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Ochs ME, McWhirter RM, Unckless RL, Miller DM, Lundquist EA. Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration. BMC Genomics 2022; 23:13. [PMID: 34986795 PMCID: PMC8734324 DOI: 10.1186/s12864-021-08217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/23/2021] [Indexed: 11/18/2022] Open
Abstract
Migration of neuroblasts and neurons from their birthplace is central to the formation of neural circuits and networks. ETR-1 is the Caenorhabditis elegans homolog of the CELF1 (CUGBP, ELAV-like family 1) RNA-processing factor involved in neuromuscular disorders. etr-1 regulates body wall muscle differentiation. Our previous work showed that etr-1 in muscle has a non-autonomous role in neuronal migration, suggesting that ETR-1 is involved in the production of a signal emanating from body wall muscle that controls neuroblast migration and that interacts with Wnt signaling. etr-1 is extensively alternatively-spliced, and we identified the viable etr-1(lq61) mutant, caused by a stop codon in alternatively-spliced exon 8 and only affecting etr-1 isoforms containing exon 8. We took advantage of viable etr-1(lq61) to identify potential RNA targets of ETR-1 in body wall muscle using a combination of fluorescence activated cell sorting (FACS) of body wall muscles from wild-type and etr-1(lq61) and subsequent RNA-seq. This analysis revealed genes whose splicing and transcript levels were controlled by ETR-1 exon 8 isoforms, and represented a broad spectrum of genes involved in muscle differentiation, myofilament lattice structure, and physiology. Genes with transcripts underrepresented in etr-1(lq61) included those involved in ribosome function and translation, similar to potential CELF1 targets identified in chick cardiomyocytes. This suggests that at least some targets of ETR-1 might be conserved in vertebrates, and that ETR-1 might generally stimulate translation in muscles. As proof-of-principle, a functional analysis of a subset of ETR-1 targets revealed genes involved in AQR and PQR neuronal migration. One such gene, lev-11/tropomyosin, requires ETR-1 for alternative splicing, and another, unc-52/perlecan, requires ETR-1 for the production of long isoforms containing 3' exons. In sum, these studies identified gene targets of ETR-1/CELF1 in muscles, which included genes involved in muscle development and physiology, and genes with novel roles in neuronal migration.
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Affiliation(s)
- Matthew E Ochs
- Program in Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Rebecca M McWhirter
- Department of Cell and Developmental Biology and Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37203, USA
| | - Robert L Unckless
- Program in Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - David M Miller
- Department of Cell and Developmental Biology and Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37203, USA
| | - Erik A Lundquist
- Program in Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.
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2
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Tang LTH, Trivedi M, Freund J, Salazar CJ, Rahman M, Ramirez-Suarez NJ, Lee G, Wang Y, Grant BD, Bülow HE. The CATP-8/P5A-type ATPase functions in multiple pathways during neuronal patterning. PLoS Genet 2021; 17:e1009475. [PMID: 34197450 PMCID: PMC8279360 DOI: 10.1371/journal.pgen.1009475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 06/10/2021] [Indexed: 11/18/2022] Open
Abstract
The assembly of neuronal circuits involves the migrations of neurons from their place of birth to their final location in the nervous system, as well as the coordinated growth and patterning of axons and dendrites. In screens for genes required for patterning of the nervous system, we identified the catp-8/P5A-ATPase as an important regulator of neural patterning. P5A-ATPases are part of the P-type ATPases, a family of proteins known to serve a conserved function as transporters of ions, lipids and polyamines in unicellular eukaryotes, plants, and humans. While the function of many P-type ATPases is relatively well understood, the function of P5A-ATPases in metazoans remained elusive. We show here, that the Caenorhabditis elegans ortholog catp-8/P5A-ATPase is required for defined aspects of nervous system development. Specifically, the catp-8/P5A-ATPase serves functions in shaping the elaborately sculpted dendritic trees of somatosensory PVD neurons. Moreover, catp-8/P5A-ATPase is required for axonal guidance and repulsion at the midline, as well as embryonic and postembryonic neuronal migrations. Interestingly, not all axons at the midline require catp-8/P5A-ATPase, although the axons run in the same fascicles and navigate the same space. Similarly, not all neuronal migrations require catp-8/P5A-ATPase. A CATP-8/P5A-ATPase reporter is localized to the ER in most, if not all, tissues and catp-8/P5A-ATPase can function both cell-autonomously and non-autonomously to regulate neuronal development. Genetic analyses establish that catp-8/P5A-ATPase can function in multiple pathways, including the Menorin pathway, previously shown to control dendritic patterning in PVD, and Wnt signaling, which functions to control neuronal migrations. Lastly, we show that catp-8/P5A-ATPase is required for localizing select transmembrane proteins necessary for dendrite morphogenesis. Collectively, our studies suggest that catp-8/P5A-ATPase serves diverse, yet specific, roles in different genetic pathways and may be involved in the regulation or localization of transmembrane and secreted proteins to specific subcellular compartments.
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Affiliation(s)
- Leo T. H. Tang
- Department of Genetics Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Meera Trivedi
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jenna Freund
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Christopher J. Salazar
- Department of Genetics Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Maisha Rahman
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Nelson J. Ramirez-Suarez
- Department of Genetics Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Garrett Lee
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yu Wang
- Department of Molecular Biology & Biochemistry, Rutgers Center for Lipid Research, Rutgers University, Piscataway, New Jersey, United States of America
| | - Barth D. Grant
- Department of Molecular Biology & Biochemistry, