1
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Poole RJ, Flames N, Cochella L. Neurogenesis in Caenorhabditis elegans. Genetics 2024; 228:iyae116. [PMID: 39167071 PMCID: PMC11457946 DOI: 10.1093/genetics/iyae116] [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: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/23/2024] Open
Abstract
Animals rely on their nervous systems to process sensory inputs, integrate these with internal signals, and produce behavioral outputs. This is enabled by the highly specialized morphologies and functions of neurons. Neuronal cells share multiple structural and physiological features, but they also come in a large diversity of types or classes that give the nervous system its broad range of functions and plasticity. This diversity, first recognized over a century ago, spurred classification efforts based on morphology, function, and molecular criteria. Caenorhabditis elegans, with its precisely mapped nervous system at the anatomical level, an extensive molecular description of most of its neurons, and its genetic amenability, has been a prime model for understanding how neurons develop and diversify at a mechanistic level. Here, we review the gene regulatory mechanisms driving neurogenesis and the diversification of neuron classes and subclasses in C. elegans. We discuss our current understanding of the specification of neuronal progenitors and their differentiation in terms of the transcription factors involved and ensuing changes in gene expression and chromatin landscape. The central theme that has emerged is that the identity of a neuron is defined by modules of gene batteries that are under control of parallel yet interconnected regulatory mechanisms. We focus on how, to achieve these terminal identities, cells integrate information along their developmental lineages. Moreover, we discuss how neurons are diversified postembryonically in a time-, genetic sex-, and activity-dependent manner. Finally, we discuss how the understanding of neuronal development can provide insights into the evolution of neuronal diversity.
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Affiliation(s)
- Richard J Poole
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia 46012, Spain
| | - Luisa Cochella
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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2
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Catela C, Assimacopoulos S, Chen Y, Tsioras K, Feng W, Kratsios P. The Iroquois ( Iro/Irx) homeobox genes are conserved Hox targets involved in motor neuron development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596714. [PMID: 38853975 PMCID: PMC11160718 DOI: 10.1101/2024.05.30.596714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Iroquois (Iro/Irx) homeobox genes encode transcription factors with fundamental roles in animal development. Despite their link to various congenital conditions in humans, our understanding of Iro/Irx gene expression, function, and regulation remains incomplete. Here, we conducted a systematic expression analysis of all six mouse Irx genes in the embryonic spinal cord. We found five Irx genes (Irx1, Irx2, Irx3, Irx5, and Irx6) to be confined mostly to ventral spinal domains, offering new molecular markers for specific groups of post-mitotic motor neurons (MNs). Further, we engineered Irx2, Irx5, and Irx6 mouse mutants and uncovered essential but distinct roles for Irx2 and Irx6 in MN development. Last, we found that the highly conserved regulators of MN development across species, the HOX proteins, directly control Irx gene expression both in mouse and C. elegans MNs, critically expanding the repertoire of HOX target genes in the developing nervous system. Altogether, our study provides important insights into Iro/Irx expression and function in the developing spinal cord, and uncovers an ancient gene regulatory relationship between HOX and Iro/Irx genes.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Stavroula Assimacopoulos
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Konstantinos Tsioras
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
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3
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Moreira P, Papatheodorou P, Deng S, Gopal S, Handley A, Powell DR, Pocock R. Nuclear factor Y is a pervasive regulator of neuronal gene expression. Cell Rep 2023; 42:113582. [PMID: 38096055 DOI: 10.1016/j.celrep.2023.113582] [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: 02/12/2023] [Revised: 10/12/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Nervous system function relies on the establishment of complex gene expression programs that provide neuron-type-specific and core pan-neuronal features. These complementary regulatory paradigms are controlled by terminal selector and parallel-acting transcription factors (TFs), respectively. Here, we identify the nuclear factor Y (NF-Y) TF as a pervasive direct and indirect regulator of both neuron-type-specific and pan-neuronal gene expression. Mapping global NF-Y targets reveals direct binding to the cis-regulatory regions of pan-neuronal genes and terminal selector TFs. We show that NFYA-1 controls pan-neuronal gene expression directly through binding to CCAAT boxes in target gene promoters and indirectly by regulating the expression of terminal selector TFs. Further, we find that NFYA-1 regulation of neuronal gene expression is important for neuronal activity and motor function. Thus, our research sheds light on how global neuronal gene expression programs are buffered through direct and indirect regulatory mechanisms.
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Affiliation(s)
- Pedro Moreira
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Paul Papatheodorou
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Shuer Deng
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Ava Handley
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia.
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4
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Cuentas-Condori A, Chen S, Krout M, Gallik KL, Tipps J, Gailey C, Flautt L, Kim H, Mulcahy B, Zhen M, Richmond JE, Miller DM. The epithelial Na + channel UNC-8 promotes an endocytic mechanism that recycles presynaptic components to new boutons in remodeling neurons. Cell Rep 2023; 42:113327. [PMID: 37906594 PMCID: PMC10921563 DOI: 10.1016/j.celrep.2023.113327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 06/01/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
Circuit refinement involves the formation of new presynaptic boutons as others are dismantled. Nascent presynaptic sites can incorporate material from recently eliminated synapses, but the recycling mechanisms remain elusive. In early-stage C. elegans larvae, the presynaptic boutons of GABAergic DD neurons are removed and new outputs established at alternative sites. Here, we show that developmentally regulated expression of the epithelial Na+ channel (ENaC) UNC-8 in remodeling DD neurons promotes a Ca2+ and actin-dependent mechanism, involving activity-dependent bulk endocytosis (ADBE), that recycles presynaptic material for reassembly at nascent DD synapses. ADBE normally functions in highly active neurons to accelerate local recycling of synaptic vesicles. In contrast, we find that an ADBE-like mechanism results in the distal recycling of synaptic material from old to new synapses. Thus, our findings suggest that a native mechanism (ADBE) can be repurposed to dismantle presynaptic terminals for reassembly at new, distant locations.
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Affiliation(s)
- Andrea Cuentas-Condori
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Siqi Chen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Mia Krout
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kristin L Gallik
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - John Tipps
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Casey Gailey
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Leah Flautt
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Hongkyun Kim
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Janet E Richmond
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA; Neurosience Program, Vanderbilt University, Nashville, TN 37240, USA.
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5
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Sun H, Hobert O. Temporal transitions in the postembryonic nervous system of the nematode Caenorhabditis elegans: Recent insights and open questions. Semin Cell Dev Biol 2023; 142:67-80. [PMID: 35688774 DOI: 10.1016/j.semcdb.2022.05.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
After the generation, differentiation and integration into functional circuitry, post-mitotic neurons continue to change certain phenotypic properties throughout postnatal juvenile stages until an animal has reached a fully mature state in adulthood. We will discuss such changes in the context of the nervous system of the nematode C. elegans, focusing on recent descriptions of anatomical and molecular changes that accompany postembryonic maturation of neurons. We summarize the characterization of genetic timer mechanisms that control these temporal transitions or maturational changes, and discuss that many but not all of these transitions relate to sexual maturation of the animal. We describe how temporal, spatial and sex-determination pathways are intertwined to sculpt the emergence of cell-type specific maturation events. Finally, we lay out several unresolved questions that should be addressed to move the field forward, both in C. elegans and in vertebrates.
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Affiliation(s)
- Haosheng Sun
- Department of Cell, Developmental, and Integrative Biology. University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, USA
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6
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Mizumoto K, Jin Y, Bessereau JL. Synaptogenesis: unmasking molecular mechanisms using Caenorhabditis elegans. Genetics 2023; 223:iyac176. [PMID: 36630525 PMCID: PMC9910414 DOI: 10.1093/genetics/iyac176] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/22/2022] [Indexed: 01/13/2023] Open
Abstract
The nematode Caenorhabditis elegans is a research model organism particularly suited to the mechanistic understanding of synapse genesis in the nervous system. Armed with powerful genetics, knowledge of complete connectomics, and modern genomics, studies using C. elegans have unveiled multiple key regulators in the formation of a functional synapse. Importantly, many signaling networks display remarkable conservation throughout animals, underscoring the contributions of C. elegans research to advance the understanding of our brain. In this chapter, we will review up-to-date information of the contribution of C. elegans to the understanding of chemical synapses, from structure to molecules and to synaptic remodeling.
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Affiliation(s)
- Kota Mizumoto
- Department of Zoology, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Yishi Jin
- Department of Neurobiology, University of California San Diego, La Jolla, CA 92093, USA
| | - Jean-Louis Bessereau
- Univ Lyon, University Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U 1314, Melis, 69008 Lyon, France
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7
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Tocco C, Øvsthus M, Bjaalie JG, Leergaard TB, Studer M. The topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1. Development 2022; 149:274658. [PMID: 35262177 PMCID: PMC8959144 DOI: 10.1242/dev.200026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/20/2021] [Indexed: 12/27/2022]
Abstract
Axonal projections from layer V neurons of distinct neocortical areas are topographically organized into discrete clusters within the pontine nuclei during the establishment of voluntary movements. However, the molecular determinants controlling corticopontine connectivity are insufficiently understood. Here, we show that an intrinsic cortical genetic program driven by Nr2f1 graded expression is directly implicated in the organization of corticopontine topographic mapping. Transgenic mice lacking cortical expression of Nr2f1 and exhibiting areal organization defects were used as model systems to investigate the arrangement of corticopontine projections. By combining three-dimensional digital brain atlas tools, Cre-dependent mouse lines and axonal tracing, we show that Nr2f1 expression in postmitotic neurons spatially and temporally controls somatosensory topographic projections, whereas expression in progenitor cells influences the ratio between corticopontine and corticospinal fibres passing the pontine nuclei. We conclude that cortical gradients of area-patterning genes are directly implicated in the establishment of a topographic somatotopic mapping from the cortex onto pontine nuclei. Summary: Cortical gradient expression of the area patterning gene Nr2f1 spatially and temporally controls corticopontine topographic connectivity in layer V projection neurons.
