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Sukumar SK, Antonydhason V, Molander L, Sandakly J, Kleit M, Umapathy G, Mendoza-Garcia P, Masudi T, Schlosser A, Nässel DR, Wegener C, Shirinian M, Palmer RH. The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neuropeptide precursor in the Drosophila central nervous system. eLife 2024; 12:RP88985. [PMID: 38904987 PMCID: PMC11196111 DOI: 10.7554/elife.88985] [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: 06/22/2024] Open
Abstract
Numerous roles for the Alk receptor tyrosine kinase have been described in Drosophila, including functions in the central nervous system (CNS), however the molecular details are poorly understood. To gain mechanistic insight, we employed Targeted DamID (TaDa) transcriptional profiling to identify targets of Alk signaling in the larval CNS. TaDa was employed in larval CNS tissues, while genetically manipulating Alk signaling output. The resulting TaDa data were analyzed together with larval CNS scRNA-seq datasets performed under similar conditions, identifying a role for Alk in the transcriptional regulation of neuroendocrine gene expression. Further integration with bulk and scRNA-seq datasets from larval brains in which Alk signaling was manipulated identified a previously uncharacterized Drosophila neuropeptide precursor encoded by CG4577 as an Alk signaling transcriptional target. CG4577, which we named Sparkly (Spar), is expressed in a subset of Alk-positive neuroendocrine cells in the developing larval CNS, including circadian clock neurons. In agreement with our TaDa analysis, overexpression of the Drosophila Alk ligand Jeb resulted in increased levels of Spar protein in the larval CNS. We show that Spar protein is expressed in circadian (clock) neurons, and flies lacking Spar exhibit defects in sleep and circadian activity control. In summary, we report a novel activity regulating neuropeptide precursor gene that is regulated by Alk signaling in the Drosophila CNS.
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Affiliation(s)
- Sanjay Kumar Sukumar
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of GothenburgGothenburgSweden
| | - Vimala Antonydhason
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of GothenburgGothenburgSweden
| | - Linnea Molander
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of GothenburgGothenburgSweden
| | - Jawdat Sandakly
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of BeirutBeirutLebanon
| | - Malak Kleit
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of BeirutBeirutLebanon
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of GothenburgGothenburgSweden
| | - Patricia Mendoza-Garcia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of GothenburgGothenburgSweden
| | - Tafheem Masudi
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of GothenburgGothenburgSweden
| | - Andreas Schlosser
- Julius-Maximilians-Universität Würzburg, Rudolf-Virchow-Center, Center for Integrative and Translational BioimagingWürzburgGermany
| | - Dick R Nässel
- Department of Zoology, Stockholm UniversityStockholmSweden
| | - Christian Wegener
- Julius-Maximilians-Universität Würzburg, Biocenter, Theodor-Boveri-Institute, Neurobiology and GeneticsWürzburgGermany
| | - Margret Shirinian
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of BeirutBeirutLebanon
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of GothenburgGothenburgSweden
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2
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Gupta S, Heinrichs E, Novitch BG, Butler SJ. Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses. Development 2024; 151:dev202209. [PMID: 38804879 PMCID: PMC11166460 DOI: 10.1242/dev.202209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
Abstract
Dorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itchiness and proprioception. Previous studies using genetic strategies in animal models have revealed important insights into dI development, but the molecular details of how dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification by combining a single-cell RNA-Seq atlas of mouse embryonic stem cell-derived dIs with pseudotime analyses. To validate this in silico resource as a useful tool, we used it to first identify genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them using in situ hybridization analyses in the developing mouse spinal cord in vivo. We have also identified an endpoint of the dI5 lineage trajectory and found that dIs become more transcriptionally homogeneous during terminal differentiation. This study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and demonstrates its utility in clarifying dI lineage relationships.
