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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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2
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Wolfe Z, Liska D, Norris A. Deep Transcriptomics Reveals Cell-Specific Isoforms of Pan-Neuronal Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594572. [PMID: 38826410 PMCID: PMC11142100 DOI: 10.1101/2024.05.16.594572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Profiling gene expression in single neurons using single-cell RNA-Seq is a powerful method for understanding the molecular diversity of the nervous system. Profiling alternative splicing in single neurons using these methods is more challenging, however, due to low capture efficiency and sensitivity. As a result, we know much less about splicing patterns and regulation across neurons than we do about gene expression. Here we leverage unique attributes of the C. elegans nervous system to investigate deep cell-specific transcriptomes complete with biological replicates generated by the CeNGEN consortium, enabling high-confidence assessment of splicing across neuron types even for lowly-expressed genes. Global splicing maps reveal several striking observations, including pan-neuronal genes that harbor cell-specific splice variants, abundant differential intron retention across neuron types, and a single neuron highly enriched for upstream alternative 3' splice sites. We develop an algorithm to identify unique cell-specific expression patterns and use it to discover both cell-specific isoforms and potential regulatory RNA binding proteins that establish these isoforms. Genetic interrogation of these RNA binding proteins in vivo identifies three distinct regulatory factors employed to establish unique splicing patterns in a single neuron. Finally, we develop a user-friendly platform for spatial transcriptomic visualization of these splicing patterns with single-neuron resolution.
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3
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Smith JJ, Taylor SR, Blum JA, Feng W, Collings R, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. Cell Rep 2024; 43:113857. [PMID: 38421866 PMCID: PMC11091551 DOI: 10.1016/j.celrep.2024.113857] [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: 08/18/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Motor neurons (MNs) constitute an ancient cell type targeted by multiple adult-onset diseases. It is therefore important to define the molecular makeup of adult MNs in animal models and extract organizing principles. Here, we generate a comprehensive molecular atlas of adult Caenorhabditis elegans MNs and a searchable database. Single-cell RNA sequencing of 13,200 cells reveals that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. Extending C. elegans Neuronal Gene Expression Map and Network (CeNGEN) findings, all MN subclasses are delineated by distinct expression codes of either neuropeptide or transcription factor gene families. Strikingly, combinatorial codes of homeodomain transcription factor genes succinctly delineate adult MN diversity in both C. elegans and mice. Further, molecularly defined MN subclasses in C. elegans display distinct patterns of connectivity. Hence, our study couples the connectivity map of the C. elegans motor circuit with a molecular atlas of its constituent MNs and uncovers organizing principles and conserved molecular codes of adult MN diversity.
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Affiliation(s)
- Jayson J Smith
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Rebecca Collings
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Program in Neuroscience, Vanderbilt University, Nashville, TN 37240, USA.
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA.
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4
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Stefanakis N, Jiang J, Liang Y, Shaham S. LET-381/FoxF and its target UNC-30/Pitx2 specify and maintain the molecular identity of C. elegans mesodermal glia that regulate motor behavior. EMBO J 2024; 43:956-992. [PMID: 38360995 PMCID: PMC10943081 DOI: 10.1038/s44318-024-00049-w] [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: 09/07/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
While most glial cell types in the central nervous system (CNS) arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which envelop the brain neuropil and separate it from the circulatory system cavity. Transcriptome analysis shows that GLR glia combine astrocytic and endothelial characteristics, which are relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor also expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, the UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naive cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and promotes salt-induced paralysis, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neuronal differentiation, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
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Affiliation(s)
- Nikolaos Stefanakis
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Jessica Jiang
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Yupu Liang
- Research Bioinformatics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Alexion Pharmaceuticals, Boston, MA, 02135, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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5
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Xu C, Ramos TB, Rogers EM, Reiser MB, Doe CQ. Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity. eLife 2024; 12:RP90133. [PMID: 38180023 PMCID: PMC10942767 DOI: 10.7554/elife.90133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
How our brain generates diverse neuron types that assemble into precise neural circuits remains unclear. Using Drosophila lamina neuron types (L1-L5), we show that the primary homeodomain transcription factor (HDTF) brain-specific homeobox (Bsh) is initiated in progenitors and maintained in L4/L5 neurons to adulthood. Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates while repressing the HDTF Zfh1 to prevent ectopic L1/L3 fates (control: L1-L5; Bsh-knockdown: L1-L3), thereby generating lamina neuronal diversity for normal visual sensitivity. Subsequently, in L4 neurons, Bsh and Ap function in a feed-forward loop to activate the synapse recognition molecule DIP-β, thereby bridging neuronal fate decision to synaptic connectivity. Expression of a Bsh:Dam, specifically in L4, reveals Bsh binding to the DIP-β locus and additional candidate L4 functional identity genes. We propose that HDTFs function hierarchically to coordinate neuronal molecular identity, circuit formation, and function. Hierarchical HDTFs may represent a conserved mechanism for linking neuronal diversity to circuit assembly and function.
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Affiliation(s)
- Chundi Xu
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Tyler B Ramos
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Edward M Rogers
- Janelia Research Campus, Howard Hughes Medical Institute, Helix DriveAshburnUnited States
| | - Michael B Reiser
- Janelia Research Campus, Howard Hughes Medical Institute, Helix DriveAshburnUnited States
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
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6
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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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7
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Boeglin M, Leyva-Díaz E, Hobert O. Expression and function of Caenorhabditis elegans UNCP-18, a paralog of the SM protein UNC-18. Genetics 2023; 225:iyad180. [PMID: 37793339 PMCID: PMC10697816 DOI: 10.1093/genetics/iyad180] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/01/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Sec1/Munc18 (SM) proteins are important regulators of SNARE complex assembly during exocytosis throughout all major animal tissue types. However, expression of a founding member of the SM family, UNC-18, is mostly restricted to the nervous system of the nematode Caenorhabditis elegans, where it is important for synaptic transmission. Moreover, unc-18 null mutants do not display the lethality phenotype associated with (a) loss of all Drosophila and mouse orthologs of unc-18 and (b) with complete elimination of synaptic transmission in C. elegans. We investigated whether a previously uncharacterized unc-18 paralog, which we named uncp-18, may be able to explain the restricted expression and limited phenotypes of unc-18 null mutants. A reporter allele shows ubiquitous expression of uncp-18. Analysis of uncp-18 null mutants, unc-18 and uncp-18 double null mutants, as well as overexpression of uncp-18 in an unc-18 null mutant background, shows that these 2 genes can functionally compensate for one another and are redundantly required for embryonic viability. Our results indicate that the synaptic transmission defects of unc-18 null mutants cannot necessarily be interpreted as constituting a null phenotype for SM protein function at the synapse.
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Affiliation(s)
- Marion Boeglin
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, NewYork, NY 10027, USA
- Department of Development and Stem Cells, IGBMC, CNRS UMR 7104/INSERM U1258, Université de Strasbourg, Strasbourg 67081, France
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, NewYork, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, NewYork, NY 10027, USA
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8
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Bastien BL, Cowen MH, Hart MP. Distinct neurexin isoforms cooperate to initiate and maintain foraging activity. Transl Psychiatry 2023; 13:367. [PMID: 38036526 PMCID: PMC10689797 DOI: 10.1038/s41398-023-02668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/24/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Neurexins are synaptic adhesion molecules that play diverse roles in synaptic development, function, maintenance, and plasticity. Neurexin genes have been associated with changes in human behavior, where variants in NRXN1 are associated with autism, schizophrenia, and Tourette syndrome. While NRXN1, NRXN2, and NRXN3 all encode major α and β isoforms, NRXN1 uniquely encodes a γ isoform, for which mechanistic roles in behavior have yet to be defined. Here, we show that both α and γ isoforms of neurexin/nrx-1 are required for the C. elegans behavioral response to food deprivation, a sustained period of hyperactivity upon food loss. We find that the γ isoform regulates initiation and the α isoform regulates maintenance of the behavioral response to food deprivation, demonstrating cooperative function of multiple nrx-1 isoforms in regulating a sustained behavior. The γ isoform alters monoamine signaling via octopamine, relies on specific expression of NRX-1 isoforms throughout the relevant circuit, and is independent of neuroligin/nlg-1, the canonical trans-synaptic partner of nrx-1. The α isoform regulates the pre-synaptic structure of the octopamine producing RIC neuron and its maintenance role is conditional on neuroligin/nlg-1. Collectively, these results demonstrate that neurexin isoforms can have separate behavioral roles and act cooperatively across neuronal circuits to modify behavior, highlighting the need to directly analyze and consider all isoforms when defining the contribution of neurexins to behavior.
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Affiliation(s)
- Brandon L Bastien
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mara H Cowen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael P Hart
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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9
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Stefanakis N, Jiang J, Liang Y, Shaham S. LET-381/FoxF and UNC-30/Pitx2 control the development of C. elegans mesodermal glia that regulate motor behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563501. [PMID: 37961181 PMCID: PMC10634723 DOI: 10.1101/2023.10.23.563501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
While most CNS glia arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which ensheath the brain neuropil and separate it from the circulatory-system cavity. Transcriptome analysis suggests GLR glia merge astrocytic and endothelial characteristics relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naïve cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and induces salt hypersensitivity, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neurons, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
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10
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Tee LF, Young JJ, Maruyama K, Kimura S, Suzuki R, Endo Y, Kimura KD. Electric shock causes a fleeing-like persistent behavioral response in the nematode Caenorhabditis elegans. Genetics 2023; 225:iyad148. [PMID: 37595066 PMCID: PMC10550322 DOI: 10.1093/genetics/iyad148] [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: 04/11/2023] [Accepted: 07/27/2023] [Indexed: 08/20/2023] Open
Abstract
Behavioral persistency reflects internal brain states, which are the foundations of multiple brain functions. However, experimental paradigms enabling genetic analyses of behavioral persistency and its associated brain functions have been limited. Here, we report novel persistent behavioral responses caused by electric stimuli in the nematode Caenorhabditis elegans. When the animals on bacterial food are stimulated by alternating current, their movement speed suddenly increases 2- to 3-fold, persisting for more than 1 minute even after a 5-second stimulation. Genetic analyses reveal that voltage-gated channels in the neurons are required for the response, possibly as the sensors, and neuropeptide signaling regulates the duration of the persistent response. Additional behavioral analyses implicate that the animal's response to electric shock is scalable and has a negative valence. These properties, along with persistence, have been recently regarded as essential features of emotion, suggesting that C. elegans response to electric shock may reflect a form of emotion, akin to fear.
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Affiliation(s)
- Ling Fei Tee
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - Jared J Young
- Mills College at Northeastern University, Oakland, CA 94613, USA
| | - Keisuke Maruyama
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - Sota Kimura
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - Ryoga Suzuki
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - Yuto Endo
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Koutarou D Kimura
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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11
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Smith JJ, Taylor SR, Blum JA, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552048. [PMID: 37577463 PMCID: PMC10418256 DOI: 10.1101/2023.08.04.552048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Motor neurons (MNs) constitute an ancient cell type targeted by multiple adult-onset diseases. It is therefore important to define the molecular makeup of adult MNs in animal models and extract organizing principles. Here, we generated a comprehensive molecular atlas of adult Caenorhabditis elegans MNs and a searchable database (http://celegans.spinalcordatlas.org). Single-cell RNA-sequencing of 13,200 cells revealed that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. All subclasses are delineated by unique expression codes of either neuropeptide or transcription factor gene families. Strikingly, we found that combinatorial codes of homeodomain transcription factor genes define adult MN diversity both in C. elegans and mice. Further, molecularly defined MN subclasses in C. elegans display distinct patterns of connectivity. Hence, our study couples the connectivity map of the C. elegans motor circuit with a molecular atlas of its constituent MNs, and uncovers organizing principles and conserved molecular codes of adult MN diversity.
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Affiliation(s)
- Jayson J. Smith
- Department of Neurobiology, University of Chicago, Chicago, IL, 60637, USA
- University of Chicago Neuroscience Institute, Chicago, IL, 60637, USA
| | - Seth R. Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, 84602, USA
| | - Jacob A. Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M. Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Program in Neuroscience, Vanderbilt University, Nashville, TN, 37240, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, 60637, USA
- University of Chicago Neuroscience Institute, Chicago, IL, 60637, USA
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12
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Brocal-Ruiz R, Esteve-Serrano A, Mora-Martínez C, Franco-Rivadeneira ML, Swoboda P, Tena JJ, Vilar M, Flames N. Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans. eLife 2023; 12:e89702. [PMID: 37449480 PMCID: PMC10393296 DOI: 10.7554/elife.89702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cilia, either motile or non-motile (a.k.a primary or sensory), are complex evolutionarily conserved eukaryotic structures composed of hundreds of proteins required for their assembly, structure and function that are collectively known as the ciliome. Ciliome gene mutations underlie a group of pleiotropic genetic diseases known as ciliopathies. Proper cilium function requires the tight coregulation of ciliome gene transcription, which is only fragmentarily understood. RFX transcription factors (TF) have an evolutionarily conserved role in the direct activation of ciliome genes both in motile and non-motile cilia cell-types. In vertebrates, FoxJ1 and FoxN4 Forkhead (FKH) TFs work with RFX in the direct activation of ciliome genes, exclusively in motile cilia cell-types. No additional TFs have been described to act together with RFX in primary cilia cell-types in any organism. Here we describe FKH-8, a FKH TF, as a direct regulator of the sensory ciliome genes in Caenorhabditis elegans. FKH-8 is expressed in all ciliated neurons in C. elegans, binds the regulatory regions of ciliome genes, regulates ciliome gene expression, cilium morphology and a wide range of behaviors mediated by sensory ciliated neurons. FKH-8 and DAF-19 (C. elegans RFX) physically interact and synergistically regulate ciliome gene expression. C. elegans FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 but not by other members of other mouse FKH subfamilies. In conclusion, RFX and FKH TF families act jointly as direct regulators of ciliome genes also in sensory ciliated cell types suggesting that this regulatory logic could be an ancient trait predating functional cilia sub-specialization.
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Affiliation(s)
- Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Ainara Esteve-Serrano
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | | | - Peter Swoboda
- Department of Biosciences and Nutrition. Karolinska Institute. Campus FlemingsbergStockholmSweden
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de OlavideSevilleSpain
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
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13
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Ramirez M, Robert R, Yeung J, Wu J, Abdalla-Wyse A, Goldowitz D. Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis. BMC Genomics 2023; 24:351. [PMID: 37365500 DOI: 10.1186/s12864-023-09368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The development of the brain requires precise coordination of molecular processes across many cell-types. Underpinning these events are gene expression programs which require intricate regulation by non-coding regulatory sequences known as enhancers. In the context of the developing brain, transcribed enhancers (TEs) regulate temporally-specific expression of genes critical for cell identity and differentiation. Transcription of non-coding RNAs at active enhancer sequences, known as enhancer RNAs (eRNAs), is tightly associated with enhancer activity and has been correlated with target gene expression. TEs have been characterized in a multitude of developing tissues, however their regulatory role has yet to be described in the context of embryonic and early postnatal brain development. In this study, eRNA transcription was analyzed to identify TEs active during cerebellar development, as a proxy for the developing brain. Cap Analysis of Gene Expression followed by sequencing (CAGE-seq) was conducted at 12 stages throughout embryonic and early postnatal cerebellar development. RESULTS Temporal analysis of eRNA transcription identified clusters of TEs that peak in activity during either embryonic or postnatal times, highlighting their importance for temporally specific developmental events. Functional analysis of putative target genes identified molecular mechanisms under TE regulation revealing that TEs regulate genes involved in biological processes specific to neurons. We validate enhancer activity using in situ hybridization of eRNA expression from TEs predicted to regulate Nfib, a gene critical for cerebellar granule cell differentiation. CONCLUSIONS The results of this analysis provide a valuable dataset for the identification of cerebellar enhancers and provide insight into the molecular mechanisms critical for brain development under TE regulation. This dataset is shared with the community through an online resource ( https://goldowitzlab.shinyapps.io/trans-enh-app/ ).
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Remi Robert
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada.
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada.
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14
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Kenis S, Istiban MN, Van Damme S, Vandewyer E, Watteyne J, Schoofs L, Beets I. Ancestral glycoprotein hormone-receptor pathway controls growth in C. elegans. Front Endocrinol (Lausanne) 2023; 14:1200407. [PMID: 37409228 PMCID: PMC10319355 DOI: 10.3389/fendo.2023.1200407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/23/2023] [Indexed: 07/07/2023] Open
Abstract
In vertebrates, thyrostimulin is a highly conserved glycoprotein hormone that, besides thyroid stimulating hormone (TSH), is a potent ligand of the TSH receptor. Thyrostimulin is considered the most ancestral glycoprotein hormone and orthologs of its subunits, GPA2 and GPB5, are widely conserved across vertebrate and invertebrate animals. Unlike TSH, however, the functions of the thyrostimulin neuroendocrine system remain largely unexplored. Here, we identify a functional thyrostimulin-like signaling system in Caenorhabditis elegans. We show that orthologs of GPA2 and GPB5, together with thyrotropin-releasing hormone (TRH) related neuropeptides, constitute a neuroendocrine pathway that promotes growth in C. elegans. GPA2/GPB5 signaling is required for normal body size and acts through activation of the glycoprotein hormone receptor ortholog FSHR-1. C. elegans GPA2 and GPB5 increase cAMP signaling by FSHR-1 in vitro. Both subunits are expressed in enteric neurons and promote growth by signaling to their receptor in glial cells and the intestine. Impaired GPA2/GPB5 signaling causes bloating of the intestinal lumen. In addition, mutants lacking thyrostimulin-like signaling show an increased defecation cycle period. Our study suggests that the thyrostimulin GPA2/GPB5 pathway is an ancient enteric neuroendocrine system that regulates intestinal function in ecdysozoans, and may ancestrally have been involved in the control of organismal growth.