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Affiliation(s)
- Chiara Tocco
- University Côte d'Azur, CNRS, Inserm, iBV, Nice 06108, France
| | - Martin Øvsthus
- Institute of Basic Medical Sciences, University of Oslo, Oslo N-0317, Norway
| | - Jan G Bjaalie
- Institute of Basic Medical Sciences, University of Oslo, Oslo N-0317, Norway
| | - Trygve B Leergaard
- Institute of Basic Medical Sciences, University of Oslo, Oslo N-0317, Norway
| | - Michèle Studer
- University Côte d'Azur, CNRS, Inserm, iBV, Nice 06108, France
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8
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Tocco C, Bertacchi M, Studer M. Structural and Functional Aspects of the Neurodevelopmental Gene NR2F1: From Animal Models to Human Pathology. Front Mol Neurosci 2022; 14:767965. [PMID: 34975398 PMCID: PMC8715095 DOI: 10.3389/fnmol.2021.767965] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 01/28/2023] Open
Abstract
The assembly and maturation of the mammalian brain result from an intricate cascade of highly coordinated developmental events, such as cell proliferation, migration, and differentiation. Any impairment of this delicate multi-factorial process can lead to complex neurodevelopmental diseases, sharing common pathogenic mechanisms and molecular pathways resulting in multiple clinical signs. A recently described monogenic neurodevelopmental syndrome named Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) is caused by NR2F1 haploinsufficiency. The NR2F1 gene, coding for a transcriptional regulator belonging to the steroid/thyroid hormone receptor superfamily, is known to play key roles in several brain developmental processes, from proliferation and differentiation of neural progenitors to migration and identity acquisition of neocortical neurons. In a clinical context, the disruption of these cellular processes could underlie the pathogenesis of several symptoms affecting BBSOAS patients, such as intellectual disability, visual impairment, epilepsy, and autistic traits. In this review, we will introduce NR2F1 protein structure, molecular functioning, and expression profile in the developing mouse brain. Then, we will focus on Nr2f1 several functions during cortical development, from neocortical area and cell-type specification to maturation of network activity, hippocampal development governing learning behaviors, assembly of the visual system, and finally establishment of cortico-spinal descending tracts regulating motor execution. Whenever possible, we will link experimental findings in animal or cellular models to corresponding features of the human pathology. Finally, we will highlight some of the unresolved questions on the diverse functions played by Nr2f1 during brain development, in order to propose future research directions. All in all, we believe that understanding BBSOAS mechanisms will contribute to further unveiling pathophysiological mechanisms shared by several neurodevelopmental disorders and eventually lead to effective treatments.
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Affiliation(s)
- Chiara Tocco
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
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9
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Wang T, Wang Z, de Fabritus L, Tao J, Saied EM, Lee HJ, Ramazanov BR, Jackson B, Burkhardt D, Parker M, Gleinich AS, Wang Z, Seo DE, Zhou T, Xu S, Alecu I, Azadi P, Arenz C, Hornemann T, Krishnaswamy S, van de Pavert SA, Kaech SM, Ivanova NB, Santori FR. 1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development. Dev Cell 2021; 56:3128-3145.e15. [PMID: 34762852 PMCID: PMC8628544 DOI: 10.1016/j.devcel.2021.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/30/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022]
Abstract
Identification of physiological modulators of nuclear hormone receptor (NHR) activity is paramount for understanding the link between metabolism and transcriptional networks that orchestrate development and cellular physiology. Using libraries of metabolic enzymes alongside their substrates and products, we identify 1-deoxysphingosines as modulators of the activity of NR2F1 and 2 (COUP-TFs), which are orphan NHRs that are critical for development of the nervous system, heart, veins, and lymphatic vessels. We show that these non-canonical alanine-based sphingolipids bind to the NR2F1/2 ligand-binding domains (LBDs) and modulate their transcriptional activity in cell-based assays at physiological concentrations. Furthermore, inhibition of sphingolipid biosynthesis phenocopies NR2F1/2 deficiency in endothelium and cardiomyocytes, and increases in 1-deoxysphingosine levels activate NR2F1/2-dependent differentiation programs. Our findings suggest that 1-deoxysphingosines are physiological regulators of NR2F1/2-mediated transcription.
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Affiliation(s)
- Ting Wang
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA; Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zheng Wang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong 266071, China; Department of Reproductive Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Lauriane de Fabritus
- Aix-Marseille Universite, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13288 Marseille Cedex 9, France
| | - Jinglian Tao
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China; Center for Molecular Medicine, Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Essa M Saied
- Institut für Chemie, Humboldt Universität zu Berlin, Berlin 12489, Germany; Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Ho-Joon Lee
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Bulat R Ramazanov
- Department of Cell Biology, Yale University, New Haven, CT 06520, USA
| | - Benjamin Jackson
- Center for Molecular Medicine, Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Daniel Burkhardt
- Department of Genetics, Yale University, New Haven, CT 06520, USA
| | - Mikhail Parker
- Center for Molecular Medicine, Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Anne S Gleinich
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Zhirui Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Dong Eun Seo
- Center for Molecular Medicine, Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Ting Zhou
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Shihao Xu
- NOMIS Center for Immunobiology and Microbial Pathogenesis, the Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Irina Alecu
- Neural Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Christoph Arenz
- Institut für Chemie, Humboldt Universität zu Berlin, Berlin 12489, Germany
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University and University Hospital of Zurich, Zurich 8091, Switzerland
| | | | - Serge A van de Pavert
- Aix-Marseille Universite, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), 13288 Marseille Cedex 9, France
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, the Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Natalia B Ivanova
- Center for Molecular Medicine, Department of Genetics, University of Georgia, Athens, GA 30602, USA.
| | - Fabio R Santori
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA.
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10
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Hobert O. Homeobox genes and the specification of neuronal identity. Nat Rev Neurosci 2021; 22:627-636. [PMID: 34446866 DOI: 10.1038/s41583-021-00497-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2021] [Indexed: 12/27/2022]
Abstract
The enormous diversity of cell types that characterizes any animal nervous system is defined by neuron-type-specific gene batteries that endow cells with distinct anatomical and functional properties. To understand how such cellular diversity is genetically specified, one needs to understand the gene regulatory programmes that control the expression of cell-type-specific gene batteries. The small nervous system of the nematode Caenorhabditis elegans has been comprehensively mapped at the cellular and molecular levels, which has enabled extensive, nervous system-wide explorations into whether there are common underlying mechanisms that specify neuronal cell-type diversity. One principle that emerged from these studies is that transcription factors termed 'terminal selectors' coordinate the expression of individual members of neuron-type-specific gene batteries, thereby assigning unique identities to individual neuron types. Systematic mutant analyses and recent nervous system-wide expression analyses have revealed that one transcription factor family, the homeobox gene family, is broadly used throughout the entire C. elegans nervous system to specify neuronal identity as terminal selectors. I propose that the preponderance of homeobox genes in neuronal identity control is a reflection of an evolutionary trajectory in which an ancestral neuron type was specified by one or more ancestral homeobox genes, and that this functional linkage then duplicated and diversified to generate distinct cell types in an evolving nervous system.
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Affiliation(s)
- Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY, USA.
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11
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Miller-Fleming TW, Cuentas-Condori A, Manning L, Palumbos S, Richmond JE, Miller DM. Transcriptional Control of Parallel-Acting Pathways That Remove Specific Presynaptic Proteins in Remodeling Neurons. J Neurosci 2021; 41:5849-5866. [PMID: 34045310 PMCID: PMC8265810 DOI: 10.1523/jneurosci.0893-20.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/29/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
Synapses are actively dismantled to mediate circuit refinement, but the developmental pathways that regulate synaptic disassembly are largely unknown. We have previously shown that the epithelial sodium channel ENaC/UNC-8 triggers an activity-dependent mechanism that drives the removal of presynaptic proteins liprin-α/SYD-2, Synaptobrevin/SNB-1, RAB-3, and Endophilin/UNC-57 in remodeling GABAergic neurons in Caenorhabditis elegans (Miller-Fleming et al., 2016). Here, we report that the conserved transcription factor Iroquois/IRX-1 regulates UNC-8 expression as well as an additional pathway, independent of UNC-8, that functions in parallel to dismantle functional presynaptic terminals. We show that the additional IRX-1-regulated pathway is selectively required for the removal of the presynaptic proteins, Munc13/UNC-13 and ELKS, which normally mediate synaptic vesicle (SV) fusion and neurotransmitter release. Our findings are notable because they highlight the key role of transcriptional regulation in synapse elimination during development and reveal parallel-acting pathways that coordinate synaptic disassembly by removing specific active zone proteins.SIGNIFICANCE STATEMENT Synaptic pruning is a conserved feature of developing neural circuits but the mechanisms that dismantle the presynaptic apparatus are largely unknown. We have determined that synaptic disassembly is orchestrated by parallel-acting mechanisms that target distinct components of the active zone. Thus, our finding suggests that synaptic disassembly is not accomplished by en masse destruction but depends on mechanisms that dismantle the structure in an organized process.
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Affiliation(s)
| | - Andrea Cuentas-Condori
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37212
| | - Laura Manning
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Sierra Palumbos
- Neuroscience Program, Vanderbilt University, Nashville, Tennessee 37212
| | - Janet E Richmond
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
| | - David M Miller
- Neuroscience Program, Vanderbilt University, Nashville, Tennessee 37212
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37212
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12
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Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM. Molecular topography of an entire nervous system. Cell 2021; 184:4329-4347.e23. [PMID: 34237253 DOI: 10.1016/j.cell.2021.06.023] [Citation(s) in RCA: 305] [Impact Index Per Article: 101.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/09/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses distinct codes of ∼23 neuropeptide genes and ∼36 neuropeptide receptors, delineating a complex and expansive "wireless" signaling network. To demonstrate the utility of this comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression and (2) reveal adhesion proteins with potential roles in process placement and synaptic specificity. Our expression data are available at https://cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity, and function throughout the C. elegans nervous system.
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Affiliation(s)
- Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Alexis Weinreb
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Alec Barrett
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Chuan Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Erdem Varol
- Department of Statistics, Columbia University, New York, NY, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Lori Glenwinkel
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Abigail Poff
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Manasa Basavaraju
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Steven J Cook
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Alexander Abrams
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Berta Vidal
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Cyril Cros
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Marc Hammarlund
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA.
