabolic switch remain unclear. Here, we show that the IRE1/XBP1 endoplasmic reticulum (ER) stress signaling module mediates metabolic adaptation upon DR in flies by promoting triglyceride synthesis and accumulation in enterocytes (ECs) of the Drosophila midgut. Consistently, IRE1/XBP1 function in ECs is required for increased longevity upon DR. We further identify sugarbabe, a Gli-like zinc-finger transcription factor, as a key mediator of the IRE1/XBP1-regulated induction of de novo lipogenesis in ECs. Overexpression of sugarbabe rescues metabolic and lifespan phenotypes of IRE1 loss-of-function conditions. Our study highlights the critical role of metabolic adaptation of the intestinal epithelium for DR-induced lifespan extension and explores the IRE1/XBP1 signaling pathway regulating this adaptation and influencing lifespan.
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Affiliation(s)
- Nuno Miguel Luis
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA.
| | - Lifen Wang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - Mauricio Ortega
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - Hansong Deng
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - Subhash D Katewa
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - Patrick Wai-Lun Li
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - Jason Karpac
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Heinrich Jasper
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA; Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena 07745, Germany.
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA.
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44
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Gracida X, Calarco JA. Cell type-specific transcriptome profiling in C. elegans using the Translating Ribosome Affinity Purification technique. Methods 2017. [PMID: 28648677 DOI: 10.1016/j.ymeth.2017.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Organs and specific cell types execute specialized functions in multicellular organisms, in large part through customized gene expression signatures. Thus, profiling the transcriptomes of specific cell and tissue types remains an important tool for understanding how cells become specialized. Methodological approaches to detect gene expression differences have utilized samples from whole animals, dissected tissues, and more recently single cells. Despite these advances, there is still a challenge and a need in most laboratories to implement less invasive yet powerful cell-type specific transcriptome profiling methods. Here, we describe the use of the Translating Ribosome Affinity Purification (TRAP) method for C. elegans to detect cell type-specific gene expression patterns at the level of translating mRNAs. In TRAP, a ribosomal protein is fused to a tag (GFP) and is expressed under cell type-specific promoters to mark genetically defined cell types in vivo. Affinity purification of lysates of animals expressing the tag enriches for ribosome-associated mRNAs of the targeted tissue. The purified mRNAs are used for making cDNA libraries subjected to high-throughput sequencing to obtain genome-wide profiles of transcripts from the targeted cell type. The ease of exposing C. elegans to diverse stimuli, coupled with available cell type specific promoters, makes TRAP a useful approach to enable the discovery of molecular components in response to external or genetic perturbations.
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Affiliation(s)
- Xicotencatl Gracida
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States; Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States.
| | - John A Calarco
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States; Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5, Canada.
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Whitworth GB, Misaghi BC, Rosenthal DM, Mills EA, Heinen DJ, Watson AH, Ives CW, Ali SH, Bezold K, Marsh-Armstrong N, Watson FL. Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis. Dev Biol 2017; 426:360-373. [PMID: 27471010 PMCID: PMC5897040 DOI: 10.1016/j.ydbio.2016.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 11/29/2022]
Abstract
Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.
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Affiliation(s)
- G B Whitworth
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - B C Misaghi
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - D M Rosenthal
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - E A Mills
- Johns Hopkins University School of Medicine, Solomon H. Snyder Dept. of Neuroscience and Hugo Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
| | - D J Heinen
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - A H Watson
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - C W Ives
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - S H Ali
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - K Bezold
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - N Marsh-Armstrong
- Johns Hopkins University School of Medicine, Solomon H. Snyder Dept. of Neuroscience and Hugo Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
| | - F L Watson
- Department of Biology, Washington and Lee University, Lexington, VA, United States.