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Affiliation(s)
- Signe Kenis
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Majdulin Nabil Istiban
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Sara Van Damme
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Elke Vandewyer
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jan Watteyne
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Isabel Beets
- Neural Signaling and Circuit Plasticity Group, Department of Biology, KU Leuven, Leuven, Belgium
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15
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Fletcher A, Wunderlich Z, Enciso G. Shadow enhancers mediate trade-offs between transcriptional noise and fidelity. PLoS Comput Biol 2023; 19:e1011071. [PMID: 37205714 DOI: 10.1371/journal.pcbi.1011071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/03/2023] [Indexed: 05/21/2023] Open
Abstract
Enhancers are stretches of regulatory DNA that bind transcription factors (TFs) and regulate the expression of a target gene. Shadow enhancers are two or more enhancers that regulate the same target gene in space and time and are associated with most animal developmental genes. These multi-enhancer systems can drive more consistent transcription than single enhancer systems. Nevertheless, it remains unclear why shadow enhancer TF binding sites are distributed across multiple enhancers rather than within a single large enhancer. Here, we use a computational approach to study systems with varying numbers of TF binding sites and enhancers. We employ chemical reaction networks with stochastic dynamics to determine the trends in transcriptional noise and fidelity, two key performance objectives of enhancers. This reveals that while additive shadow enhancers do not differ in noise and fidelity from their single enhancer counterparts, sub- and superadditive shadow enhancers have noise and fidelity trade-offs not available to single enhancers. We also use our computational approach to compare the duplication and splitting of a single enhancer as mechanisms for the generation of shadow enhancers and find that the duplication of enhancers can decrease noise and increase fidelity, although at the metabolic cost of increased RNA production. A saturation mechanism for enhancer interactions similarly improves on both of these metrics. Taken together, this work highlights that shadow enhancer systems may exist for several reasons: genetic drift or the tuning of key functions of enhancers, including transcription fidelity, noise and output.
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Affiliation(s)
- Alvaro Fletcher
- Mathematical, Computational, and Systems Biology, University of California, Irvine, Irvine, CA, United States of America
| | - Zeba Wunderlich
- Department of Biology, Boston University, Boston, MA, United States of America
- Biological Design Center, Boston University, Boston, MA, United States of America
| | - German Enciso
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States of America
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16
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Rusin LY. Evolution of homology: From archetype towards a holistic concept of cell type. J Morphol 2023; 284:e21569. [PMID: 36789784 DOI: 10.1002/jmor.21569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The concept of homology lies in the heart of comparative biological science. The distinction between homology as structure and analogy as function has shaped the evolutionary paradigm for a century and formed the axis of comparative anatomy and embryology, which accept the identity of structure as a ground measure of relatedness. The advent of single-cell genomics overturned the classical view of cell homology by establishing a backbone regulatory identity of cell types, the basic biological units bridging the molecular and phenotypic dimensions, to reveal that the cell is the most flexible unit of living matter and that many approaches of classical biology need to be revised to understand evolution and diversity at the cellular level. The emerging theory of cell types explicitly decouples cell identity from phenotype, essentially allowing for the divergence of evolutionarily related morphotypes beyond recognition, as well as it decouples ontogenetic cell lineage from cell-type phylogeny, whereby explicating that cell types can share common descent regardless of their structure, function or developmental origin. The article succinctly summarizes current progress and opinion in this field and formulates a more generalistic view of biological cell types as avatars, transient or terminal cell states deployed in a continuum of states by the developmental programme of one and the same omnipotent cell, capable of changing or combining identities with distinct evolutionary histories or inventing ad hoc identities that never existed in evolution or development. It highlights how the new logic grounded in the regulatory nature of cell identity transforms the concepts of cell homology and phenotypic stability, suggesting that cellular evolution is inherently and massively network-like, with one-to-one homologies being rather uncommon and restricted to shallower levels of the animal tree of life.
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Affiliation(s)
- Leonid Y Rusin
- Laboratory for Mathematic Methods and Models in Bioinformatics, Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- EvoGenome Analytics LLC, Odintsovo, Moscow Region, Russia
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17
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Froehlich JJ, Rajewsky N. C. elegans Gene Regulatory Alleles and Reporter Bashing Studies. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000709. [PMID: 36748042 PMCID: PMC9898812 DOI: 10.17912/micropub.biology.000709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/08/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023]
Abstract
Gene regulation has been studied in C. elegans for over 30 years. In this analysis of 102 publications, we find that most transcriptional cis-regulatory elements are located within 5,000 bp of the transcription start site. Over 75% of studies conclude that transcriptional elements and 5'UTRs activate-, while 3'UTRs repress gene expression. While gene regulatory mutations make up less than 0.8% of alleles in forward genetics screens, recent CRISPR-Cas approaches are increasing the number of tested mutations. This work provides a resource of known gene regulatory sequences in C.elegans .
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Affiliation(s)
- Jonathan J Froehlich
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
,
Current affiliation: Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
,
Correspondence to: Jonathan J Froehlich (
)
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
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18
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Masoudi N, Schnabel R, Yemini E, Leyva-Díaz E, Hobert O. Cell-specific effects of the sole C. elegans Daughterless/E protein homolog, HLH-2, on nervous system development. Development 2023; 150:286219. [PMID: 36595352 PMCID: PMC10108603 DOI: 10.1242/dev.201366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 01/04/2023]
Abstract
Are there common mechanisms of neurogenesis used throughout an entire nervous system? We explored to what extent canonical proneural class I/II bHLH complexes are responsible for neurogenesis throughout the entire Caenorhabditis elegans nervous system. Distinct, lineage-specific proneural class II bHLH factors are generally thought to operate via interaction with a common, class I bHLH subunit, encoded by Daughterless in flies, the E proteins in vertebrates and HLH-2 in C. elegans. To eliminate function of all proneuronal class I/II bHLH complexes, we therefore genetically removed maternal and zygotic hlh-2 gene activity. We observed broad effects on neurogenesis, but still detected normal neurogenesis in many distinct neuron-producing lineages of the central and peripheral nervous system. Moreover, we found that hlh-2 selectively affects some aspects of neuron differentiation while leaving others unaffected. Although our studies confirm the function of proneuronal class I/II bHLH complexes in many different lineages throughout a nervous system, we conclude that their function is not universal, but rather restricted by lineage, cell type and components of differentiation programs affected.
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Affiliation(s)
- Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA.,University of Massachusetts, Department of Neurobiology, Worcester, MA 1605-2324, USA
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
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19
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Özel MN, Gibbs CS, Holguera I, Soliman M, Bonneau R, Desplan C. Coordinated control of neuronal differentiation and wiring by sustained transcription factors. Science 2022; 378:eadd1884. [PMID: 36480601 DOI: 10.1126/science.add1884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The large diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of on average 10 continuously expressed transcription factors. We show that targeted modifications of this terminal selector code induce predictable conversions of neuronal fates that appear morphologically and transcriptionally complete. Cis-regulatory analysis of open chromatin links one of these genes to an upstream patterning factor that specifies neuronal fates in stem cells. Experimentally validated network models describe the synergistic regulation of downstream effectors by terminal selectors and ecdysone signaling during brain wiring. Our results provide a generalizable framework of how specific fates are implemented in postmitotic neurons.
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Affiliation(s)
| | - Claudia Skok Gibbs
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Isabel Holguera
- Department of Biology, New York University, New York, NY 10003, USA
| | - Mennah Soliman
- Department of Biology, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA.,Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA.,New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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20
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Konzman D, Fukushige T, Dagnachew M, Krause M, Hanover JA. O-GlcNAc transferase plays a non-catalytic role in C. elegans male fertility. PLoS Genet 2022; 18:e1010273. [PMID: 36383567 PMCID: PMC9710795 DOI: 10.1371/journal.pgen.1010273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/30/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022] Open
Abstract
Animal behavior is influenced by the competing drives to maintain energy and to reproduce. The balance between these evolutionary pressures and how nutrient signaling pathways intersect with mating remains unclear. The nutrient sensor O-GlcNAc transferase, which post-translationally modifies intracellular proteins with a single monosaccharide, is responsive to cellular nutrient status and regulates diverse biological processes. Though essential in most metazoans, O-GlcNAc transferase (ogt-1) is dispensable in Caenorhabditis elegans, allowing genetic analysis of its physiological roles. Compared to control, ogt-1 males had a four-fold reduction in mean offspring, with nearly two thirds producing zero progeny. Interestingly, we found that ogt-1 males transferred sperm less often, and virgin males had reduced sperm count. ogt-1 males were also less likely to engage in mate-searching and mate-response behaviors. Surprisingly, we found normal fertility for males with hypodermal expression of ogt-1 and for ogt-1 strains with catalytic-dead mutations. This suggests OGT-1 serves a non-catalytic function in the hypodermis impacting male fertility and mating behavior. This study builds upon research on the nutrient sensor O-GlcNAc transferase and demonstrates a role it plays in the interplay between the evolutionary drives for reproduction and survival.
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Affiliation(s)
- Daniel Konzman
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mesgana Dagnachew
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John A. Hanover
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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21
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Feng W, Destain H, Smith JJ, Kratsios P. Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism. Nat Commun 2022; 13:6097. [PMID: 36243871 PMCID: PMC9569373 DOI: 10.1038/s41467-022-33781-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Hox transcription factors play fundamental roles during early patterning, but they are also expressed continuously, from embryonic stages through adulthood, in the nervous system. However, the functional significance of their sustained expression remains unclear. In C. elegans motor neurons (MNs), we find that LIN-39 (Scr/Dfd/Hox4-5) is continuously required during post-embryonic life to maintain neurotransmitter identity, a core element of neuronal function. LIN-39 acts directly to co-regulate genes that define cholinergic identity (e.g., unc-17/VAChT, cho-1/ChT). We further show that LIN-39, MAB-5 (Antp/Hox6-8) and the transcription factor UNC-3 (Collier/Ebf) operate in a positive feedforward loop to ensure continuous and robust expression of cholinergic identity genes. Finally, we identify a two-component design principle for homeostatic control of Hox gene expression in adult MNs: Hox transcriptional autoregulation is counterbalanced by negative UNC-3 feedback. These findings uncover a noncanonical role for Hox proteins during post-embryonic life, critically broadening their functional repertoire from early patterning to the control of neurotransmitter identity.