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13
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Berghoff EG, Glenwinkel L, Bhattacharya A, Sun H, Varol E, Mohammadi N, Antone A, Feng Y, Nguyen K, Cook SJ, Wood JF, Masoudi N, Cros CC, Ramadan YH, Ferkey DM, Hall DH, Hobert O. The Prop1-like homeobox gene unc-42 specifies the identity of synaptically connected neurons. eLife 2021; 10:e64903. [PMID: 34165428 PMCID: PMC8225392 DOI: 10.7554/elife.64903] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Many neuronal identity regulators are expressed in distinct populations of cells in the nervous system, but their function is often analyzed only in specific isolated cellular contexts, thereby potentially leaving overarching themes in gene function undiscovered. We show here that the Caenorhabditis elegans Prop1-like homeobox gene unc-42 is expressed in 15 distinct sensory, inter- and motor neuron classes throughout the entire C. elegans nervous system. Strikingly, all 15 neuron classes expressing unc-42 are synaptically interconnected, prompting us to investigate whether unc-42 controls the functional properties of this circuit and perhaps also the assembly of these neurons into functional circuitry. We found that unc-42 defines the routes of communication between these interconnected neurons by controlling the expression of neurotransmitter pathway genes, neurotransmitter receptors, neuropeptides, and neuropeptide receptors. Anatomical analysis of unc-42 mutant animals reveals defects in axon pathfinding and synaptic connectivity, paralleled by expression defects of molecules involved in axon pathfinding, cell-cell recognition, and synaptic connectivity. We conclude that unc-42 establishes functional circuitry by acting as a terminal selector of functionally connected neuron types. We identify a number of additional transcription factors that are also expressed in synaptically connected neurons and propose that terminal selectors may also function as 'circuit organizer transcription factors' to control the assembly of functional circuitry throughout the nervous system. We hypothesize that such organizational properties of transcription factors may be reflective of not only ontogenetic, but perhaps also phylogenetic trajectories of neuronal circuit establishment.
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Affiliation(s)
- Emily G Berghoff
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Lori Glenwinkel
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Abhishek Bhattacharya
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - HaoSheng Sun
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Erdem Varol
- Department of Statistics, Zuckerman Institute, Columbia UniversityNew YorkUnited States
| | - Nicki Mohammadi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Amelia Antone
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Yi Feng
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Ken Nguyen
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
| | - Steven J Cook
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Jordan F Wood
- Department of Biological Sciences, University at Buffalo, The State University of New YorkBuffaloUnited States
| | - Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Cyril C Cros
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Yasmin H Ramadan
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, The State University of New YorkBuffaloUnited States
| | - David H Hall
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
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14
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Chen C, Fu H, He P, Yang P, Tu H. Extracellular Matrix Muscle Arm Development Defective Protein Cooperates with the One Immunoglobulin Domain Protein To Suppress Precocious Synaptic Remodeling. ACS Chem Neurosci 2021; 12:2045-2056. [PMID: 34019371 DOI: 10.1021/acschemneuro.1c00194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Synaptic remodeling plays important roles in health and neural disorders. Although previous studies revealed that several transcriptional programs control synaptic remodeling in the nematode Caenorhabditis elegans, the molecular mechanisms of the dorsal D-type (DD) synaptic remodeling are poorly understood. Here we show that extracellular matrix molecule muscle arm development defective protein-4 (MADD-4) cooperates with the one immunoglobulin domain protein-1 (OIG-1) to defer precocious DD synaptic remodeling. Specifically, loss of MADD-4 exhibited the precocious DD synaptic remodeling. The long isoform MADD-4L is dynamically expressed while the short isoform MADD-4B is persistently expressed in DD neurons of L1 stage. In the unc-30 mutant lacking the Pitx-type homeodomain transcription factor UNC-30, the expression levels of both MADD-4B and -L isoforms were dramatically downregulated in DD neurons of the L1 stage. Our further data showed that MADD-4B and -L isoforms physically interact with OIG-1 and madd-4 acts in the oig-1 genetic pathway to modulate the DD synaptic remodeling. Our findings demonstrated that the extracellular matrix plays a novel role in synaptic plasticity.
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Affiliation(s)
- Chunhong Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Neuroscience, College of Biology, Hunan University, 410082 Changsha, Hunan, China
| | - Huiyuan Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Neuroscience, College of Biology, Hunan University, 410082 Changsha, Hunan, China
| | - Ping He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Neuroscience, College of Biology, Hunan University, 410082 Changsha, Hunan, China
| | - Peng Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Neuroscience, College of Biology, Hunan University, 410082 Changsha, Hunan, China
| | - Haijun Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Neuroscience, College of Biology, Hunan University, 410082 Changsha, Hunan, China
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15
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Tsironis I, Paganos P, Gouvi G, Tsimpos P, Stamopoulou A, Arnone MI, Flytzanis CN. Coup-TF: A maternal factor essential for differentiation along the embryonic axes in the sea urchin Paracentrotus lividus. Dev Biol 2021; 475:131-144. [PMID: 33484706 DOI: 10.1016/j.ydbio.2020.12.012] [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: 07/04/2020] [Revised: 11/27/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
Coup-TF, a member of the nuclear receptor super-family, is present in the pool of maternal mRNAs and proteins in the sea urchin egg. The presence of this protein seems to be essential for the execution of the early developmental program, leading to all three embryonic layers. Our results demonstrate that Pl-Coup-TF morphants, i.e. Pl-Coup-TF morpholino knockdown embryos, resemble blastulae that lack archenteron at 24 hpf (hours post fertilization), a stage at which normal embryos reach the end of gastrulation in Paracentrotus lividus. At 48 hpf, when normal embryos reach the pluteus larva stage, the morphants are seemingly underdeveloped and lack the characteristic skeletal rods. Nevertheless, the morphant embryos express vegetal endomesodermal marker genes, such as Pl-Blimp1, Pl-Endo16, Pl-Alx1 and Pl-Tbr as judged by in situ hybridization experiments. The anterior neuroectoderm genes, Pl-FoxQ2, Pl-Six3 and Pl-Pax6, are also expressed in the morphant embryos, but Pl-Hbn and Pl-Fez mRNAs, which encode proteins significant for the differentiation of serotonergic neurons, are not detected. Consequently, Pl-Coup-TF morphants at 48 hpf lack serotonergic neurons, whereas normal 48 hpf plutei exhibit the formation of two bilateral pairs of such neurons in the apical organ. Furthermore, genes indicative of the ciliary band formation, Pl-Hnf6, Pl-Dri, Pl-FoxG and Pl-Otx, are not expressed in Pl-Coup-TF morphants, suggesting the disruption of this neurogenic territory as well. In addition, the Pl-SynB gene, a marker of differentiated neurons, is silent leading to the hypothesis that Pl-Coup-TF morphants might lack all types of neurons. On the contrary, the genes expressing signaling molecules, which establish the ventral/dorsal axis, Pl-Nodal and Pl-Lefty show the characteristic ventral lateral expression pattern, Pl-Bmp2/4, which activates the dorsal ectoderm GRN is down-regulated and Pl-Chordin is aberrantly over-expressed in the entire ectoderm. The identity of ectodermal cells in Pl-Coup-TF morphant embryos, was probed for expression of the ventral marker Pl-Gsc which was over-expressed and dorsal markers, Pl-IrxA and Pl-Hox7, which were silent. Therefore, we propose that maternal Pl-Coup-TF is essential for correct dissemination of the early embryonic signaling along both animal/vegetal and ventral/dorsal axes. Limiting Pl-Coup-TF's quantity, results in an embryo without digestive and nervous systems, skeleton and ciliary band that cannot survive past the initial 48 h of development.
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Affiliation(s)
- Ioannis Tsironis
- Department of Biology, University of Patras, Patras, 26500, Greece
| | - Periklis Paganos
- Department of Biology, University of Patras, Patras, 26500, Greece; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Georgia Gouvi
- Department of Biology, University of Patras, Patras, 26500, Greece
| | | | | | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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16
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Rossillo M, Ringstad N. Development of specialized sensory neurons engages a nuclear receptor required for functional plasticity. Genes Dev 2020; 34:1666-1679. [PMID: 33184226 PMCID: PMC7706712 DOI: 10.1101/gad.342212.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022]
Abstract
In this study, Rossillo and Ringstad sought to determine mechanisms that support the physiology and plasticity of BAG neurons, which are specialized neurons that sense the respiratory gas carbon dioxide (CO2) and, in a context-dependent manner, switch from mediating avoidance of CO2 to supporting CO2 attraction in C. elegans. They used tandem ChIP-seq and cell targeted RNA-seq to identify gene targets of the transcription factor ETS-5, which is required for BAG development, and their functional screen of ETS-5 targets revealed that NHR-6, the sole C. elegans NR4A-type nuclear receptor, is required for BAG-mediated avoidance of CO2 and regulates expression of a subset of BAG-specific genes. During development, the nervous system generates neurons that serve highly specialized roles and, accordingly, possess unique functional attributes. The chemosensory BAG neurons of C. elegans are striking exemplars of this. BAGs sense the respiratory gas carbon dioxide (CO2) and, in a context-dependent manner, switch from mediating avoidance of CO2 to supporting CO2 attraction. To determine mechanisms that support the physiology and plasticity of BAG neurons, we used tandem ChIP-seq and cell targeted RNA-seq to identify gene targets of the transcription factor ETS-5, which is required for BAG development. A functional screen of ETS-5 targets revealed that NHR-6, the sole C. elegans NR4A-type nuclear receptor, is required for BAG-mediated avoidance of CO2 and regulates expression of a subset of BAG-specific genes. Unlike ets-5 mutants, which are defective for both attraction to and avoidance of CO2, nhr-6 mutants are fully competent for attraction. These data indicate that the remarkable ability of BAGs to adaptively assign positive or negative valence to a chemosensory stimulus requires a gene-regulatory program supported by an evolutionarily conserved type of nuclear receptor. We suggest that NHR-6 might be an example of a developmental mechanism for modular encoding of functional plasticity in the nervous system.