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Affiliation(s)
- Sandeep Gupta
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Heinrichs
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Genetics and Genomics Graduate Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bennett G. Novitch
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samantha J. Butler
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Komori H, Rastogi G, Bugay JP, Luo H, Lin S, Angers S, Smibert CA, Lipshitz HD, Lee CY. Post-transcriptional regulatory pre-complex assembly drives timely cell-state transitions during differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591706. [PMID: 38746105 PMCID: PMC11092521 DOI: 10.1101/2024.04.29.591706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Complexes that control mRNA stability and translation promote timely cell-state transitions during differentiation by ensuring appropriate expression patterns of key developmental regulators. The Drosophila RNA-binding protein Brain tumor (Brat) promotes degradation of target transcripts during the maternal-to-zygotic transition in syncytial embryos and in uncommitted intermediate neural progenitors (immature INPs). We identified Ubiquitin-specific protease 5 (Usp5) as a Brat interactor essential for the degradation of Brat target mRNAs in both cell types. Usp5 promotes Brat-dedadenylase pre-complex assembly in mitotic neural stem cells (neuroblasts) by bridging Brat and the scaffolding components of deadenylase complexes lacking their catalytic subunits. The adaptor protein Miranda binds the RNA-binding domain of Brat, limiting its ability to bind target mRNAs in mitotic neuroblasts. Cortical displacement of Miranda activates Brat-mediated mRNA decay in immature INPs. We propose that the assembly of an enzymatically inactive and RNA-binding-deficient pre-complex poises mRNA degradation machineries for rapid activation driving timely developmental transitions.
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4
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Gupta S, Heinrichs E, Novitch BG, Butler SJ. Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.24.550380. [PMID: 37546781 PMCID: PMC10402035 DOI: 10.1101/2023.07.24.550380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Dorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itch, and proprioception. While previous studies using genetic strategies in animal models have revealed important insights into dI development, the molecular details by which dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification by combining a single-cell RNA-Seq atlas of mouse ESC-derived dIs with pseudotime analyses. To validate this in silico resource as a useful tool, we used it to first identify novel genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them using in situ hybridization analyses in the developing mouse spinal cord in vivo . We have also identified a novel endpoint of the dI5 lineage trajectory and found that dIs become more transcriptionally homogenous during terminal differentiation. Together, this study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and demonstrates its utility clarifying dI lineage relationships. Summary statement Pseudotime analyses of embryonic stem cell-derived dorsal spinal interneurons reveals both novel regulators and lineage relationships between different interneuron populations.
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5
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Cai W, Zhang W, Zheng Q, Hor CC, Pan T, Fatima M, Dong X, Duan B, Xu XZS. The kainate receptor GluK2 mediates cold sensing in mice. Nat Neurosci 2024; 27:679-688. [PMID: 38467901 DOI: 10.1038/s41593-024-01585-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/23/2024] [Indexed: 03/13/2024]
Abstract
Thermosensors expressed in peripheral somatosensory neurons sense a wide range of environmental temperatures. While thermosensors detecting cool, warm and hot temperatures have all been extensively characterized, little is known about those sensing cold temperatures. Though several candidate cold sensors have been proposed, none has been demonstrated to mediate cold sensing in somatosensory neurons in vivo, leaving a knowledge gap in thermosensation. Here we characterized mice lacking the kainate-type glutamate receptor GluK2, a mammalian homolog of the Caenorhabditis elegans cold sensor GLR-3. While GluK2 knockout mice respond normally to heat and mechanical stimuli, they exhibit a specific deficit in sensing cold but not cool temperatures. Further analysis supports a key role for GluK2 in sensing cold temperatures in somatosensory DRG neurons in the periphery. Our results reveal that GluK2-a glutamate-sensing chemoreceptor mediating synaptic transmission in the central nervous system-is co-opted as a cold-sensing thermoreceptor in the periphery.
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Affiliation(s)
- Wei Cai
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Wenwen Zhang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Qin Zheng
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chia Chun Hor
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tong Pan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Mahar Fatima
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bo Duan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - X Z Shawn Xu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.