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Affiliation(s)
- Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jayson J Smith
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA.
- University of Chicago Neuroscience Institute, Chicago, IL, USA.
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA.
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22
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Rashid A, Tevlin M, Lu Y, Shaham S. A developmental pathway for epithelial-to-motoneuron transformation in C. elegans. Cell Rep 2022; 40:111414. [PMID: 36170838 PMCID: PMC9579992 DOI: 10.1016/j.celrep.2022.111414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/18/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Motoneurons and motoneuron-like pancreatic β cells arise from radial glia and ductal cells, respectively, both tube-lining progenitors that share molecular regulators. To uncover programs underlying motoneuron formation, we studied a similar, cell-division-independent transformation of the C. elegans tube-lining Y cell into the PDA motoneuron. We find that lin-12/Notch acts through ngn-1/Ngn and its regulator hlh-16/Olig to control transformation timing. lin-12 loss blocks transformation, while lin-12(gf) promotes precocious PDA formation. Early basal expression of ngn-1/Ngn and hlh-16/Olig depends on sem-4/Sall and egl-5/Hox. Later, coincident with Y cell morphological changes, ngn-1/Ngn expression is upregulated in a sem-4/Sall and egl-5/Hox-dependent but hlh-16/Olig-independent manner. Subsequently, Y cell retrograde extension forms an anchored process priming PDA axon extension. Extension requires ngn-1-dependent expression of the cytoskeleton organizers UNC-119, UNC-44/ANK, and UNC-33/CRMP, which also activate PDA terminal-gene expression. Our findings uncover cell-division-independent regulatory events leading to motoneuron generation, suggesting a conserved pathway for epithelial-to-motoneuron/motoneuron-like cell differentiation. Rashid et al. report on a conserved epithelial-to-motoneuron transformation pathway in C. elegans requiring ngn-1/Ngn and hlh-16/Olig. lin-12/Notch regulates transformation timing through these genes, while ngn-1/Ngn and hlh-16/Olig expression levels are regulated by sem-4/Sall and egl-5/Hox. Unexpectedly, the cytoskeleton organizers UNC-119, UNC-44, and UNC-33, which are ngn-1/Ngn targets, promote motoneuron terminal identity.
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Affiliation(s)
- Alina Rashid
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Maya Tevlin
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yun Lu
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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23
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Lin JM, Mitchell TA, Rothstein M, Pehl A, Taroc EZM, Katreddi RR, Parra KE, Zuloaga DG, Simoes-Costa M, Forni PE. Sociosexual behavior requires both activating and repressive roles of Tfap2e/AP-2ε in vomeronasal sensory neurons. eLife 2022; 11:e77259. [PMID: 36111787 PMCID: PMC9525060 DOI: 10.7554/elife.77259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Neuronal identity dictates the position in an epithelium, and the ability to detect, process, and transmit specific signals to specified targets. Transcription factors (TFs) determine cellular identity via direct modulation of genetic transcription and recruiting chromatin modifiers. However, our understanding of the mechanisms that define neuronal identity and their magnitude remain a critical barrier to elucidate the etiology of congenital and neurodegenerative disorders. The rodent vomeronasal organ provides a unique system to examine in detail the molecular mechanisms underlying the differentiation and maturation of chemosensory neurons. Here, we demonstrated that the identity of postmitotic/maturing vomeronasal sensory neurons (VSNs), and vomeronasal-dependent behaviors can be reprogrammed through the rescue of Tfap2e/AP-2ε expression in the Tfap2eNull mice, and partially reprogrammed by inducing ectopic Tfap2e expression in mature apical VSNs. We suggest that the TF Tfap2e can reprogram VSNs bypassing cellular plasticity restrictions, and that it directly controls the expression of batteries of vomeronasal genes.
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Affiliation(s)
- Jennifer M Lin
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Tyler A Mitchell
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Megan Rothstein
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Alison Pehl
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Ed Zandro M Taroc
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Raghu R Katreddi
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Katherine E Parra
- Department of Psychology, University at Albany, State University of New YorkAlbanyUnited States
| | - Damian G Zuloaga
- Department of Psychology, University at Albany, State University of New YorkAlbanyUnited States
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Paolo Emanuele Forni
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
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24
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Godini R, Fallahi H, Pocock R. The regulatory landscape of neurite development in Caenorhabditis elegans. Front Mol Neurosci 2022; 15:974208. [PMID: 36090252 PMCID: PMC9453034 DOI: 10.3389/fnmol.2022.974208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Neuronal communication requires precise connectivity of neurite projections (axons and dendrites). Developing neurites express cell-surface receptors that interpret extracellular cues to enable correct guidance toward, and connection with, target cells. Spatiotemporal regulation of neurite guidance molecule expression by transcription factors (TFs) is critical for nervous system development and function. Here, we review how neurite development is regulated by TFs in the Caenorhabditis elegans nervous system. By collecting publicly available transcriptome and ChIP-sequencing data, we reveal gene expression dynamics during neurite development, providing insight into transcriptional mechanisms governing construction of the nervous system architecture.
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Affiliation(s)
- Rasoul Godini
- Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- *Correspondence: Rasoul Godini,
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Roger Pocock
- Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Roger Pocock,
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25
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Skuhersky M, Wu T, Yemini E, Nejatbakhsh A, Boyden E, Tegmark M. Toward a more accurate 3D atlas of C. elegans neurons. BMC Bioinformatics 2022; 23:195. [PMID: 35643434 PMCID: PMC9145532 DOI: 10.1186/s12859-022-04738-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Determining cell identity in volumetric images of tagged neuronal nuclei is an ongoing challenge in contemporary neuroscience. Frequently, cell identity is determined by aligning and matching tags to an “atlas” of labeled neuronal positions and other identifying characteristics. Previous analyses of such C. elegans datasets have been hampered by the limited accuracy of such atlases, especially for neurons present in the ventral nerve cord, and also by time-consuming manual elements of the alignment process.
Results
We present a novel automated alignment method for sparse and incomplete point clouds of the sort resulting from typical C. elegans fluorescence microscopy datasets. This method involves a tunable learning parameter and a kernel that enforces biologically realistic deformation. We also present a pipeline for creating alignment atlases from datasets of the recently developed NeuroPAL transgene. In combination, these advances allow us to label neurons in volumetric images with confidence much higher than previous methods.
Conclusions
We release, to the best of our knowledge, the most complete full-body C. elegans 3D positional neuron atlas, incorporating positional variability derived from at least 7 animals per neuron, for the purposes of cell-type identity prediction for myriad applications (e.g., imaging neuronal activity, gene expression, and cell-fate).
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26
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Driesschaert B, Temmerman L. The Q system for conditional gene expression is leaky and lacks dynamic range in C. elegans neurons. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000573. [PMID: 35601753 PMCID: PMC9115586 DOI: 10.17912/micropub.biology.000573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022]
Abstract
The Q system allows for conditional gene expression in several organisms, including
C. elegans
. We aimed to apply this system in
C. elegans
neurons to obtain temporally-resolved, tissue-specific expression of a fluorescent reporter. We report that, in our hands, there is undesired expression of the reporter in conditions where expression is supposed to be repressed. In addition, in this setup, the signal‑to‑noise ratio of the Q system is unfavorable. We conclude that the Q system is far from optimal in the
C. elegans
nervous system, and advise cautious use.
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Affiliation(s)
| | - Liesbet Temmerman
- Katholieke Universiteit Leuven, Leuven, Belgium
,
Correspondence to: Liesbet Temmerman (
)
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27
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Rapti G. Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration. Front Neurosci 2022; 15:787753. [PMID: 35321480 PMCID: PMC8934944 DOI: 10.3389/fnins.2021.787753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Nervous system cells, the building blocks of circuits, have been studied with ever-progressing resolution, yet neural circuits appear still resistant to schemes of reductionist classification. Due to their sheer numbers, complexity and diversity, their systematic study requires concrete classifications that can serve reduced dimensionality, reproducibility, and information integration. Conventional hierarchical schemes transformed through the history of neuroscience by prioritizing criteria of morphology, (electro)physiological activity, molecular content, and circuit function, influenced by prevailing methodologies of the time. Since the molecular biology revolution and the recent advents in transcriptomics, molecular profiling gains ground toward the classification of neurons and glial cell types. Yet, transcriptomics entails technical challenges and more importantly uncovers unforeseen spatiotemporal heterogeneity, in complex and simpler nervous systems. Cells change states dynamically in space and time, in response to stimuli or throughout their developmental trajectory. Mapping cell type and state heterogeneity uncovers uncharted terrains in neurons and especially in glial cell biology, that remains understudied in many aspects. Examining neurons and glial cells from the perspectives of molecular neuroscience, physiology, development and evolution highlights the advantage of multifaceted classification schemes. Among the amalgam of models contributing to neuroscience research, Caenorhabditis elegans combines nervous system anatomy, lineage, connectivity and molecular content, all mapped at single-cell resolution, and can provide valuable insights for the workflow and challenges of the multimodal integration of cell type features. This review reflects on concepts and practices of neuron and glial cells classification and how research, in C. elegans and beyond, guides nervous system experimentation through integrated multidimensional schemes. It highlights underlying principles, emerging themes, and open frontiers in the study of nervous system development, regulatory logic and evolution. It proposes unified platforms to allow integrated annotation of large-scale datasets, gene-function studies, published or unpublished findings and community feedback. Neuroscience is moving fast toward interdisciplinary, high-throughput approaches for combined mapping of the morphology, physiology, connectivity, molecular function, and the integration of information in multifaceted schemes. A closer look in mapped neural circuits and understudied terrains offers insights for the best implementation of these approaches.