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Affiliation(s)
- Mary Rossillo
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Niels Ringstad
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, New York 10016, USA
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17
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Cuentas-Condori A, Miller Rd DM. Synaptic remodeling, lessons from C. elegans. J Neurogenet 2020; 34:307-322. [PMID: 32808848 PMCID: PMC7855814 DOI: 10.1080/01677063.2020.1802725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023]
Abstract
Sydney Brenner's choice of Caenorhabditis elegans as a model organism for understanding the nervous system has accelerated discoveries of gene function in neural circuit development and behavior. In this review, we discuss a striking example of synaptic remodeling in the C. elegans motor circuit in which DD class motor neurons effectively reverse polarity as presynaptic and postsynaptic domains at opposite ends of the DD neurite switch locations. Originally revealed by EM reconstruction conducted over 40 years ago, DD remodeling has since been investigated by live cell imaging methods that exploit the power of C. elegans genetics to reveal key effectors of synaptic plasticity. Although synapses are also extensively rewired in developing mammalian circuits, the underlying remodeling mechanisms are largely unknown. Here, we highlight the possibility that studies in C. elegans can reveal pathways that orchestrate synaptic remodeling in more complex organisms. Specifically, we describe (1) transcription factors that regulate DD remodeling, (2) the cellular and molecular cascades that drive synaptic remodeling and (3) examples of circuit modifications in vertebrate neurons that share some similarities with synaptic remodeling in C. elegans DD neurons.
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18
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Lorenzo R, Onizuka M, Defrance M, Laurent P. Combining single-cell RNA-sequencing with a molecular atlas unveils new markers for Caenorhabditis elegans neuron classes. Nucleic Acids Res 2020; 48:7119-7134. [PMID: 32542321 PMCID: PMC7367206 DOI: 10.1093/nar/gkaa486] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) of the Caenorhabditis elegans nervous system offers the unique opportunity to obtain a partial expression profile for each neuron within a known connectome. Building on recent scRNA-seq data and on a molecular atlas describing the expression pattern of ∼800 genes at the single cell resolution, we designed an iterative clustering analysis aiming to match each cell-cluster to the ∼100 anatomically defined neuron classes of C. elegans. This heuristic approach successfully assigned 97 of the 118 neuron classes to a cluster. Sixty two clusters were assigned to a single neuron class and 15 clusters grouped neuron classes sharing close molecular signatures. Pseudotime analysis revealed a maturation process occurring in some neurons (e.g. PDA) during the L2 stage. Based on the molecular profiles of all identified neurons, we predicted cell fate regulators and experimentally validated unc-86 for the normal differentiation of RMG neurons. Furthermore, we observed that different classes of genes functionally diversify sensory neurons, interneurons and motorneurons. Finally, we designed 15 new neuron class-specific promoters validated in vivo. Amongst them, 10 represent the only specific promoter reported to this day, expanding the list of neurons amenable to genetic manipulations.
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Affiliation(s)
- Ramiro Lorenzo
- Laboratory of Neurophysiology, ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Michiho Onizuka
- Laboratory of Neurophysiology, ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Matthieu Defrance
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Patrick Laurent
- Laboratory of Neurophysiology, ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Brussels, Belgium
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19
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Cuentas-Condori A, Mulcahy B, He S, Palumbos S, Zhen M, Miller DM. C. elegans neurons have functional dendritic spines. eLife 2019; 8:e47918. [PMID: 31584430 PMCID: PMC6802951 DOI: 10.7554/elife.47918] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022] Open
Abstract
Dendritic spines are specialized postsynaptic structures that transduce presynaptic signals, are regulated by neural activity and correlated with learning and memory. Most studies of spine function have focused on the mammalian nervous system. However, spine-like protrusions have been reported in C. elegans (Philbrook et al., 2018), suggesting that the experimental advantages of smaller model organisms could be exploited to study the biology of dendritic spines. Here, we used super-resolution microscopy, electron microscopy, live-cell imaging and genetics to show that C. elegans motor neurons have functional dendritic spines that: (1) are structurally defined by a dynamic actin cytoskeleton; (2) appose presynaptic dense projections; (3) localize ER and ribosomes; (4) display calcium transients triggered by presynaptic activity and propagated by internal Ca++ stores; (5) respond to activity-dependent signals that regulate spine density. These studies provide a solid foundation for a new experimental paradigm that exploits the power of C. elegans genetics and live-cell imaging for fundamental studies of dendritic spine morphogenesis and function.
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Affiliation(s)
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research InstituteUniversity of TorontoTorontoCanada
| | - Siwei He
- Neuroscience ProgramVanderbilt UniversityNashvilleUnited States
| | - Sierra Palumbos
- Neuroscience ProgramVanderbilt UniversityNashvilleUnited States
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research InstituteUniversity of TorontoTorontoCanada
| | - David M Miller
- Department of Cell and Developmental BiologyVanderbilt UniversityNashvilleUnited States
- Neuroscience ProgramVanderbilt UniversityNashvilleUnited States
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20
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Catela C, Kratsios P. Transcriptional mechanisms of motor neuron development in vertebrates and invertebrates. Dev Biol 2019; 475:193-204. [PMID: 31479648 DOI: 10.1016/j.ydbio.2019.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 07/08/2019] [Accepted: 08/29/2019] [Indexed: 02/04/2023]
Abstract
Across phylogeny, motor neurons (MNs) represent a single but often remarkably diverse neuronal class composed of a multitude of subtypes required for vital behaviors, such as eating and locomotion. Over the past decades, seminal studies in multiple model organisms have advanced our molecular understanding of the early steps of MN development, such as progenitor specification and acquisition of MN subtype identity, by revealing key roles for several evolutionarily conserved transcription factors. However, very little is known about the molecular strategies that allow distinct MN subtypes to maintain their identity- and function-defining features during the late steps of development and postnatal life. Here, we provide an overview of invertebrate and vertebrate studies on transcription factor-based strategies that control early and late steps of MN development, aiming to highlight evolutionarily conserved gene regulatory principles necessary for establishment and maintenance of neuronal identity.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, IL, 60637, USA; The Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, 60637, USA; The Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA.
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21
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Ferguson GD, Bridge WJ. The glutathione system and the related thiol network in Caenorhabditis elegans. Redox Biol 2019. [DOI: 10.1110.1016/j.redox.2019.101171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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22
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Ferguson GD, Bridge WJ. The glutathione system and the related thiol network in Caenorhabditis elegans. Redox Biol 2019; 24:101171. [PMID: 30901603 PMCID: PMC6429583 DOI: 10.1016/j.redox.2019.101171] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/07/2019] [Accepted: 03/13/2019] [Indexed: 01/09/2023] Open
Abstract
Advances in the field of redox biology have contributed to the understanding of the complexity of the thiol-based system in mediating signal transduction. The redox environment is the overall spatiotemporal balance of oxidation-reduction systems within the integrated compartments of the cell, tissues and whole organisms. The ratio of the reduced to disulfide glutathione redox couple (GSH:GSSG) is a key indicator of the redox environment and its associated cellular health. The reaction mechanisms of glutathione-dependent and related thiol-based enzymes play a fundamental role in the function of GSH as a redox regulator. Glutathione homeostasis is maintained by the balance of GSH synthesis (de novo and salvage pathways) and its utilization through its detoxification, thiol signalling, and antioxidant defence functions via GSH-dependent enzymes and free radical scavenging. As such, GSH acts in concert with the entire redox network to maintain reducing conditions in the cell. Caenorhabditis elegans offers a simple model to facilitate further understanding at the multicellular level of the physiological functions of GSH and the GSH-dependent redox network. This review discusses the C. elegans studies that have investigated glutathione and related systems of the redox network including; orthologs to the protein-encoding genes of GSH synthesis; glutathione peroxidases; glutathione-S-transferases; and the glutaredoxin, thioredoxin and peroxiredoxin systems.
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Affiliation(s)
- Gavin Douglas Ferguson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Wallace John Bridge
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.
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23
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Philbrook A, Ramachandran S, Lambert CM, Oliver D, Florman J, Alkema MJ, Lemons M, Francis MM. Neurexin directs partner-specific synaptic connectivity in C. elegans. eLife 2018; 7:35692. [PMID: 30039797 PMCID: PMC6057746 DOI: 10.7554/elife.35692] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/21/2018] [Indexed: 01/14/2023] Open
Abstract
In neural circuits, individual neurons often make projections onto multiple postsynaptic partners. Here, we investigate molecular mechanisms by which these divergent connections are generated, using dyadic synapses in C. elegans as a model. We report that C. elegans nrx-1/neurexin directs divergent connectivity through differential actions at synapses with partnering neurons and muscles. We show that cholinergic outputs onto neurons are, unexpectedly, located at previously undefined spine-like protrusions from GABAergic dendrites. Both these spine-like features and cholinergic receptor clustering are strikingly disrupted in the absence of nrx-1. Excitatory transmission onto GABAergic neurons, but not neuromuscular transmission, is also disrupted. Our data indicate that NRX-1 located at presynaptic sites specifically directs postsynaptic development in GABAergic neurons. Our findings provide evidence that individual neurons can direct differential patterns of connectivity with their post-synaptic partners through partner-specific utilization of synaptic organizers, offering a novel view into molecular control of divergent connectivity. Nervous systems are complex networks of interconnected cells called neurons. These networks vary in size from a few hundred cells in worms, to tens of billions in the human brain. Within these networks, each individual neuron forms connections – called synapses – with many others. But these partner neurons are not necessarily alike. In fact, they may be different cell types. How neurons form distinct connections with different partner cells remains unclear. Part of the answer may lie in specialized proteins called cell adhesion molecules. These proteins occur on the cell surface and enable neurons to recognize one another. This helps ensure that the cells form appropriate connections via synapses. Cell adhesion molecules are therefore also known as synaptic organizers. Philbrook et al. have now examined the role of synaptic organizers in wiring up the nervous system of the nematode worm and model organism Caenorhabditis elegans. Motor neurons form connections with two types of partner cell: muscle cells and neurons. Philbrook et al. screened C. elegans that have mutations in genes encoding various synaptic organizers. This revealed that a protein called neurexin must be present for motor neurons to form synapses with other neurons. By contrast, neurexin is not required for the same neurons to establish synapses with muscles. Philbrook et al. found that neuron-to-neuron synapses arise at specialized finger-like projections. These resemble the dendritic spines at which synapses form in the brains of mammals, and had not been previously identified in C. elegans. In worms that lack neurexin, these spine-like structures do not form correctly, disrupting the formation of neuron-to-neuron connections. Previous work has implicated neurexin in synapse formation in the mammalian brain. But this is the first study to reveal a role for neurexin in establishing partner-specific synaptic connections. Mutations in synaptic organizers, including neurexin, contribute to disorders of brain development. These include schizophrenia and autism spectrum disorders. Learning more about how neurexin helps establish specific synaptic connections may help us understand how these disorders arise.