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6
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Wang X, Zhai Y, Zheng H. Deciphering the cellular heterogeneity of the insect brain with single-cell RNA sequencing. INSECT SCIENCE 2024; 31:314-327. [PMID: 37702319 DOI: 10.1111/1744-7917.13270] [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: 04/24/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
Insects show highly complicated adaptive and sophisticated behaviors, including spatial orientation skills, learning ability, and social interaction. These behaviors are controlled by the insect brain, the central part of the nervous system. The tiny insect brain consists of millions of highly differentiated and interconnected cells forming a complex network. Decades of research has gone into an understanding of which parts of the insect brain possess particular behaviors, but exactly how they modulate these functional consequences needs to be clarified. Detailed description of the brain and behavior is required to decipher the complexity of cell types, as well as their connectivity and function. Single-cell RNA-sequencing (scRNA-seq) has emerged recently as a breakthrough technology to understand the transcriptome at cellular resolution. With scRNA-seq, it is possible to uncover the cellular heterogeneity of brain cells and elucidate their specific functions and state. In this review, we first review the basic structure of insect brains and the links to insect behaviors mainly focusing on learning and memory. Then the scRNA applications on insect brains are introduced by representative studies. Single-cell RNA-seq has allowed researchers to classify cell subpopulations within different insect brain regions, pinpoint single-cell developmental trajectories, and identify gene regulatory networks. These developments empower the advances in neuroscience and shed light on the intricate problems in understanding insect brain functions and behaviors.
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Affiliation(s)
- Xiaofei Wang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and In-sect Pests, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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7
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Sun C, Shao Y, Iqbal J. Insect Insights at the Single-Cell Level: Technologies and Applications. Cells 2023; 13:91. [PMID: 38201295 PMCID: PMC10777908 DOI: 10.3390/cells13010091] [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: 11/22/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Single-cell techniques are a promising way to unravel the complexity and heterogeneity of transcripts at the cellular level and to reveal the composition of different cell types and functions in a tissue or organ. In recent years, advances in single-cell RNA sequencing (scRNA-seq) have further changed our view of biological systems. The application of scRNA-seq in insects enables the comprehensive characterization of both common and rare cell types and cell states, the discovery of new cell types, and revealing how cell types relate to each other. The recent application of scRNA-seq techniques to insect tissues has led to a number of exciting discoveries. Here we provide an overview of scRNA-seq and its application in insect research, focusing on biological applications, current challenges, and future opportunities to make new discoveries with scRNA-seq in insects.
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Affiliation(s)
- Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Yongqi Shao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junaid Iqbal
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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8
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Rajan A, Anhezini L, Rives-Quinto N, Chhabra JY, Neville MC, Larson ED, Goodwin SF, Harrison MM, Lee CY. Low-level repressive histone marks fine-tune gene transcription in neural stem cells. eLife 2023; 12:e86127. [PMID: 37314324 PMCID: PMC10344426 DOI: 10.7554/elife.86127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/11/2023] [Indexed: 06/15/2023] Open
Abstract
Coordinated regulation of gene activity by transcriptional and translational mechanisms poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of gene transcription is lacking due to the compensatory effect of translational control. We used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). We demonstrate that the transcription factor FruitlessC (FruC) binds cis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss of fruC function alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. FruC negatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in gene cis-regulatory regions. Identical to fruC loss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. We propose low-level H3K27me3 enrichment fine-tunes gene transcription in stem cells, a mechanism likely conserved from flies to humans.
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Affiliation(s)
- Arjun Rajan
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Lucas Anhezini
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Noemi Rives-Quinto
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Jay Y Chhabra
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Megan C Neville
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Stephen F Goodwin
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
- Department of Cell and Developmental Biology, University of Michigan Medical SchoolAnn ArborUnited States
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical SchoolAnn ArborUnited States
- Rogel Cancer Center, University of Michigan Medical SchoolAnn ArborUnited States
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9
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Marques GS, Teles-Reis J, Konstantinides N, Brito PH, Homem CCF. Asynchronous transcription and translation of neurotransmitter-related genes characterize the initial stages of neuronal maturation in Drosophila. PLoS Biol 2023; 21:e3002115. [PMID: 37205703 PMCID: PMC10234549 DOI: 10.1371/journal.pbio.3002115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 06/01/2023] [Accepted: 04/06/2023] [Indexed: 05/21/2023] Open
Abstract
Neuron specification and maturation are essential for proper central nervous system development. However, the precise mechanisms that govern neuronal maturation, essential to shape and maintain neuronal circuitry, remain poorly understood. Here, we analyse early-born secondary neurons in the Drosophila larval brain, revealing that the early maturation of secondary neurons goes through 3 consecutive phases: (1) Immediately after birth, neurons express pan-neuronal markers but do not transcribe terminal differentiation genes; (2) Transcription of terminal differentiation genes, such as neurotransmitter-related genes VGlut, ChAT, or Gad1, starts shortly after neuron birth, but these transcripts are, however, not translated; (3) Translation of neurotransmitter-related genes only begins several hours later in mid-pupa stages in a coordinated manner with animal developmental stage, albeit in an ecdysone-independent manner. These results support a model where temporal regulation of transcription and translation of neurotransmitter-related genes is an important mechanism to coordinate neuron maturation with brain development.