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28
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Jimeno-Martín A, Sousa E, Brocal-Ruiz R, Daroqui N, Maicas M, Flames N. Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity. Genome Res 2022; 32:459-473. [PMID: 35074859 PMCID: PMC8896470 DOI: 10.1101/gr.275623.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022]
Abstract
To systematically investigate the complexity of neuron specification regulatory networks, we performed an RNA interference (RNAi) screen against all 875 transcription factors (TFs) encoded in Caenorhabditis elegans genome and searched for defects in nine different neuron types of the monoaminergic (MA) superclass and two cholinergic motoneurons. We identified 91 TF candidates to be required for correct generation of these neuron types, of which 28 were confirmed by mutant analysis. We found that correct reporter expression in each individual neuron type requires at least nine different TFs. Individual neuron types do not usually share TFs involved in their specification but share a common pattern of TFs belonging to the five most common TF families: homeodomain (HD), basic helix loop helix (bHLH), zinc finger (ZF), basic leucine zipper domain (bZIP), and nuclear hormone receptors (NHR). HD TF members are overrepresented, supporting a key role for this family in the establishment of neuronal identities. These five TF families are also prevalent when considering mutant alleles with previously reported neuronal phenotypes in C. elegans, Drosophila, and mouse. In addition, we studied terminal differentiation complexity focusing on the dopaminergic terminal regulatory program. We found two HD TFs (UNC-62 and VAB-3) that work together with known dopaminergic terminal selectors (AST-1, CEH-43, CEH-20). Combined TF binding sites for these five TFs constitute a cis-regulatory signature enriched in the regulatory regions of dopaminergic effector genes. Our results provide new insights on neuron-type regulatory programs in C. elegans that could help better understand neuron specification and evolution of neuron types.
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Affiliation(s)
- Angela Jimeno-Martín
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Noemi Daroqui
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
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29
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Leyva-Díaz E, Hobert O. Robust regulatory architecture of pan-neuronal gene expression. Curr Biol 2022; 32:1715-1727.e8. [PMID: 35259341 PMCID: PMC9050922 DOI: 10.1016/j.cub.2022.02.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 12/17/2022]
Abstract
Pan-neuronally expressed genes, such as genes involved in the synaptic vesicle cycle or in neuropeptide maturation, are critical for proper function of all neurons, but the transcriptional control mechanisms that direct such genes to all neurons of a nervous system remain poorly understood. We show here that six members of the CUT family of homeobox genes control pan-neuronal identity specification in Caenorhabditis elegans. Single CUT mutants show barely any effects on pan-neuronal gene expression or global nervous system function, but such effects become apparent and progressively worsen upon removal of additional CUT family members, indicating a critical role of gene dosage. Overexpression of each individual CUT gene rescued the phenotype of compound mutants, corroborating that gene dosage, rather than the activity of specific members of the gene family, is critical for CUT gene family function. Genome-wide binding profiles, as well as mutation of CUT homeodomain binding sites by CRISPR/Cas9 genome engineering show that CUT genes directly control the expression of pan-neuronal features. Moreover, CUT genes act in conjunction with neuron-type-specific transcription factors to control pan-neuronal gene expression. Our study, therefore, provides a previously missing key insight into how neuronal gene expression programs are specified and reveals a highly buffered and robust mechanism that controls the most critical functional features of all neuronal cell types.
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30
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Closser M, Guo Y, Wang P, Patel T, Jang S, Hammelman J, De Nooij JC, Kopunova R, Mazzoni EO, Ruan Y, Gifford DK, Wichterle H. An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity. Neuron 2022; 110:70-85.e6. [PMID: 34727520 PMCID: PMC8738133 DOI: 10.1016/j.neuron.2021.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
Proper assembly and function of the nervous system requires the generation of a uniquely diverse population of neurons expressing a cell-type-specific combination of effector genes that collectively define neuronal morphology, connectivity, and function. How countless partially overlapping but cell-type-specific patterns of gene expression are controlled at the genomic level remains poorly understood. Here we show that neuronal genes are associated with highly complex gene regulatory systems composed of independent cell-type- and cell-stage-specific regulatory elements that reside in expanded non-coding genomic domains. Mapping enhancer-promoter interactions revealed that motor neuron enhancers are broadly distributed across the large chromatin domains. This distributed regulatory architecture is not a unique property of motor neurons but is employed throughout the nervous system. The number of regulatory elements increased dramatically during the transition from invertebrates to vertebrates, suggesting that acquisition of new enhancers might be a fundamental process underlying the evolutionary increase in cellular complexity.
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Affiliation(s)
- Michael Closser
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yuchun Guo
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Tulsi Patel
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sumin Jang
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jennifer Hammelman
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Joriene C De Nooij
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel Kopunova
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA.
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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31
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Sousa E, Flames N. Transcriptional regulation of neuronal identity. Eur J Neurosci 2021; 55:645-660. [PMID: 34862697 PMCID: PMC9306894 DOI: 10.1111/ejn.15551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Neuronal diversity is an intrinsic feature of the nervous system. Transcription factors (TFs) are key regulators in the establishment of different neuronal identities; how are the actions of different TFs coordinated to orchestrate this diversity? Are there common features shared among the different neuron types of an organism or even among different animal groups? In this review, we provide a brief overview on common traits emerging on the transcriptional regulation of neuron type diversification with a special focus on the comparison between mouse and Caenorhabditis elegans model systems. In the first part, we describe general concepts on neuronal identity and transcriptional regulation of gene expression. In the second part of the review, TFs are classified in different categories according to their key roles at specific steps along the protracted process of neuronal specification and differentiation. The same TF categories can be identified both in mammals and nematodes. Importantly, TFs are very pleiotropic: Depending on the neuron type or the time in development, the same TF can fulfil functions belonging to different categories. Finally, we describe the key role of transcriptional repression at all steps controlling neuronal diversity and propose that acquisition of neuronal identities could be considered a metastable process.
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Affiliation(s)
- Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
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32
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Sonobe Y, Aburas J, Krishnan G, Fleming AC, Ghadge G, Islam P, Warren EC, Gu Y, Kankel MW, Brown AEX, Kiskinis E, Gendron TF, Gao FB, Roos RP, Kratsios P. A C. elegans model of C9orf72-associated ALS/FTD uncovers a conserved role for eIF2D in RAN translation. Nat Commun 2021; 12:6025. [PMID: 34654821 PMCID: PMC8519953 DOI: 10.1038/s41467-021-26303-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/28/2021] [Indexed: 12/31/2022] Open
Abstract
A hexanucleotide repeat expansion GGGGCC in the non-coding region of C9orf72 is the most common cause of inherited amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Toxic dipeptide repeats (DPRs) are synthesized from GGGGCC via repeat-associated non-AUG (RAN) translation. Here, we develop C. elegans models that express, either ubiquitously or exclusively in neurons, 75 GGGGCC repeats flanked by intronic C9orf72 sequence. The worms generate DPRs (poly-glycine-alanine [poly-GA], poly-glycine-proline [poly-GP]) and poly-glycine-arginine [poly-GR]), display neurodegeneration, and exhibit locomotor and lifespan defects. Mutation of a non-canonical translation-initiating codon (CUG) upstream of the repeats selectively reduces poly-GA steady-state levels and ameliorates disease, suggesting poly-GA is pathogenic. Importantly, loss-of-function mutations in the eukaryotic translation initiation factor 2D (eif-2D/eIF2D) reduce poly-GA and poly-GP levels, and increase lifespan in both C. elegans models. Our in vitro studies in mammalian cells yield similar results. Here, we show a conserved role for eif-2D/eIF2D in DPR expression.