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Affiliation(s)
- Alison Philbrook
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Shankar Ramachandran
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Christopher M Lambert
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Devyn Oliver
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Jeremy Florman
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Mark J Alkema
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Michele Lemons
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States.,Department of Natural Sciences, Assumption College, Worcester, United States
| | - Michael M Francis
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
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24
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Jin Y, Qi YB. Building stereotypic connectivity: mechanistic insights into structural plasticity from C. elegans. Curr Opin Neurobiol 2017; 48:97-105. [PMID: 29182952 DOI: 10.1016/j.conb.2017.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 11/07/2017] [Accepted: 11/14/2017] [Indexed: 01/10/2023]
Abstract
The ability of neurons to modify or remodel their synaptic connectivity is critical for the function of neural circuitry throughout the life of an animal. Understanding the mechanisms underlying neuronal structural changes is central to our knowledge of how the nervous system is shaped for complex behaviors and how it further adapts to developmental and environmental demands. Caenorhabditis elegans provides a powerful model for examining developmental processes and for discovering mechanisms controlling neural plasticity. Recent findings have identified conserved themes underlying neural plasticity in development and under environmental stress.
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Affiliation(s)
- Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Yingchuan B Qi
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
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25
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Yu B, Wang X, Wei S, Fu T, Dzakah EE, Waqas A, Walthall WW, Shan G. Convergent Transcriptional Programs Regulate cAMP Levels in C. elegans GABAergic Motor Neurons. Dev Cell 2017; 43:212-226.e7. [PMID: 29033363 DOI: 10.1016/j.devcel.2017.09.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/26/2017] [Accepted: 09/15/2017] [Indexed: 02/07/2023]
Abstract
Both transcriptional regulation and signaling pathways play crucial roles in neuronal differentiation and plasticity. Caenorhabditis elegans possesses 19 GABAergic motor neurons (MNs) called D MNs, which are divided into two subgroups: DD and VD. DD, but not VD, MNs reverse their cellular polarity in a developmental process called respecification. UNC-30 and UNC-55 are two critical transcription factors in D MNs. By using chromatin immunoprecipitation with CRISPR/Cas9 knockin of GFP fusion, we uncovered the global targets of UNC-30 and UNC-55. UNC-30 and UNC-55 are largely converged to regulate over 1,300 noncoding and coding genes, and genes in multiple biological processes, including cAMP metabolism, are co-regulated. Increase in cAMP levels may serve as a timing signal for respecification, whereas UNC-55 regulates genes such as pde-4 to keep the cAMP levels low in VD. Other genes modulating DD respecification such as lin-14, irx-1, and oig-1 are also found to affect cAMP levels.
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Affiliation(s)
- Bin Yu
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Xiaolin Wang
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Shuai Wei
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Tao Fu
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Emmanuel Enoch Dzakah
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Ahmed Waqas
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Walter W Walthall
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China.
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26
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Meng J, Ma X, Tao H, Jin X, Witvliet D, Mitchell J, Zhu M, Dong MQ, Zhen M, Jin Y, Qi YB. Myrf ER-Bound Transcription Factors Drive C. elegans Synaptic Plasticity via Cleavage-Dependent Nuclear Translocation. Dev Cell 2017; 41:180-194.e7. [PMID: 28441531 DOI: 10.1016/j.devcel.2017.03.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 01/20/2017] [Accepted: 02/24/2017] [Indexed: 11/16/2022]
Abstract
Synaptic refinement is a critical step in nervous system maturation, requiring a carefully timed reorganization and refinement of neuronal connections. We have identified myrf-1 and myrf-2, two C. elegans homologs of Myrf family transcription factors, as key regulators of synaptic rewiring. MYRF-1 and its paralog MYRF-2 are functionally redundant specifically in synaptic rewiring. They co-exist in the same protein complex and act cooperatively to regulate synaptic rewiring. We find that the MYRF proteins localize to the ER membrane and that they are cleaved into active N-terminal fragments, which then translocate into the nucleus to drive synaptic rewiring. Overexpression of active forms of MYRF is sufficient to accelerate synaptic rewiring. MYRF-1 and MYRF-2 are the first genes identified to be indispensable for promoting synaptic rewiring in C. elegans. These findings reveal a molecular mechanism underlying synaptic rewiring and developmental circuit plasticity.
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Affiliation(s)
- Jun Meng
- Institute of Developmental and Regenerative Biology, Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xiaoxia Ma
- Institute of Developmental and Regenerative Biology, Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Huaping Tao
- Institute of Developmental and Regenerative Biology, Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xia Jin
- Institute of Developmental and Regenerative Biology, Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Daniel Witvliet
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - James Mitchell
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Mei Zhen
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yishi Jin
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yingchuan B Qi
- Institute of Developmental and Regenerative Biology, Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
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27
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Zuckerman B, Abergel Z, Zelmanovich V, Romero L, Abergel R, Livshits L, Smith Y, Gross E. Characterization of gene expression associated with the adaptation of the nematode C. elegans to hypoxia and reoxygenation stress reveals an unexpected function of the neuroglobin GLB-5 in innate immunity. Free Radic Biol Med 2017; 108:858-873. [PMID: 28495447 DOI: 10.1016/j.freeradbiomed.2017.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 04/27/2017] [Accepted: 05/07/2017] [Indexed: 01/05/2023]
Abstract
Oxygen (O2) is a double-edged sword to cells, for while it is vital for energy production in all aerobic animals and insufficient O2 (hypoxia) can lead to cell death, the reoxygenation of hypoxic tissues may trigger the generation of reactive oxygen species (ROS) that can destroy any biological molecule. Indeed, both hypoxia and hypoxia-reoxygenation (H/R) stress are harmful, and may play a critical role in the pathophysiology of many human diseases, such as myocardial ischemia and stroke. Therefore, understanding how animals adapt to hypoxia and H/R stress is critical for developing better treatments for these diseases. Previous studies showed that the neuroglobin GLB-5(Haw) is essential for the fast recovery of the nematode Caenorhabditis elegans (C. elegans) from H/R stress. Here, we characterize the changes in neuronal gene expression during the adaptation of worms to hypoxia and recovery from H/R stress. Our analysis shows that innate immunity genes are differentially expressed during both adaptation to hypoxia and recovery from H/R stress. Moreover, we reveal that the prolyl hydroxylase EGL-9, a known regulator of both adaptation to hypoxia and the innate immune response, inhibits the fast recovery from H/R stress through its activity in the O2-sensing neurons AQR, PQR, and URX. Finally, we show that GLB-5(Haw) acts in AQR, PQR, and URX to increase the tolerance of worms to Pseudomonas aeruginosa pathogenesis. Together, our studies suggest that innate immunity and recovery from H/R stress are regulated by overlapping signaling pathways.
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Affiliation(s)
- Binyamin Zuckerman
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, P.O. Box 12271, Jerusalem, 9112102 Israel
| | - Zohar Abergel
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, P.O. Box 12271, Jerusalem, 9112102 Israel
| | - Veronica Zelmanovich
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, P.O. Box 12271, Jerusalem, 9112102 Israel
| | - Leonor Romero
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, P.O. Box 12271, Jerusalem, 9112102 Israel
| | - Rachel Abergel
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, P.O. Box 12271, Jerusalem, 9112102 Israel
| | - Leonid Livshits
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, P.O. Box 12271, Jerusalem, 9112102 Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University - Hadassah Medical School, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Einav Gross
- Dept. of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, P.O. Box 12271, Jerusalem, 9112102 Israel.
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28
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Campbell RF, Walthall WW. Meis/UNC-62 isoform dependent regulation of CoupTF-II/UNC-55 and GABAergic motor neuron subtype differentiation. Dev Biol 2016; 419:250-261. [PMID: 27634571 DOI: 10.1016/j.ydbio.2016.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/24/2016] [Accepted: 09/09/2016] [Indexed: 11/28/2022]
Abstract
Gene regulatory networks orchestrate the assembly of functionally related cells within a cellular network. Subtle differences often exist among functionally related cells within such networks. How differences are created among cells with similar functions has been difficult to determine due to the complexity of both the gene and the cellular networks. In Caenorhabditis elegans, the DD and VD motor neurons compose a cross-inhibitory, GABAergic network that coordinates dorsal and ventral muscle contractions during locomotion. The Pitx2 homologue, UNC-30, acts as a terminal selector gene to create similarities and the Coup-TFII homologue, UNC-55, is necessary for creating differences between the two motor neuron classes. What is the organizing gene regulatory network responsible for initiating the expression of UNC-55 and thus creating differences between the DD and VD motor neurons? We show that the unc-55 promoter has modules that contain Meis/UNC-62 binding sites. These sites can be subdivided into regions that are capable of activating or repressing UNC-55 expression in different motor neurons. Interestingly, different isoforms of UNC-62 are responsible for the activation and the stabilization of unc-55 transcription. Furthermore, specific isoforms of UNC-62 are required for proper synaptic patterning of the VD motor neurons. Isoform specific regulation of differentiating neurons is a relatively unexplored area of research and presents a mechanism for creating differences among functionally related cells within a network.