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Pankova K, Borst A. Transgenic line for the identification of cholinergic release sites in Drosophila melanogaster. ACTA ACUST UNITED AC 2017; 220:1405-1410. [PMID: 28167805 PMCID: PMC5413067 DOI: 10.1242/jeb.149369] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/31/2017] [Indexed: 01/12/2023]
Abstract
The identification of neurotransmitter type used by a neuron is important for the functional dissection of neuronal circuits. In the model organism Drosophila melanogaster, several methods for discerning the neurotransmitter systems are available. Here, we expanded the toolbox for the identification of cholinergic neurons by generating a new line FRT-STOP-FRT-VAChT::HA that is a conditional tagged knock-in of the vesicular acetylcholine transporter (VAChT) gene in its endogenous locus. Importantly, in comparison to already available tools for the detection of cholinergic neurons, the FRT-STOP-FRT-VAChT::HA allele also allows for identification of the subcellular localization of the cholinergic presynaptic release sites in a cell-specific manner. We used the newly generated FRT-STOP-FRT-VAChT::HA line to characterize the Mi1 and Tm3 neurons in the fly visual system and found that VAChT is present in the axons of both cell types, suggesting that Mi1 and Tm3 neurons provide cholinergic input to the elementary motion detectors, the T4 neurons. Summary: A new transgenic Drosophila melanogaster line for the cell-type-specific identification of cholinergic release sites expands the available methods toolbox for discerning the neurotransmitter systems in the fly nervous system.
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Affiliation(s)
- Katarina Pankova
- Max Planck Institute of Neurobiology, 82152 Martinsried, Germany .,Graduate School of Systemic Neurosciences, LMU Munich, 80539 Munich, Germany
| | - Alexander Borst
- Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
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Ng FS, Sengupta S, Huang Y, Yu AM, You S, Roberts MA, Iyer LK, Yang Y, Jackson FR. TRAP-seq Profiling and RNAi-Based Genetic Screens Identify Conserved Glial Genes Required for Adult Drosophila Behavior. Front Mol Neurosci 2016; 9:146. [PMID: 28066175 PMCID: PMC5177635 DOI: 10.3389/fnmol.2016.00146] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/30/2016] [Indexed: 01/06/2023] Open
Abstract
Although, glial cells have well characterized functions in the developing and mature brain, it is only in the past decade that roles for these cells in behavior and plasticity have been delineated. Glial astrocytes and glia-neuron signaling, for example, are now known to have important modulatory functions in sleep, circadian behavior, memory and plasticity. To better understand mechanisms of glia-neuron signaling in the context of behavior, we have conducted cell-specific, genome-wide expression profiling of adult Drosophila astrocyte-like brain cells and performed RNA interference (RNAi)-based genetic screens to identify glial factors that regulate behavior. Importantly, our studies demonstrate that adult fly astrocyte-like cells and mouse astrocytes have similar molecular signatures; in contrast, fly astrocytes and surface glia-different classes of glial cells-have distinct expression profiles. Glial-specific expression of 653 RNAi constructs targeting 318 genes identified multiple factors associated with altered locomotor activity, circadian rhythmicity and/or responses to mechanical stress (bang sensitivity). Of interest, 1 of the relevant genes encodes a vesicle recycling factor, 4 encode secreted proteins and 3 encode membrane transporters. These results strongly support the idea that glia-neuron communication is vital for adult behavior.
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Affiliation(s)
- Fanny S Ng
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - Sukanya Sengupta
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - Yanmei Huang
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - Amy M Yu
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - Samantha You
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - Mary A Roberts
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - Lakshmanan K Iyer
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - Yongjie Yang
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
| | - F Rob Jackson
- Department of Neuroscience, Sackler Program in Biomedical Sciences, Tufts University School of Medicine Boston, MA, USA
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Liu B, Bossing T. Single neuron transcriptomics identify SRSF/SR protein B52 as a regulator of axon growth and Choline acetyltransferase splicing. Sci Rep 2016; 6:34952. [PMID: 27725692 PMCID: PMC5057162 DOI: 10.1038/srep34952] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/21/2016] [Indexed: 01/14/2023] Open
Abstract
We removed single identified neurons from living Drosophila embryos to gain insight into the transcriptional control of developing neuronal networks. The microarray analysis of the transcriptome of two sibling neurons revealed seven differentially expressed transcripts between both neurons (threshold: log21.4). One transcript encodes the RNA splicing factor B52. Loss of B52 increases growth of axon branches. B52 function is also required for Choline acetyltransferase (ChAT ) splicing. At the end of embryogenesis, loss of B52 function impedes splicing of ChAT, reduces acetylcholine synthesis, and extends the period of uncoordinated muscle twitches during larval hatching. ChAT regulation by SRSF proteins may be a conserved feature since changes in SRSF5 expression and increased acetylcholine levels in brains of bipolar disease patients have been reported recently.