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Affiliation(s)
- Graça S. Marques
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa; Lisboa, Portugal
| | - José Teles-Reis
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa; Lisboa, Portugal
| | | | - Patrícia H. Brito
- Applied Molecular Biosciences Unit-UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Catarina C. F. Homem
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa; Lisboa, Portugal
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10
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Models of Congenital Adrenal Hyperplasia for Gene Therapies Testing. Int J Mol Sci 2023; 24:ijms24065365. [PMID: 36982440 PMCID: PMC10049562 DOI: 10.3390/ijms24065365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/26/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
The adrenal glands are important endocrine organs that play a major role in the stress response. Some adrenal glands abnormalities are treated with hormone replacement therapy, which does not address physiological requirements. Modern technologies make it possible to develop gene therapy drugs that can completely cure diseases caused by mutations in specific genes. Congenital adrenal hyperplasia (CAH) is an example of such a potentially treatable monogenic disease. CAH is an autosomal recessive inherited disease with an overall incidence of 1:9500–1:20,000 newborns. To date, there are several promising drugs for CAH gene therapy. At the same time, it remains unclear how new approaches can be tested, as there are no models for this disease. The present review focuses on modern models for inherited adrenal gland insufficiency and their detailed characterization. In addition, the advantages and disadvantages of various pathological models are discussed, and ways of further development are suggested.
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11
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Kozlov EN, Tokmatcheva EV, Khrustaleva AM, Grebenshchikov ES, Deev RV, Gilmutdinov RA, Lebedeva LA, Zhukova M, Savvateeva-Popova EV, Schedl P, Shidlovskii YV. Long-Term Memory Formation in Drosophila Depends on the 3'UTR of CPEB Gene orb2. Cells 2023; 12:cells12020318. [PMID: 36672258 PMCID: PMC9856895 DOI: 10.3390/cells12020318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/30/2022] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Activation of local translation in neurites in response to stimulation is an important step in the formation of long-term memory (LTM). CPEB proteins are a family of translation factors involved in LTM formation. The Drosophila CPEB protein Orb2 plays an important role in the development and function of the nervous system. Mutations of the coding region of the orb2 gene have previously been shown to impair LTM formation. We found that a deletion of the 3'UTR of the orb2 gene similarly results in loss of LTM in Drosophila. As a result of the deletion, the content of the Orb2 protein remained the same in the neuron soma, but significantly decreased in synapses. Using RNA immunoprecipitation followed by high-throughput sequencing, we detected more than 6000 potential Orb2 mRNA targets expressed in the Drosophila brain. Importantly, deletion of the 3'UTR of orb2 mRNA also affected the localization of the Csp, Pyd, and Eya proteins, which are encoded by putative mRNA targets of Orb2. Therefore, the 3'UTR of the orb2 mRNA is important for the proper localization of Orb2 and other proteins in synapses of neurons and the brain as a whole, providing a molecular basis for LTM formation.