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MESH Headings
- Animals
- Animals, Genetically Modified
- CRISPR-Cas Systems
- Caenorhabditis elegans/genetics
- Caenorhabditis elegans/physiology
- Caenorhabditis elegans Proteins/biosynthesis
- Caenorhabditis elegans Proteins/physiology
- GABAergic Neurons/cytology
- Gene Expression Regulation, Developmental
- Gene Regulatory Networks/genetics
- Genes, Reporter
- Homeodomain Proteins/physiology
- Motor Neurons/classification
- Motor Neurons/cytology
- Neurogenesis/genetics
- Promoter Regions, Genetic/genetics
- Protein Isoforms/physiology
- RNA, Helminth/biosynthesis
- RNA, Helminth/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/physiology
- Receptors, Cytoplasmic and Nuclear/biosynthesis
- Receptors, Cytoplasmic and Nuclear/physiology
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Transcription Factors
- Transcription, Genetic/genetics
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Richard F Campbell
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Walter W Walthall
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States.
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29
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Miller-Fleming TW, Petersen SC, Manning L, Matthewman C, Gornet M, Beers A, Hori S, Mitani S, Bianchi L, Richmond J, Miller DM. The DEG/ENaC cation channel protein UNC-8 drives activity-dependent synapse removal in remodeling GABAergic neurons. eLife 2016; 5. [PMID: 27403890 PMCID: PMC4980115 DOI: 10.7554/elife.14599] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/11/2016] [Indexed: 12/30/2022] Open
Abstract
Genetic programming and neural activity drive synaptic remodeling in developing neural circuits, but the molecular components that link these pathways are poorly understood. Here we show that the C. elegans Degenerin/Epithelial Sodium Channel (DEG/ENaC) protein, UNC-8, is transcriptionally controlled to function as a trigger in an activity-dependent mechanism that removes synapses in remodeling GABAergic neurons. UNC-8 cation channel activity promotes disassembly of presynaptic domains in DD type GABA neurons, but not in VD class GABA neurons where unc-8 expression is blocked by the COUP/TF transcription factor, UNC-55. We propose that the depolarizing effect of UNC-8-dependent sodium import elevates intracellular calcium in a positive feedback loop involving the voltage-gated calcium channel UNC-2 and the calcium-activated phosphatase TAX-6/calcineurin to initiate a caspase-dependent mechanism that disassembles the presynaptic apparatus. Thus, UNC-8 serves as a link between genetic and activity-dependent pathways that function together to promote the elimination of GABA synapses in remodeling neurons. DOI:http://dx.doi.org/10.7554/eLife.14599.001 The brain contains billions of nerve cells, or neurons, that communicate with one another through connections called synapses. As the brain develops, these circuits are extensively modified as new synapses are created and others are removed. Neurological disorders may emerge if these processes are not regulated correctly. Identifying the biological pathways that control the addition and removal of synapses could therefore provide new insights into how to treat human brain diseases. To communicate across a synapse, the signaling neuron releases chemicals called neurotransmitters that alter the activity of the receiving neuron. Some neurotransmitters, such as GABA, inhibit the activity of the receiving neuron. The activity of a neuron – and hence how often it releases neurotransmitters – depends on different ions moving into and out of the neuron through proteins called ion channels that are embedded in the cell membrane. For example, the movement of calcium ions into the neuron can trigger the release of neurotransmitters. The roundworm Caenorhabditis elegans is often used as a model organism to study how the brain develops. During development, the worm nervous system eliminates synapses that release GABA and reassembles them at new locations. However, the nervous system does not eliminate these synapses at random. Miller-Fleming, Petersen et al. now show that a C. elegans protein called UNC-8 is responsible for this effect. UNC-8 forms part of an ion channel that allows sodium ions to enter the neuron and is selectively produced in GABA neurons that are destined for remodeling. Miller-Fleming, Petersen et al. found that inside GABA-releasing neurons, calcium ions stimulate an enzyme called calcineurin that may in turn activate UNC-8. Sodium ions then enter the neuron through UNC-8 channels. This boosts the activity of the calcium ion channels, which further increases how many calcium ions enter the cell. Ultimately, the amount of calcium inside the neuron becomes high enough to activate an additional pathway that eliminates the synapse. This downstream pathway involves components of a cell-killing (or “apoptotic”) mechanism that is repurposed in this case to remove the GABA release apparatus at the synapse. Other proteins are likely to help UNC-8 sense the activity of neurons and destroy synapses in response. Further work is required to investigate these additional components and to determine how they work with UNC-8 to remove synapses in the nervous system during development. DOI:http://dx.doi.org/10.7554/eLife.14599.002
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Affiliation(s)
| | - Sarah C Petersen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Laura Manning
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States
| | - Cristina Matthewman
- Department of Physiology and Biophysics, University of Miami, Miami, United States
| | - Megan Gornet
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Allison Beers
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Sayaka Hori
- Department of Physiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Laura Bianchi
- Department of Physiology and Biophysics, University of Miami, Miami, United States
| | - Janet Richmond
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States
| | - David M Miller
- Neuroscience Program, Vanderbilt University, Nashville, United States.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
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30
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Hobert O. A map of terminal regulators of neuronal identity in Caenorhabditis elegans. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:474-98. [PMID: 27136279 PMCID: PMC4911249 DOI: 10.1002/wdev.233] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/07/2016] [Accepted: 02/21/2016] [Indexed: 12/31/2022]
Abstract
Our present day understanding of nervous system development is an amalgam of insights gained from studying different aspects and stages of nervous system development in a variety of invertebrate and vertebrate model systems, with each model system making its own distinctive set of contributions. One aspect of nervous system development that has been among the most extensively studied in the nematode Caenorhabditis elegans is the nature of the gene regulatory programs that specify hardwired, terminal cellular identities. I first summarize a number of maps (anatomical, functional, and molecular) that describe the terminal identity of individual neurons in the C. elegans nervous system. I then provide a comprehensive summary of regulatory factors that specify terminal identities in the nervous system, synthesizing these past studies into a regulatory map of cellular identities in the C. elegans nervous system. This map shows that for three quarters of all neurons in the C. elegans nervous system, regulatory factors that control terminal identity features are known. In-depth studies of specific neuron types have revealed that regulatory factors rarely act alone, but rather act cooperatively in neuron-type specific combinations. In most cases examined so far, distinct, biochemically unlinked terminal identity features are coregulated via cooperatively acting transcription factors, termed terminal selectors, but there are also cases in which distinct identity features are controlled in a piecemeal fashion by independent regulatory inputs. The regulatory map also illustrates that identity-defining transcription factors are reemployed in distinct combinations in different neuron types. However, the same transcription factor can drive terminal differentiation in neurons that are unrelated by lineage, unrelated by function, connectivity and neurotransmitter deployment. Lastly, the regulatory map illustrates the preponderance of homeodomain transcription factors in the control of terminal identities, suggesting that these factors have ancient, phylogenetically conserved roles in controlling terminal neuronal differentiation in the nervous system. WIREs Dev Biol 2016, 5:474-498. doi: 10.1002/wdev.233 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY, USA
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31
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Tu H, Huhtala P, Lee HM, Adams JC, Pihlajaniemi T. Membrane-associated collagens with interrupted triple-helices (MACITs): evolution from a bilaterian common ancestor and functional conservation in C. elegans. BMC Evol Biol 2015; 15:281. [PMID: 26667623 PMCID: PMC4678570 DOI: 10.1186/s12862-015-0554-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/02/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Collagens provide structural support and guidance cues within the extracellular matrix of metazoans. Mammalian collagens XIII, XXIII and XXV form a unique subgroup of type II transmembrane proteins, each comprising a short N-terminal cytosolic domain, a transmembrane domain and a largely collagenous ectodomain. We name these collagens as MACITs (Membrane-Associated Collagens with Interrupted Triple-helices), and here investigate their evolution and conserved properties. To date, these collagens have been studied only in mammals. Knowledge of the representation of MACITs in other extant metazoans is lacking. This question is of interest for understanding structural/functional relationships in the MACIT family and also for insight into the evolution of MACITs in relation to the secreted, fibrillar collagens that are present throughout the metazoa. RESULTS MACITs are restricted to bilaterians and are represented in the Ecdysozoa, Hemichordata, Urochordata and Vertebrata (Gnathostomata). They were not identified in available early-diverging metazoans, Lophotrochozoa, Echinodermata, Cephalochordata or Vertebrata (Cyclostomata). Whereas invertebrates encode a single MACIT, collagens XIII/XXIII/XXV of jawed vertebrates are paralogues that originated from the two rounds of en-bloc genome duplication occurring early in vertebrate evolution. MACITs have conserved domain architecture in which a juxta-membrane furin-cleavage site and the C-terminal 34 residues are especially highly conserved, whereas the cytoplasmic domains are weakly conserved. To study protein expression and function in a metazoan with a single MACIT gene, we focused on Caenorhabditis elegans and its col-99 gene. A col-99 cDNA was cloned and expressed as protein in mammalian CHO cells, two antibodies against COL-99 protein were generated, and a col-99-bearing fosmid gene construct col-99::egfp::flag was used to generate transgenic C. elegans lines. The encoded COL-99 polypeptide is 85 kDa in size and forms a trimeric protein. COL-99 is plasma membrane-associated and undergoes furin-dependent ectodomain cleavage and shedding. COL-99 is detected in mouth, pharynx, body wall and the tail, mostly in motor neurons and muscle systems and is enriched at neuromuscular junctions. CONCLUSIONS Through identification of MACITs in multiple metazoan phyla we developed a model for the evolution of MACITs. The experimental data demonstrate conservation of MACIT molecular and cellular properties and tissue localisations in the invertebrate, C. elegans.
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Affiliation(s)
- Hongmin Tu
- Centre of Excellence in Cell-Extracellular Matrix Research, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 5, Oulu, FIN 90014, Finland.
| | - Pirkko Huhtala
- Centre of Excellence in Cell-Extracellular Matrix Research, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 5, Oulu, FIN 90014, Finland.
| | - Hang-Mao Lee
- Centre of Excellence in Cell-Extracellular Matrix Research, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 5, Oulu, FIN 90014, Finland.
| | - Josephine C Adams
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK.
| | - Taina Pihlajaniemi
- Centre of Excellence in Cell-Extracellular Matrix Research, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 5, Oulu, FIN 90014, Finland.