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Affiliation(s)
- Yoshifumi Sonobe
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.412578.d0000 0000 8736 9513Department of Neurology, University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA
| | - Jihad Aburas
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA ,grid.170205.10000 0004 1936 7822Department of Neurobiology, University of Chicago, Chicago, IL USA
| | - Gopinath Krishnan
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Andrew C. Fleming
- grid.16753.360000 0001 2299 3507The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ghanashyam Ghadge
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.412578.d0000 0000 8736 9513Department of Neurology, University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA
| | - Priota Islam
- grid.14105.310000000122478951MRC London Institute of Medical Sciences, London, UK ,grid.7445.20000 0001 2113 8111Institute of Clinical Sciences, Imperial College London, London, UK
| | - Eleanor C. Warren
- grid.14105.310000000122478951MRC London Institute of Medical Sciences, London, UK ,grid.7445.20000 0001 2113 8111Institute of Clinical Sciences, Imperial College London, London, UK
| | - Yuanzheng Gu
- grid.417832.b0000 0004 0384 8146Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142 USA
| | - Mark W. Kankel
- grid.417832.b0000 0004 0384 8146Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142 USA
| | - André E. X. Brown
- grid.14105.310000000122478951MRC London Institute of Medical Sciences, London, UK ,grid.7445.20000 0001 2113 8111Institute of Clinical Sciences, Imperial College London, London, UK
| | - Evangelos Kiskinis
- grid.16753.360000 0001 2299 3507The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Tania F. Gendron
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, Jacksonville, FL USA
| | - Fen-Biao Gao
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Raymond P. Roos
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.412578.d0000 0000 8736 9513Department of Neurology, University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA
| | - Paschalis Kratsios
- University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL, 60637, USA. .,The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL, USA. .,Department of Neurobiology, University of Chicago, Chicago, IL, USA.
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33
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Godini R, Handley A, Pocock R. Transcription Factors That Control Behavior-Lessons From C. elegans. Front Neurosci 2021; 15:745376. [PMID: 34646119 PMCID: PMC8503520 DOI: 10.3389/fnins.2021.745376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/02/2021] [Indexed: 11/15/2022] Open
Abstract
Behavior encompasses the physical and chemical response to external and internal stimuli. Neurons, each with their own specific molecular identities, act in concert to perceive and relay these stimuli to drive behavior. Generating behavioral responses requires neurons that have the correct morphological, synaptic, and molecular identities. Transcription factors drive the specific gene expression patterns that define these identities, controlling almost every phenomenon in a cell from development to homeostasis. Therefore, transcription factors play an important role in generating and regulating behavior. Here, we describe the transcription factors, the pathways they regulate, and the neurons that drive chemosensation, mechanosensation, thermosensation, osmolarity sensing, complex, and sex-specific behaviors in the animal model Caenorhabditis elegans. We also discuss the current limitations in our knowledge, particularly our minimal understanding of how transcription factors contribute to the adaptive behavioral responses that are necessary for organismal survival.
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34
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Pham K, Masoudi N, Leyva-Díaz E, Hobert O. A nervous system-specific subnuclear organelle in Caenorhabditis elegans. Genetics 2021; 217:1-17. [PMID: 33683371 DOI: 10.1093/genetics/iyaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/12/2020] [Indexed: 12/26/2022] Open
Abstract
We describe here phase-separated subnuclear organelles in the nematode Caenorhabditis elegans, which we term NUN (NUclear Nervous system-specific) bodies. Unlike other previously described subnuclear organelles, NUN bodies are highly cell type specific. In fully mature animals, 4-10 NUN bodies are observed exclusively in the nucleus of neuronal, glial and neuron-like cells, but not in other somatic cell types. Based on co-localization and genetic loss of function studies, NUN bodies are not related to other previously described subnuclear organelles, such as nucleoli, splicing speckles, paraspeckles, Polycomb bodies, promyelocytic leukemia bodies, gems, stress-induced nuclear bodies, or clastosomes. NUN bodies form immediately after cell cycle exit, before other signs of overt neuronal differentiation and are unaffected by the genetic elimination of transcription factors that control many other aspects of neuronal identity. In one unusual neuron class, the canal-associated neurons, NUN bodies remodel during larval development, and this remodeling depends on the Prd-type homeobox gene ceh-10. In conclusion, we have characterized here a novel subnuclear organelle whose cell type specificity poses the intriguing question of what biochemical process in the nucleus makes all nervous system-associated cells different from cells outside the nervous system.
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Affiliation(s)
- Kenneth Pham
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Neda Masoudi
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
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35
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Chakraborty K, Anees P, Surana S, Martin S, Aburas J, Moutel S, Perez F, Koushika SP, Kratsios P, Krishnan Y. Tissue-specific targeting of DNA nanodevices in a multicellular living organism. eLife 2021; 10:67830. [PMID: 34318748 PMCID: PMC8360651 DOI: 10.7554/elife.67830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Nucleic acid nanodevices present great potential as agents for logic-based therapeutic intervention as well as in basic biology. Often, however, the disease targets that need corrective action are localized in specific organs, and thus realizing the full potential of DNA nanodevices also requires ways to target them to specific cell types in vivo. Here, we show that by exploiting either endogenous or synthetic receptor-ligand interactions and leveraging the biological barriers presented by the organism, we can target extraneously introduced DNA nanodevices to specific cell types in Caenorhabditis elegans, with subcellular precision. The amenability of DNA nanostructures to tissue-specific targeting in vivo significantly expands their utility in biomedical applications and discovery biology.
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Affiliation(s)
- Kasturi Chakraborty
- Department of Chemistry, The University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, United States
| | - Palapuravan Anees
- Department of Chemistry, The University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, United States
| | - Sunaina Surana
- Department of Chemistry, The University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, United States
| | - Simona Martin
- Department of Chemistry, The University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, United States
| | - Jihad Aburas
- Department of Neurobiology, The University of Chicago, Chicago, United States
| | - Sandrine Moutel
- Recombinant Antibody Platform (TAb-IP), Institut Curie, PSL Research University, CNRS UMR144, Paris, France.,Cell Biology and Cancer Unit, Institut Curie, PSL Research University, CNRS UMR144, Paris, France
| | - Franck Perez
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, CNRS UMR144, Paris, France
| | - Sandhya P Koushika
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Paschalis Kratsios
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, United States.,Department of Neurobiology, The University of Chicago, Chicago, United States
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, United States.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, United States
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36
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Rapti G. A perspective on C. elegans neurodevelopment: from early visionaries to a booming neuroscience research. J Neurogenet 2021; 34:259-272. [PMID: 33446023 DOI: 10.1080/01677063.2020.1837799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The formation of the nervous system and its striking complexity is a remarkable feat of development. C. elegans served as a unique model to dissect the molecular events in neurodevelopment, from its early visionaries to the current booming neuroscience community. Soon after being introduced as a model, C. elegans was mapped at the level of genes, cells, and synapses, providing the first metazoan with a complete cell lineage, sequenced genome, and connectome. Here, I summarize mechanisms underlying C. elegans neurodevelopment, from the generation and diversification of neural components to their navigation and connectivity. I point out recent noteworthy findings in the fields of glia biology, sex dimorphism and plasticity in neurodevelopment, highlighting how current research connects back to the pioneering studies by Brenner, Sulston and colleagues. Multifaceted investigations in model organisms, connecting genes to cell function and behavior, expand our mechanistic understanding of neurodevelopment while allowing us to formulate emerging questions for future discoveries.
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Affiliation(s)
- Georgia Rapti
- European Molecular Biology Laboratory, Unit of Developmental Biology, Heidelberg, Germany
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37
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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: 247] [Impact Index Per Article: 82.3] [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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Masoudi N, Yemini E, Schnabel R, Hobert O. Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans. Development 2021; 148:dev199224. [PMID: 34100067 PMCID: PMC8217713 DOI: 10.1242/dev.199224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/29/2021] [Indexed: 11/20/2022]
Abstract
Cells of the same type can be generated by distinct cellular lineages that originate in different parts of the developing embryo ('lineage convergence'). Several Caenorhabditis elegans neuron classes composed of left/right or radially symmetric class members display such lineage convergence. We show here that the C. elegans Atonal homolog lin-32 is differentially expressed in neuronal lineages that give rise to left/right or radially symmetric class members. Loss of lin-32 results in the selective loss of the expression of pan-neuronal markers and terminal selector-type transcription factors that confer neuron class-specific features. Another basic helix-loop-helix (bHLH) gene, the Achaete-Scute homolog hlh-14, is expressed in a mirror image pattern relative to lin-32 and is required to induce neuronal identity and terminal selector expression on the contralateral side of the animal. These findings demonstrate that distinct lineage histories converge via different bHLH factors at the level of induction of terminal selector identity determinants, which thus serve as integrators of distinct lineage histories. We also describe neuron-to-neuron identity transformations in lin-32 mutants, which we propose to also be the result of misregulation of terminal selector gene expression.
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Affiliation(s)
- Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
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Abstract
Shadow enhancers are seemingly redundant transcriptional cis-regulatory elements that regulate the same gene and drive overlapping expression patterns. Recent studies have shown that shadow enhancers are remarkably abundant and control most developmental gene expression in both invertebrates and vertebrates, including mammals. Shadow enhancers might provide an important mechanism for buffering gene expression against mutations in non-coding regulatory regions of genes implicated in human disease. Technological advances in genome editing and live imaging have shed light on how shadow enhancers establish precise gene expression patterns and confer phenotypic robustness. Shadow enhancers can interact in complex ways and may also help to drive the formation of transcriptional hubs within the nucleus. Despite their apparent redundancy, the prevalence and evolutionary conservation of shadow enhancers underscore their key role in emerging metazoan gene regulatory networks.