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Affiliation(s)
- Eugene N. Kozlov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elena V. Tokmatcheva
- Institute of Physiology, Russian Academy of Sciences, 188680 St. Petersburg, Russia
| | - Anastasia M. Khrustaleva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Eugene S. Grebenshchikov
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| | - Roman V. Deev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Rudolf A. Gilmutdinov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Lyubov A. Lebedeva
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Mariya Zhukova
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | | | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton University, Princeton, NJ 08544-1014, USA
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
- Correspondence:
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12
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Sato M, Suzuki T. Cutting edge technologies expose the temporal regulation of neurogenesis in the Drosophila nervous system. Fly (Austin) 2022; 16:222-232. [PMID: 35549651 PMCID: PMC9116403 DOI: 10.1080/19336934.2022.2073158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 11/23/2022] Open
Abstract
During the development of the central nervous system (CNS), extremely large numbers of neurons are produced in a regular fashion to form precise neural circuits. During this process, neural progenitor cells produce different neurons over time due to their intrinsic gene regulatory mechanisms as well as extrinsic mechanisms. The Drosophila CNS has played an important role in elucidating the temporal mechanisms that control neurogenesis over time. It has been shown that a series of temporal transcription factors are sequentially expressed in neural progenitor cells and regulate the temporal specification of neurons in the embryonic CNS. Additionally, similar mechanisms are found in the developing optic lobe and central brain in the larval CNS. However, it is difficult to elucidate the function of numerous molecules in many different cell types solely by molecular genetic approaches. Recently, omics analysis using single-cell RNA-seq and other methods has been used to study the Drosophila nervous system on a large scale and is making a significant contribution to the understanding of the temporal mechanisms of neurogenesis. In this article, recent findings on the temporal patterning of neurogenesis and the contributions of cutting-edge technologies will be reviewed.
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Affiliation(s)
- Makoto Sato
- Mathematical Neuroscience Unit, Institute for Frontier Science Initiative,Laboratory of Developmental Neurobiology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Takumi Suzuki
- College of Science, Department of Science, Ibaraki University, Ibaraki, Japan
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13
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Transcriptional profiling from whole embryos to single neuroblast lineages in Drosophila. Dev Biol 2022; 489:21-33. [PMID: 35660371 PMCID: PMC9805786 DOI: 10.1016/j.ydbio.2022.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/06/2022] [Accepted: 05/25/2022] [Indexed: 01/03/2023]
Abstract
Embryonic development results in the production of distinct tissue types, and different cell types within each tissue. A major goal of developmental biology is to uncover the "parts list" of cell types that comprise each organ. Here we perform single cell RNA sequencing (scRNA-seq) of the Drosophila embryo to identify the genes that characterize different cell and tissue types during development. We assay three different timepoints, revealing a coordinated change in gene expression within each tissue. Interestingly, we find that the elav and Mhc genes, whose protein products are widely used as markers for neurons and muscles, respectively, show broad pan-embryonic expression, indicating the importance of post-transcriptional regulation. We next focus on the central nervous system (CNS), where we identify genes whose expression is enriched at each stage of neuronal differentiation: from neural progenitors, called neuroblasts, to their immediate progeny ganglion mother cells (GMCs), followed by new-born neurons, young neurons, and the most mature neurons. Finally, we ask whether the clonal progeny of a single neuroblast (NB7-1) share a similar transcriptional identity. Surprisingly, we find that clonal identity does not lead to transcriptional clustering, showing that neurons within a lineage are diverse, and that neurons with a similar transcriptional profile (e.g. motor neurons, glia) are distributed among multiple neuroblast lineages. Although each lineage consists of diverse progeny, we were able to identify a previously uncharacterized gene, Fer3, as an excellent marker for the NB7-1 lineage. Within the NB7-1 lineage, neurons which share a temporal identity (e.g. Hunchback, Kruppel, Pdm, and Castor temporal transcription factors in the NB7-1 lineage) have shared transcriptional features, allowing for the identification of candidate novel temporal factors or targets of the temporal transcription factors. In conclusion, we have characterized the embryonic transcriptome for all major tissue types and for three stages of development, as well as the first transcriptomic analysis of a single, identified neuroblast lineage, finding a lineage-enriched transcription factor.
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14
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Dillon N, Cocanougher B, Sood C, Yuan X, Kohn AB, Moroz LL, Siegrist SE, Zlatic M, Doe CQ. Single cell RNA-seq analysis reveals temporally-regulated and quiescence-regulated gene expression in Drosophila larval neuroblasts. Neural Dev 2022; 17:7. [PMID: 36002894 PMCID: PMC9404614 DOI: 10.1186/s13064-022-00163-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanisms that generate neural diversity during development remains largely unknown. Here, we use scRNA-seq methodology to discover new features of the Drosophila larval CNS across several key developmental timepoints. We identify multiple progenitor subtypes - both stem cell-like neuroblasts and intermediate progenitors - that change gene expression across larval development, and report on new candidate markers for each class of progenitors. We identify a pool of quiescent neuroblasts in newly hatched larvae and show that they are transcriptionally primed to respond to the insulin signaling pathway to exit from quiescence, including relevant pathway components in the adjacent glial signaling cell type. We identify candidate "temporal transcription factors" (TTFs) that are expressed at different times in progenitor lineages. Our work identifies many cell type specific genes that are candidates for functional roles, and generates new insight into the differentiation trajectory of larval neurons.