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Affiliation(s)
- Boyin Liu
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Torsten Bossing
- School of Biomedical and Healthcare Sciences, Plymouth University, John Bull Building, Plymouth, PL6 8BU, U.K
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Neurons That Underlie Drosophila melanogaster Reproductive Behaviors: Detection of a Large Male-Bias in Gene Expression in fruitless-Expressing Neurons. G3-GENES GENOMES GENETICS 2016; 6:2455-65. [PMID: 27247289 PMCID: PMC4978899 DOI: 10.1534/g3.115.019265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Male and female reproductive behaviors in Drosophila melanogaster are vastly different, but neurons that express sex-specifically spliced fruitless transcripts (fru P1) underlie these behaviors in both sexes. How this set of neurons can generate such different behaviors between the two sexes is an unresolved question. A particular challenge is that fru P1-expressing neurons comprise only 2-5% of the adult nervous system, and so studies of adult head tissue or whole brain may not reveal crucial differences. Translating Ribosome Affinity Purification (TRAP) identifies the actively translated pool of mRNAs from fru P1-expressing neurons, allowing a sensitive, cell-type-specific assay. We find four times more male-biased than female-biased genes in TRAP mRNAs from fru P1-expressing neurons. This suggests a potential mechanism to generate dimorphism in behavior. The male-biased genes may direct male behaviors by establishing cell fate in a similar context of gene expression observed in females. These results suggest a possible global mechanism for how distinct behaviors can arise from a shared set of neurons.
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50
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Marshall OJ, Southall TD, Cheetham SW, Brand AH. Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing. Nat Protoc 2016; 11:1586-98. [PMID: 27490632 DOI: 10.1038/nprot.2016.084] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This protocol is an extension to: Nat. Protoc. 2, 1467-1478 (2007); doi:10.1038/nprot.2007.148; published online 7 June 2007The ability to profile transcription and chromatin binding in a cell-type-specific manner is a powerful aid to understanding cell-fate specification and cellular function in multicellular organisms. We recently developed targeted DamID (TaDa) to enable genome-wide, cell-type-specific profiling of DNA- and chromatin-binding proteins in vivo without cell isolation. As a protocol extension, this article describes substantial modifications to an existing protocol, and it offers additional applications. TaDa builds upon DamID, a technique for detecting genome-wide DNA-binding profiles of proteins, by coupling it with the GAL4 system in Drosophila to enable both temporal and spatial resolution. TaDa ensures that Dam-fusion proteins are expressed at very low levels, thus avoiding toxicity and potential artifacts from overexpression. The modifications to the core DamID technique presented here also increase the speed of sample processing and throughput, and adapt the method to next-generation sequencing technology. TaDa is robust, reproducible and highly sensitive. Compared with other methods for cell-type-specific profiling, the technique requires no cell-sorting, cross-linking or antisera, and binding profiles can be generated from as few as 10,000 total induced cells. By profiling the genome-wide binding of RNA polymerase II (Pol II), TaDa can also identify transcribed genes in a cell-type-specific manner. Here we describe a detailed protocol for carrying out TaDa experiments and preparing the material for next-generation sequencing. Although we developed TaDa in Drosophila, it should be easily adapted to other organisms with an inducible expression system. Once transgenic animals are obtained, the entire experimental procedure-from collecting tissue samples to generating sequencing libraries-can be accomplished within 5 d.
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Affiliation(s)
- Owen J Marshall
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Tony D Southall
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Seth W Cheetham
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Andrea H Brand
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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