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40
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Robinson-Thiewes S, Dufour B, Martel PO, Lechasseur X, Brou AAD, Roy V, Chen Y, Kimble J, Narbonne P. Non-autonomous regulation of germline stem cell proliferation by somatic MPK-1/MAPK activity in C. elegans. Cell Rep 2021; 35:109162. [PMID: 34038716 PMCID: PMC8182673 DOI: 10.1016/j.celrep.2021.109162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/17/2021] [Accepted: 04/30/2021] [Indexed: 11/03/2022] Open
Abstract
Extracellular-signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) is a major positive regulator of cell proliferation, which is often upregulated in cancer. However, few studies have addressed ERK/MAPK regulation of proliferation within a complete organism. The Caenorhabditis elegans ERK/MAPK ortholog MPK-1 is best known for its control of somatic organogenesis and germline differentiation, but it also stimulates germline stem cell proliferation. Here, we show that the germline-specific MPK-1B isoform promotes germline differentiation but has no apparent role in germline stem cell proliferation. By contrast, the soma-specific MPK-1A isoform promotes germline stem cell proliferation non-autonomously. Indeed, MPK-1A functions in the intestine or somatic gonad to promote germline proliferation independent of its other known roles. We propose that a non-autonomous role of ERK/MAPK in stem cell proliferation may be conserved across species and various tissue types, with major clinical implications for cancer and other diseases. The prevailing paradigm is that ERK/MAPK functions autonomously to promote cell proliferation upon mitogen stimulation. Robinson-Thiewes et al. now demonstrate that C. elegans ERK/MAPK acts within somatic tissues to non-autonomously promote the proliferation of germline stem cells. Germline ERK/MAPK is thus dispensable for germline stem cell proliferation.
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Affiliation(s)
| | - Benjamin Dufour
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Pier-Olivier Martel
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Xavier Lechasseur
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Amani Ange Danielle Brou
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Vincent Roy
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; Département de Biologie Moléculaire, de Biochimie Médicale et de pathologie, Faculté de Médecine, Université Laval, QC G1R 3S3, Canada
| | - Yunqing Chen
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Judith Kimble
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706-1580, USA
| | - Patrick Narbonne
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; Département de Biologie Moléculaire, de Biochimie Médicale et de pathologie, Faculté de Médecine, Université Laval, QC G1R 3S3, Canada.
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41
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Aghayeva U, Bhattacharya A, Sural S, Jaeger E, Churgin M, Fang-Yen C, Hobert O. DAF-16/FoxO and DAF-12/VDR control cellular plasticity both cell-autonomously and via interorgan signaling. PLoS Biol 2021; 19:e3001204. [PMID: 33891586 PMCID: PMC8099054 DOI: 10.1371/journal.pbio.3001204] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/05/2021] [Accepted: 03/23/2021] [Indexed: 01/08/2023] Open
Abstract
Many cell types display the remarkable ability to alter their cellular phenotype in response to specific external or internal signals. Such phenotypic plasticity is apparent in the nematode Caenorhabditis elegans when adverse environmental conditions trigger entry into the dauer diapause stage. This entry is accompanied by structural, molecular, and functional remodeling of a number of distinct tissue types of the animal, including its nervous system. The transcription factor (TF) effectors of 3 different hormonal signaling systems, the insulin-responsive DAF-16/FoxO TF, the TGFβ-responsive DAF-3/SMAD TF, and the steroid nuclear hormone receptor, DAF-12/VDR, a homolog of the vitamin D receptor (VDR), were previously shown to be required for entering the dauer arrest stage, but their cellular and temporal focus of action for the underlying cellular remodeling processes remained incompletely understood. Through the generation of conditional alleles that allowed us to spatially and temporally control gene activity, we show here that all 3 TFs are not only required to initiate tissue remodeling upon entry into the dauer stage, as shown before, but are also continuously required to maintain the remodeled state. We show that DAF-3/SMAD is required in sensory neurons to promote and then maintain animal-wide tissue remodeling events. In contrast, DAF-16/FoxO or DAF-12/VDR act cell-autonomously to control anatomical, molecular, and behavioral remodeling events in specific cell types. Intriguingly, we also uncover non-cell autonomous function of DAF-16/FoxO and DAF-12/VDR in nervous system remodeling, indicating the presence of several insulin-dependent interorgan signaling axes. Our findings provide novel perspectives into how hormonal systems control tissue remodeling.
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Affiliation(s)
- Ulkar Aghayeva
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Abhishek Bhattacharya
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Surojit Sural
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Eliza Jaeger
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Matthew Churgin
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- * E-mail:
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42
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Wen C, Miura T, Voleti V, Yamaguchi K, Tsutsumi M, Yamamoto K, Otomo K, Fujie Y, Teramoto T, Ishihara T, Aoki K, Nemoto T, Hillman EMC, Kimura KD. 3DeeCellTracker, a deep learning-based pipeline for segmenting and tracking cells in 3D time lapse images. eLife 2021; 10:e59187. [PMID: 33781383 PMCID: PMC8009680 DOI: 10.7554/elife.59187] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
Despite recent improvements in microscope technologies, segmenting and tracking cells in three-dimensional time-lapse images (3D + T images) to extract their dynamic positions and activities remains a considerable bottleneck in the field. We developed a deep learning-based software pipeline, 3DeeCellTracker, by integrating multiple existing and new techniques including deep learning for tracking. With only one volume of training data, one initial correction, and a few parameter changes, 3DeeCellTracker successfully segmented and tracked ~100 cells in both semi-immobilized and 'straightened' freely moving worm's brain, in a naturally beating zebrafish heart, and ~1000 cells in a 3D cultured tumor spheroid. While these datasets were imaged with highly divergent optical systems, our method tracked 90-100% of the cells in most cases, which is comparable or superior to previous results. These results suggest that 3DeeCellTracker could pave the way for revealing dynamic cell activities in image datasets that have been difficult to analyze.
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Affiliation(s)
- Chentao Wen
- Graduate School of Science, Nagoya City UniversityNagoyaJapan
| | - Takuya Miura
- Department of Biological Sciences, Graduate School of Science, Osaka UniversityToyonakaJapan
| | - Venkatakaushik Voleti
- Departments of Biomedical Engineering and Radiology and the Zuckerman Mind Brain Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Kazushi Yamaguchi
- Graduate School of Information Science and Technology, Hokkaido UniversitySapporoJapan
- National Institute for Physiological SciencesOkazakiJapan
| | - Motosuke Tsutsumi
- National Institute for Physiological SciencesOkazakiJapan
- Exploratory Research Center on Life and Living SystemsOkazakiJapan
| | - Kei Yamamoto
- National Institute for Basic Biology, National Institutes of Natural SciencesOkazakiJapan
- The Graduate School for Advanced StudyHayamaJapan
| | - Kohei Otomo
- National Institute for Physiological SciencesOkazakiJapan
- Exploratory Research Center on Life and Living SystemsOkazakiJapan
- The Graduate School for Advanced StudyHayamaJapan
| | - Yukako Fujie
- Department of Biological Sciences, Graduate School of Science, Osaka UniversityToyonakaJapan
| | - Takayuki Teramoto
- Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Takeshi Ishihara
- Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Kazuhiro Aoki
- Exploratory Research Center on Life and Living SystemsOkazakiJapan
- National Institute for Basic Biology, National Institutes of Natural SciencesOkazakiJapan
- The Graduate School for Advanced StudyHayamaJapan
| | - Tomomi Nemoto
- National Institute for Physiological SciencesOkazakiJapan
- Exploratory Research Center on Life and Living SystemsOkazakiJapan
- The Graduate School for Advanced StudyHayamaJapan
| | - Elizabeth MC Hillman
- Departments of Biomedical Engineering and Radiology and the Zuckerman Mind Brain Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Koutarou D Kimura
- Graduate School of Science, Nagoya City UniversityNagoyaJapan
- Department of Biological Sciences, Graduate School of Science, Osaka UniversityToyonakaJapan
- RIKEN center for Advanced Intelligence ProjectTokyoJapan
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43
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Tournière O, Dolan D, Richards GS, Sunagar K, Columbus-Shenkar YY, Moran Y, Rentzsch F. NvPOU4/Brain3 Functions as a Terminal Selector Gene in the Nervous System of the Cnidarian Nematostella vectensis. Cell Rep 2021; 30:4473-4489.e5. [PMID: 32234481 DOI: 10.1016/j.celrep.2020.03.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/08/2020] [Accepted: 03/11/2020] [Indexed: 12/27/2022] Open
Abstract
Terminal selectors are transcription factors that control the morphological, physiological, and molecular features that characterize distinct cell types. Here, we show that, in the sea anemone Nematostella vectensis, NvPOU4 is expressed in post-mitotic cells that give rise to a diverse set of neural cell types, including cnidocytes and NvElav1-expressing neurons. Morphological analyses of NvPOU4 mutants crossed to transgenic reporter lines show that the loss of NvPOU4 does not affect the initial specification of neural cells. Transcriptomes derived from the mutants and from different neural cell populations reveal that NvPOU4 is required for the execution of the terminal differentiation program of these neural cells. These findings suggest that POU4 genes have ancient functions as terminal selectors for morphologically and functionally disparate types of neurons and they provide experimental support for the relevance of terminal selectors for understanding the evolution of cell types.