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32
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Kurup N, Jin Y. Neural circuit rewiring: insights from DD synapse remodeling. WORM 2015; 5:e1129486. [PMID: 27073734 DOI: 10.1080/21624054.2015.1129486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/24/2015] [Accepted: 12/04/2015] [Indexed: 01/27/2023]
Abstract
Nervous systems exhibit many forms of neuronal plasticity during growth, learning and memory consolidation, as well as in response to injury. Such plasticity can occur across entire nervous systems as with the case of insect metamorphosis, in individual classes of neurons, or even at the level of a single neuron. A striking example of neuronal plasticity in C. elegans is the synaptic rewiring of the GABAergic Dorsal D-type motor neurons during larval development, termed DD remodeling. DD remodeling entails multi-step coordination to concurrently eliminate pre-existing synapses and form new synapses on different neurites, without changing the overall morphology of the neuron. This mini-review focuses on recent advances in understanding the cellular and molecular mechanisms driving DD remodeling.
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Affiliation(s)
- Naina Kurup
- Neurobiology Section, Division of Biological Sciences, University of California , San Diego, La Jolla, CA, USA
| | - Yishi Jin
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
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33
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He S, Philbrook A, McWhirter R, Gabel CV, Taub DG, Carter MH, Hanna IM, Francis MM, Miller DM. Transcriptional Control of Synaptic Remodeling through Regulated Expression of an Immunoglobulin Superfamily Protein. Curr Biol 2015; 25:2541-8. [PMID: 26387713 DOI: 10.1016/j.cub.2015.08.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/04/2015] [Accepted: 08/10/2015] [Indexed: 11/24/2022]
Abstract
Neural circuits are actively remodeled during brain development, but the molecular mechanisms that trigger circuit refinement are poorly understood. Here, we describe a transcriptional program in C. elegans that regulates expression of an Ig domain protein, OIG-1, to control the timing of synaptic remodeling. DD GABAergic neurons reverse polarity during larval development by exchanging the locations of pre- and postsynaptic components. In newly born larvae, DDs receive cholinergic inputs in the dorsal nerve cord. These inputs are switched to the ventral side by the end of the first larval (L1) stage. VD class GABAergic neurons are generated in the late L1 and are postsynaptic to cholinergic neurons in the dorsal nerve cord but do not remodel. We investigated remodeling of the postsynaptic apparatus in DD and VD neurons using targeted expression of the acetylcholine receptor (AChR) subunit, ACR-12::GFP. We determined that OIG-1 antagonizes the relocation of ACR-12 from the dorsal side in L1 DD neurons. During the L1/L2 transition, OIG-1 is downregulated in DD neurons by the transcription factor IRX-1/Iroquois, allowing the repositioning of synaptic inputs to the ventral side. In VD class neurons, which normally do not remodel, the transcription factor UNC-55/COUP-TF turns off IRX-1, thus maintaining high levels of OIG-1 to block the removal of dorsally located ACR-12 receptors. OIG-1 is secreted from GABA neurons, but its anti-plasticity function is cell autonomous and may not require secretion. Our study provides a novel mechanism by which synaptic remodeling is set in motion through regulated expression of an Ig domain protein.
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Affiliation(s)
- Siwei He
- Neuroscience Graduate Program, Vanderbilt International Scholar Program, Vanderbilt University, 465 21(st) Avenue South, Nashville, TN 37240-7935, USA
| | - Alison Philbrook
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21(st) Avenue South, Nashville, TN 37240-7935, USA
| | - Christopher V Gabel
- Department of Physiology and Biophysics, Boston University Medical Campus, 700 Albany Street, Boston, MA 02118, USA
| | - Daniel G Taub
- Department of Physiology and Biophysics, Boston University Medical Campus, 700 Albany Street, Boston, MA 02118, USA
| | - Maximilian H Carter
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21(st) Avenue South, Nashville, TN 37240-7935, USA
| | - Isabella M Hanna
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21(st) Avenue South, Nashville, TN 37240-7935, USA
| | - Michael M Francis
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
| | - David M Miller
- Neuroscience Graduate Program, Vanderbilt International Scholar Program, Vanderbilt University, 465 21(st) Avenue South, Nashville, TN 37240-7935, USA; Department of Cell and Developmental Biology, Vanderbilt University, 465 21(st) Avenue South, Nashville, TN 37240-7935, USA.
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Howell K, White JG, Hobert O. Spatiotemporal control of a novel synaptic organizer molecule. Nature 2015; 523:83-7. [PMID: 26083757 PMCID: PMC9134992 DOI: 10.1038/nature14545] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 05/12/2015] [Indexed: 12/13/2022]
Abstract
Synapse formation is a process tightly controlled in space and time. How gene regulatory mechanisms specify spatial and temporal aspects of synapse formation is not well understood. In the nematode C.elegans, two subtypes of the D-type inhibitory motor neuron (MN) classes, the dorsal D (DD) and ventral D (VD) neurons, extend axons along both the dorsal and ventral nerve cords 1. The embryonically generated DD MNs initially innervate ventral muscles in the first (L1) larval stage and receive their synaptic input from cholinergic MNs in the dorsal cord. They rewire by the end of the L1 molt to innervate dorsal muscles and to be innervated by newly formed ventral cholinergic MNs 1. VD MNs develop after the L1 molt; they take over the innervation of ventral muscles and receive their synaptic input from dorsal cholinergic MNs. We show here that the spatiotemporal control of synaptic wiring of the D-type neurons is controlled by an intersectional transcriptional strategy in which the UNC-30 Pitx-type homeodomain transcription factor acts together in embryonic and early larval stages with the temporally controlled LIN-14 transcription factor to prevent premature synapse rewiring of the DD MNs and, together with the UNC-55 nuclear hormone receptor, to prevent aberrant VD synaptic wiring in later larval and adult stages. A key effector of this intersectional transcription factor combination is a novel synaptic organizer molecule, the single immunoglobulin domain protein OIG-1. OIG-1 is perisynaptically localized along the synaptic outputs of the D-type MNs in a temporally controlled manner and is required for appropriate selection of both pre- and post-synaptic partners.
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Spencer WC, McWhirter R, Miller T, Strasbourger P, Thompson O, Hillier LW, Waterston RH, Miller DM. Isolation of specific neurons from C. elegans larvae for gene expression profiling. PLoS One 2014; 9:e112102. [PMID: 25372608 PMCID: PMC4221280 DOI: 10.1371/journal.pone.0112102] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/13/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The simple and well-described structure of the C. elegans nervous system offers an unprecedented opportunity to identify the genetic programs that define the connectivity and function of individual neurons and their circuits. A correspondingly precise gene expression map of C. elegans neurons would facilitate the application of genetic methods toward this goal. Here we describe a powerful new approach, SeqCeL (RNA-Seq of C. elegans cells) for producing gene expression profiles of specific larval C. elegans neurons. METHODS AND RESULTS We have exploited available GFP reporter lines for FACS isolation of specific larval C. elegans neurons for RNA-Seq analysis. Our analysis showed that diverse classes of neurons are accessible to this approach. To demonstrate the applicability of this strategy to rare neuron types, we generated RNA-Seq profiles of the NSM serotonergic neurons that occur as a single bilateral pair of cells in the C. elegans pharynx. These data detected >1,000 NSM enriched transcripts, including the majority of previously known NSM-expressed genes. SIGNIFICANCE This work offers a simple and robust protocol for expression profiling studies of post-embryonic C. elegans neurons and thus provides an important new method for identifying candidate genes for key roles in neuron-specific development and function.
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Affiliation(s)
- W. Clay Spencer
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Tyne Miller
- Program in Neuroscience, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Pnina Strasbourger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Owen Thompson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - LaDeana W. Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - David M. Miller
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Program in Neuroscience, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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Hwang H, Krajniak J, Matsunaga Y, Benian GM, Lu H. On-demand optical immobilization of Caenorhabditis elegans for high-resolution imaging and microinjection. LAB ON A CHIP 2014; 14:3498-501. [PMID: 25056343 PMCID: PMC4148454 DOI: 10.1039/c4lc00697f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
This paper describes a novel selective immobilization technique based on optical control of the sol-gel transition of thermoreversible Pluronic gel, which provides a simple, versatile, and biocompatible approach for high-resolution imaging and microinjection of Caenorhabditis elegans.
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Affiliation(s)
- Hyundoo Hwang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332-0100, USA.
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Nuclear receptors in nematode development: Natural experiments made by a phylum. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:224-37. [PMID: 24984201 DOI: 10.1016/j.bbagrm.2014.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/21/2014] [Accepted: 06/23/2014] [Indexed: 11/21/2022]
Abstract
The development of complex multicellular organisms is dependent on regulatory decisions that are necessary for the establishment of specific differentiation and metabolic cellular states. Nuclear receptors (NRs) form a large family of transcription factors that play critical roles in the regulation of development and metabolism of Metazoa. Based on their DNA binding and ligand binding domains, NRs are divided into eight NR subfamilies from which representatives of six subfamilies are present in both deuterostomes and protostomes indicating their early evolutionary origin. In some nematode species, especially in Caenorhabditis, the family of NRs expanded to a large number of genes strikingly exceeding the number of NR genes in vertebrates or insects. Nematode NRs, including the multiplied Caenorhabditis genes, show clear relation to vertebrate and insect homologues belonging to six of the eight main NR subfamilies. This review summarizes advances in research of nematode NRs and their developmental functions. Nematode NRs can reveal evolutionarily conserved mechanisms that regulate specific developmental and metabolic processes as well as new regulatory adaptations. They represent the results of a large number of natural experiments with structural and functional potential of NRs for the evolution of the phylum. The conserved and divergent character of nematode NRs adds a new dimension to our understanding of the general biology of regulation by NRs. This article is part of a Special Issue entitled: Nuclear receptors in animal development.