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Affiliation(s)
- Noah Dillon
- Institute of Neuroscience, Howard Hughes Medical Institute, University of Oregon, OR, 97403, Eugene, USA
| | - Ben Cocanougher
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Chhavi Sood
- Department of Biology, University of Virginia, VA, 22904, Charlottesville, USA
| | - Xin Yuan
- Department of Biology, University of Virginia, VA, 22904, Charlottesville, USA
| | - Andrea B Kohn
- Whitney Laboratory for Marine Biosciences, University of Florida, FL, 32080, St. Augustine, USA
| | - Leonid L Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, FL, 32080, St. Augustine, USA
| | - Sarah E Siegrist
- Department of Biology, University of Virginia, VA, 22904, Charlottesville, USA
| | - Marta Zlatic
- MRC Laboratory of Molecular Biology, Dept of Zoology, University of Cambridge, Cambridge, UK.,Janelia Research Campus, VA, Ashburn, USA
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of Oregon, OR, 97403, Eugene, USA.
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15
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Pfeifer K, Wolfstetter G, Anthonydhason V, Masudi T, Arefin B, Bemark M, Mendoza-Garcia P, Palmer RH. Patient-associated mutations in Drosophila Alk perturb neuronal differentiation and promote survival. Dis Model Mech 2022; 15:dmm049591. [PMID: 35972154 PMCID: PMC9403751 DOI: 10.1242/dmm.049591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Activating anaplastic lymphoma kinase (ALK) receptor tyrosine kinase (RTK) mutations occur in pediatric neuroblastoma and are associated with poor prognosis. To study ALK-activating mutations in a genetically controllable system, we employed CRIPSR/Cas9, incorporating orthologs of the human oncogenic mutations ALKF1174L and ALKY1278S in the Drosophila Alk locus. AlkF1251L and AlkY1355S mutant Drosophila exhibited enhanced Alk signaling phenotypes, but unexpectedly depended on the Jelly belly (Jeb) ligand for activation. Both AlkF1251L and AlkY1355S mutant larval brains displayed hyperplasia, represented by increased numbers of Alk-positive neurons. Despite this hyperplasic phenotype, no brain tumors were observed in mutant animals. We showed that hyperplasia in Alk mutants was not caused by significantly increased rates of proliferation, but rather by decreased levels of apoptosis in the larval brain. Using single-cell RNA sequencing, we identified perturbations during temporal fate specification in AlkY1355S mutant mushroom body lineages. These findings shed light on the role of Alk in neurodevelopmental processes and highlight the potential of Alk-activating mutations to perturb specification and promote survival in neuronal lineages. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kathrin Pfeifer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Georg Wolfstetter
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Vimala Anthonydhason
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Tafheem Masudi
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Badrul Arefin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Mats Bemark
- Department of Microbiology and Immunology, Mucosal Immunobiology and Vaccine Center, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Patricia Mendoza-Garcia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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16
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Tang JLY, Hakes AE, Krautz R, Suzuki T, Contreras EG, Fox PM, Brand AH. NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system. Dev Cell 2022; 57:1193-1207.e7. [PMID: 35483359 PMCID: PMC9616798 DOI: 10.1016/j.devcel.2022.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/08/2022] [Accepted: 04/05/2022] [Indexed: 11/24/2022]
Abstract
Temporal patterning of neural progenitors is an evolutionarily conserved strategy for generating neuronal diversity. Type II neural stem cells in the Drosophila central brain produce transit-amplifying intermediate neural progenitors (INPs) that exhibit temporal patterning. However, the known temporal factors cannot account for the neuronal diversity in the adult brain. To search for missing factors, we developed NanoDam, which enables rapid genome-wide profiling of endogenously tagged proteins in vivo with a single genetic cross. Mapping the targets of known temporal transcription factors with NanoDam revealed that Homeobrain and Scarecrow (ARX and NKX2.1 orthologs) are also temporal factors. We show that Homeobrain and Scarecrow define middle-aged and late INP temporal windows and play a role in cellular longevity. Strikingly, Homeobrain and Scarecrow have conserved functions as temporal factors in the developing visual system. NanoDam enables rapid cell-type-specific genome-wide profiling with temporal resolution and is easily adapted for use in higher organisms.