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Affiliation(s)
- Océane Tournière
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway
| | - David Dolan
- Computational Biology Unit, Department for Informatics, University of Bergen, 5006 Bergen, Norway
| | - Gemma Sian Richards
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway
| | - Kartik Sunagar
- Department of Ecology, Evolution and Behaviour, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel; Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Yaara Y Columbus-Shenkar
- Department of Ecology, Evolution and Behaviour, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behaviour, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway; Department for Biological Sciences, University of Bergen, 5006 Bergen, Norway.
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44
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Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, Samuel ADT, Paninski L, Venkatachalam V, Hobert O. NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans. Cell 2021; 184:272-288.e11. [PMID: 33378642 PMCID: PMC10494711 DOI: 10.1016/j.cell.2020.12.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 06/30/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering a multicolor transgene called NeuroPAL (a neuronal polychromatic atlas of landmarks). NeuroPAL worms share a stereotypical multicolor fluorescence map for the entire hermaphrodite nervous system that resolves all neuronal identities. Neurons labeled with NeuroPAL do not exhibit fluorescence in the green, cyan, or yellow emission channels, allowing the transgene to be used with numerous reporters of gene expression or neuronal dynamics. We showcase three applications that leverage NeuroPAL for nervous-system-wide neuronal identification. First, we determine the brainwide expression patterns of all metabotropic receptors for acetylcholine, GABA, and glutamate, completing a map of this communication network. Second, we uncover changes in cell fate caused by transcription factor mutations. Third, we record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding for these stimuli.
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Affiliation(s)
- Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
| | - Albert Lin
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Amin Nejatbakhsh
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Erdem Varol
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Ruoxi Sun
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Gonzalo E Mena
- Department of Statistics and Data Science Initiative, Harvard University, Cambridge, MA 02138, USA
| | - Aravinthan D T Samuel
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Liam Paninski
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | | | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
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45
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Abstract
Large amounts of effort have been invested in trying to understand how a single genome is able to specify the identity of hundreds of cell types. Inspired by some aspects of Caenorhabditis elegans biology, we implemented an in silico evolutionary strategy to produce gene regulatory networks (GRNs) that drive cell-specific gene expression patterns, mimicking the process of terminal cell differentiation. Dynamics of the gene regulatory networks are governed by a thermodynamic model of gene expression, which uses DNA sequences and transcription factor degenerate position weight matrixes as input. In a version of the model, we included chromatin accessibility. Experimentally, it has been determined that cell-specific and broadly expressed genes are regulated differently. In our in silico evolved GRNs, broadly expressed genes are regulated very redundantly and the architecture of their cis-regulatory modules is different, in accordance to what has been found in C. elegans and also in other systems. Finally, we found differences in topological positions in GRNs between these two classes of genes, which help to explain why broadly expressed genes are so resilient to mutations. Overall, our results offer an explanatory hypothesis on why broadly expressed genes are regulated so redundantly compared to cell-specific genes, which can be extrapolated to phenomena such as ChIP-seq HOT regions.
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Affiliation(s)
- Carlos Mora-Martinez
- Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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46
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The Conserved ASCL1/MASH-1 Ortholog HLH-3 Specifies Sex-Specific Ventral Cord Motor Neuron Fate in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:4201-4213. [PMID: 32973001 PMCID: PMC7642948 DOI: 10.1534/g3.120.401458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neural specification is regulated by one or many transcription factors that control expression of effector genes that mediate function and determine neuronal type. Here we identify a novel role for one conserved proneural factor, the bHLH protein HLH-3, implicated in the specification of sex-specific ventral cord motor neurons in C. elegans. Proneural genes act in early stages of neurogenesis in early progenitors, but here, we demonstrate a later role for hlh-3. First, we document that differentiation of the ventral cord type C motor neuron class (VC) within their neuron class, is dynamic in time and space. Expression of VC class-specific and subclass-specific identity genes is distinct through development and is dependent on the VC position along the A-P axis and their proximity to the vulva. Our characterization of the expression of VC class and VC subclass-specific differentiation markers in the absence of hlh-3 function reveals that VC fate specification, differentiation, and morphology requires hlh-3 function. Finally, we conclude that hlh-3 cell-autonomously specifies VC cell fate.
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47
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Molina-García L, Lloret-Fernández C, Cook SJ, Kim B, Bonnington RC, Sammut M, O'Shea JM, Gilbert SPR, Elliott DJ, Hall DH, Emmons SW, Barrios A, Poole RJ. Direct glia-to-neuron transdifferentiation gives rise to a pair of male-specific neurons that ensure nimble male mating. eLife 2020; 9:e48361. [PMID: 33138916 PMCID: PMC7609048 DOI: 10.7554/elife.48361] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
Sexually dimorphic behaviours require underlying differences in the nervous system between males and females. The extent to which nervous systems are sexually dimorphic and the cellular and molecular mechanisms that regulate these differences are only beginning to be understood. We reveal here a novel mechanism by which male-specific neurons are generated in Caenorhabditis elegans through the direct transdifferentiation of sex-shared glial cells. This glia-to-neuron cell fate switch occurs during male sexual maturation under the cell-autonomous control of the sex-determination pathway. We show that the neurons generated are cholinergic, peptidergic, and ciliated putative proprioceptors which integrate into male-specific circuits for copulation. These neurons ensure coordinated backward movement along the mate's body during mating. One step of the mating sequence regulated by these neurons is an alternative readjustment movement performed when intromission becomes difficult to achieve. Our findings reveal programmed transdifferentiation as a developmental mechanism underlying flexibility in innate behaviour.
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Affiliation(s)
- Laura Molina-García
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Carla Lloret-Fernández
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Steven J Cook
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineNew YorkUnited States
| | - Byunghyuk Kim
- Department of Genetics, Albert Einstein College of MedicineNew YorkUnited States
| | - Rachel C Bonnington
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Michele Sammut
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Jack M O'Shea
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Sophie PR Gilbert
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - David J Elliott
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - David H Hall
- Department of Genetics, Albert Einstein College of MedicineNew YorkUnited States
| | - Scott W Emmons
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineNew YorkUnited States
- Department of Genetics, Albert Einstein College of MedicineNew YorkUnited States
| | - Arantza Barrios
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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48
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cnd-1/NeuroD1 Functions with the Homeobox Gene ceh-5/Vax2 and Hox Gene ceh-13/labial To Specify Aspects of RME and DD Neuron Fate in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:3071-3085. [PMID: 32601060 PMCID: PMC7466980 DOI: 10.1534/g3.120.401515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Identifying the mechanisms behind neuronal fate specification are key to understanding normal neural development in addition to neurodevelopmental disorders such as autism and schizophrenia. In vivo cell fate specification is difficult to study in vertebrates. However, the nematode Caenorhabditis elegans, with its invariant cell lineage and simple nervous system of 302 neurons, is an ideal organism to explore the earliest stages of neural development. We used a comparative transcriptome approach to examine the role of cnd-1/NeuroD1 in C. elegans nervous system development and function. This basic helix-loop-helix transcription factor is deeply conserved across phyla and plays a crucial role in cell fate specification in both the vertebrate nervous system and pancreas. We find that cnd-1 controls expression of ceh-5, a Vax2-like homeobox class transcription factor, in the RME head motorneurons and PVQ tail interneurons. We also show that cnd-1 functions redundantly with the Hox gene ceh-13/labial in defining the fate of DD1 and DD2 embryonic ventral nerve cord motorneurons. These data highlight the utility of comparative transcriptomes for identifying transcription factor targets and understanding gene regulatory networks.
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Sae-Lee W, Scott LL, Brose L, Encarnacion AJ, Shi T, Kore P, Oyibo LO, Ye C, Rozmiarek SK, Pierce JT. APP-Induced Patterned Neurodegeneration Is Exacerbated by APOE4 in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2020; 10:2851-2861. [PMID: 32580938 PMCID: PMC7407474 DOI: 10.1534/g3.120.401486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/19/2020] [Indexed: 11/18/2022]
Abstract
Genetic and epidemiological studies have found that variations in the amyloid precursor protein (APP) and the apoliopoprotein E (APOE) genes represent major modifiers of the progressive neurodegeneration in Alzheimer's disease (AD). An extra copy of or gain-of-function mutations in APP correlate with early onset AD. Compared to the other variants (APOE2 and APOE3), the ε4 allele of APOE (APOE4) hastens and exacerbates early and late onset forms of AD. Convenient in vivo models to study how APP and APOE4 interact at the cellular and molecular level to influence neurodegeneration are lacking. Here, we show that the nematode C. elegans can model important aspects of AD including age-related, patterned neurodegeneration that is exacerbated by APOE4 Specifically, we found that APOE4, but not APOE3, acts with APP to hasten and expand the pattern of cholinergic neurodegeneration caused by APP Molecular mechanisms underlying how APP and APOE4 synergize to kill some neurons while leaving others unaffected may be uncovered using this convenient worm model of neurodegeneration.
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Affiliation(s)
- Wisath Sae-Lee
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Luisa L Scott
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Lotti Brose
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Aliyah J Encarnacion
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Ted Shi
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Pragati Kore
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Lashaun O Oyibo
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Congxi Ye
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Susan K Rozmiarek
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
| | - Jonathan T Pierce
- Center for Learning and Memory; Waggoner Center for Alcohol and Addiction Research; Cell and Molecular Biology; Department of Neuroscience, The University of Texas at Austin, TX, 78712
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50
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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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