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Wang Y, Matthewman C, Han L, Miller T, Miller DM, Bianchi L. Neurotoxic unc-8 mutants encode constitutively active DEG/ENaC channels that are blocked by divalent cations. ACTA ACUST UNITED AC 2014; 142:157-69. [PMID: 23898007 PMCID: PMC3727304 DOI: 10.1085/jgp.201310974] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ion channels of the DEG/ENaC family can induce neurodegeneration under conditions in which they become hyperactivated. The Caenorhabditis elegans DEG/ENaC channel MEC-4(d) encodes a mutant channel with a substitution in the pore domain that causes swelling and death of the six touch neurons in which it is expressed. Dominant mutations in the C. elegans DEG/ENaC channel subunit UNC-8 result in uncoordinated movement. Here we show that this unc-8 movement defect is correlated with the selective death of cholinergic motor neurons in the ventral nerve cord. Experiments in Xenopus laevis ooctyes confirm that these mutant proteins, UNC-8(G387E) and UNC-8(A586T), encode hyperactivated channels that are strongly inhibited by extracellular calcium and magnesium. Reduction of extracellular divalent cations exacerbates UNC-8(G387E) toxicity in oocytes. We suggest that inhibition by extracellular divalent cations limits UNC-8 toxicity and may contribute to the selective death of neurons that express UNC-8 in vivo.
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Affiliation(s)
- Ying Wang
- Department of Physiology and Biophysics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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39
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Alfano C, Magrinelli E, Harb K, Studer M. The nuclear receptors COUP-TF: a long-lasting experience in forebrain assembly. Cell Mol Life Sci 2014; 71:43-62. [PMID: 23525662 PMCID: PMC11114017 DOI: 10.1007/s00018-013-1320-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 02/14/2013] [Accepted: 03/04/2013] [Indexed: 12/16/2022]
Abstract
Chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are nuclear receptors belonging to the superfamily of the steroid/thyroid hormone receptors. Members of this family are internalized to the nucleus both in a ligand-dependent or -independent manner and act as strong transcriptional regulators by binding to the DNA of their target genes. COUP-TFs are defined as orphan receptors, since ligands regulating their activity have not so far been identified. From the very beginning of metazoan evolution, these molecules have been involved in various key events during embryonic development and organogenesis. In this review, we will mainly focus on their function during development and maturation of the central nervous system, which has been well characterized in various animal classes ranging from ctenophores to mammals. We will start by introducing the current knowledge on COUP-TF mechanisms of action and then focus our discussion on the crucial processes underlying forebrain ontogenesis, with special emphasis on mammalian development. Finally, the conserved roles of COUP-TFs along phylogenesis will be highlighted, and some hypotheses, worth exploring in future years to gain more insight into the mechanisms controlled by these factors, will be proposed.
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Affiliation(s)
- Christian Alfano
- Institute of Biology Valrose, iBV, UMR INSERM1091/CNRS7277/UNS, 06108 Nice, France
- University of Nice-Sophia Antipolis, UFR Sciences, 06108 Nice, France
| | - Elia Magrinelli
- Institute of Biology Valrose, iBV, UMR INSERM1091/CNRS7277/UNS, 06108 Nice, France
- University of Nice-Sophia Antipolis, UFR Sciences, 06108 Nice, France
| | - Kawssar Harb
- Institute of Biology Valrose, iBV, UMR INSERM1091/CNRS7277/UNS, 06108 Nice, France
- University of Nice-Sophia Antipolis, UFR Sciences, 06108 Nice, France
| | - Michèle Studer
- Institute of Biology Valrose, iBV, UMR INSERM1091/CNRS7277/UNS, 06108 Nice, France
- University of Nice-Sophia Antipolis, UFR Sciences, 06108 Nice, France
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40
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Stout Jr RF, Grubišić V, Parpura V. A Caenorhabditis elegans locomotion phenotype caused by transgenic repeats of the hlh-17 promoter sequence. PLoS One 2013; 8:e81771. [PMID: 24312354 PMCID: PMC3842965 DOI: 10.1371/journal.pone.0081771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/16/2013] [Indexed: 01/17/2023] Open
Abstract
Transgene technology is one of the most heavily relied upon tools in modern biological research. Expression of an exogenous gene within cells, for research and therapeutic applications, nearly always includes promoters and other regulatory sequences. We found that repeats of a non-protein coding transgenic sequence produced profound changes to the behavior of the nematode Caenorhabditis elegans. These changes were produced by a glial promoter sequence but, unexpectedly, major deficits were observed specifically in backward locomotion, a neuron-driven behavior. We also present evidence that this behavioral phenotype is transpromoter copy number-dependent and manifests early in development and is maintained into adulthood of the worm.
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Affiliation(s)
- Randy F. Stout Jr
- Department of Neurobiology, Center for Glial Biology in Medicine, Atomic Force Microscopy & Nanotechnology Laboratories, Civitan International Research Center, Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, Alabama, United States of America
| | - Vladimir Grubišić
- Department of Neurobiology, Center for Glial Biology in Medicine, Atomic Force Microscopy & Nanotechnology Laboratories, Civitan International Research Center, Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, Alabama, United States of America
| | - Vladimir Parpura
- Department of Neurobiology, Center for Glial Biology in Medicine, Atomic Force Microscopy & Nanotechnology Laboratories, Civitan International Research Center, Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, Alabama, United States of America
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- * E-mail:
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41
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Smith CJ, O'Brien T, Chatzigeorgiou M, Spencer WC, Feingold-Link E, Husson SJ, Hori S, Mitani S, Gottschalk A, Schafer WR, Miller DM. Sensory neuron fates are distinguished by a transcriptional switch that regulates dendrite branch stabilization. Neuron 2013; 79:266-80. [PMID: 23889932 DOI: 10.1016/j.neuron.2013.05.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
Abstract
Sensory neurons adopt distinct morphologies and functional modalities to mediate responses to specific stimuli. Transcription factors and their downstream effectors orchestrate this outcome but are incompletely defined. Here, we show that different classes of mechanosensory neurons in C. elegans are distinguished by the combined action of the transcription factors MEC-3, AHR-1, and ZAG-1. Low levels of MEC-3 specify the elaborate branching pattern of PVD nociceptors, whereas high MEC-3 is correlated with the simple morphology of AVM and PVM touch neurons. AHR-1 specifies AVM touch neuron fate by elevating MEC-3 while simultaneously blocking expression of nociceptive genes such as the MEC-3 target, the claudin-like membrane protein HPO-30, that promotes the complex dendritic branching pattern of PVD. ZAG-1 exercises a parallel role to prevent PVM from adopting the PVD fate. The conserved dendritic branching function of the Drosophila AHR-1 homolog, Spineless, argues for similar pathways in mammals.
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Affiliation(s)
- Cody J Smith
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232-8240, USA
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Xie X, Tang K, Yu CT, Tsai SY, Tsai MJ. Regulatory potential of COUP-TFs in development: stem/progenitor cells. Semin Cell Dev Biol 2013; 24:687-93. [PMID: 23978678 DOI: 10.1016/j.semcdb.2013.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 08/14/2013] [Accepted: 08/16/2013] [Indexed: 12/25/2022]
Abstract
The formation of complex organisms is highly dependent on the differentiation of specialized mature cells from common stem/progenitor cells. The orphan nuclear receptors chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are broadly, but not ubiquitously, expressed in multiple tissues throughout embryonic development and COUP-TFs are indispensible for proper organogenesis. Recently, growing evidence suggests a critical role of COUP-TFs in multiple aspects of stem/progenitor cell biology. In this review, we highlight the progress of COUP-TFs function and its underlying mechanism in driving stem/progenitor cell self-renewal, lineage specification, differentiation, maintenance, and cell identity in diverse tissue types. These studies provide novel insights into future clinical utilities of COUP-TFs in stem cell based therapies and in the management of diseases.
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Affiliation(s)
- Xin Xie
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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43
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Meng L, Chen L, Li Z, Wu ZX, Shan G. Roles of microRNAs in the Caenorhabditis elegans nervous system. J Genet Genomics 2013; 40:445-52. [PMID: 24053946 DOI: 10.1016/j.jgg.2013.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 12/11/2022]
Abstract
The first microRNA was discovered in Caenorhabditis elegans in 1993, and since then, thousands of microRNAs have been identified from almost all eukaryotic organisms examined. MicroRNAs function in many biological events such as cell fate determination, metabolism, apoptosis, and carcinogenesis. So far, more than 250 microRNAs have been identified in C. elegans; however, functions for most of these microRNAs are still unknown. A small number of C. elegans microRNAs are associated with known physiological roles such as developmental timing, cell differentiation, stress response, and longevity. In this review, we summarize known roles of microRNAs in neuronal differentiation and function of C. elegans, and discuss interesting perspectives for future studies.
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Affiliation(s)
- Lingfeng Meng
- School of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
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44
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The cell biology of synaptic specificity during development. Curr Opin Neurobiol 2013; 23:1018-26. [PMID: 23932598 DOI: 10.1016/j.conb.2013.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 02/05/2023]
Abstract
Proper circuit connectivity is critical for nervous system function. Connectivity derives from the interaction of two interdependent modules: synaptic specificity and synaptic assembly. Specificity involves both targeting of neurons to specific laminar regions and the formation of synapses onto defined subcellular areas. In this review, we focus discussion on recently elucidated molecular mechanisms that control synaptic specificity and link them to synapse assembly. We use these molecular pathways to underscore fundamental cell biological concepts that underpin, and help explain, the rules governing synaptic specificity.
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Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, Reis K, Janosch S, Schloissnig S, Ejsmont RK, Slightam C, Xu X, Kim SK, Reinke V, Stewart AF, Snyder M, Waterston RH, Hyman AA. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell 2012; 150:855-66. [PMID: 22901814 DOI: 10.1016/j.cell.2012.08.001] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 03/22/2012] [Accepted: 08/01/2012] [Indexed: 12/21/2022]
Abstract
Understanding the in vivo dynamics of protein localization and their physical interactions is important for many problems in biology. To enable systematic protein function interrogation in a multicellular context, we built a genome-scale transgenic platform for in vivo expression of fluorescent- and affinity-tagged proteins in Caenorhabditis elegans under endogenous cis regulatory control. The platform combines computer-assisted transgene design, massively parallel DNA engineering, and next-generation sequencing to generate a resource of 14,637 genomic DNA transgenes, which covers 73% of the proteome. The multipurpose tag used allows any protein of interest to be localized in vivo or affinity purified using standard tag-based assays. We illustrate the utility of the resource by systematic chromatin immunopurification and automated 4D imaging, which produced detailed DNA binding and cell/tissue distribution maps for key transcription factor proteins.
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Affiliation(s)
- Mihail Sarov
- TransgeneOmics Unit, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
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