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Affiliation(s)
- Jocelyn L Y Tang
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Anna E Hakes
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Robert Krautz
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Takumi Suzuki
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Esteban G Contreras
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Paul M Fox
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Andrea H Brand
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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17
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Rajan A, Ostgaard CM, Lee CY. Regulation of Neural Stem Cell Competency and Commitment during Indirect Neurogenesis. Int J Mol Sci 2021; 22:12871. [PMID: 34884676 PMCID: PMC8657492 DOI: 10.3390/ijms222312871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
Indirect neurogenesis, during which neural stem cells generate neurons through intermediate progenitors, drives the evolution of lissencephalic brains to gyrencephalic brains. The mechanisms that specify intermediate progenitor identity and that regulate stem cell competency to generate intermediate progenitors remain poorly understood despite their roles in indirect neurogenesis. Well-characterized lineage hierarchy and available powerful genetic tools for manipulating gene functions make fruit fly neural stem cell (neuroblast) lineages an excellent in vivo paradigm for investigating the mechanisms that regulate neurogenesis. Type II neuroblasts in fly larval brains repeatedly undergo asymmetric divisions to generate intermediate neural progenitors (INPs) that undergo limited proliferation to increase the number of neurons generated per stem cell division. Here, we review key regulatory genes and the mechanisms by which they promote the specification and generation of INPs, safeguarding the indirect generation of neurons during fly larval brain neurogenesis. Homologs of these regulators of INPs have been shown to play important roles in regulating brain development in vertebrates. Insight into the precise regulation of intermediate progenitors will likely improve our understanding of the control of indirect neurogenesis during brain development and brain evolution.
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Affiliation(s)
- Arjun Rajan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (A.R.); (C.M.O.)
| | - Cyrina M. Ostgaard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (A.R.); (C.M.O.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; (A.R.); (C.M.O.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Division of Genetic Medicine, Department of Internal Medicine and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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18
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Simon F, Konstantinides N. Single-cell transcriptomics in the Drosophila visual system: Advances and perspectives on cell identity regulation, connectivity, and neuronal diversity evolution. Dev Biol 2021; 479:107-122. [PMID: 34375653 DOI: 10.1016/j.ydbio.2021.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/10/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022]
Abstract
The Drosophila visual system supports complex behaviors and shares many of its anatomical and molecular features with the vertebrate brain. Yet, it contains a much more manageable number of neurons and neuronal types. In addition to the extensive Drosophila genetic toolbox, this relative simplicity has allowed decades of work to yield a detailed account of its neuronal type diversity, morphology, connectivity and specification mechanisms. In the past three years, numerous studies have applied large scale single-cell transcriptomic approaches to the Drosophila visual system and have provided access to the complete gene expression profile of most neuronal types throughout development. This makes the fly visual system particularly well suited to perform detailed studies of the genetic mechanisms underlying the evolution and development of neuronal systems. Here, we highlight how these transcriptomic resources allow exploring long-standing biological questions under a new light. We first present the efforts made to characterize neuronal diversity in the Drosophila visual system and suggest ways to further improve this description. We then discuss current advances allowed by the single-cell datasets, and envisage how these datasets can be further leveraged to address fundamental questions regarding the regulation of neuronal identity, neuronal circuit development and the evolution of neuronal diversity.
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Affiliation(s)
- Félix Simon
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Nikolaos Konstantinides
- Department of Biology, New York University, New York, NY, 10003, USA; Institut Jacques Monod, Centre National de la Recherche Scientifique-UMR 7592, Université Paris Diderot, Paris, France.
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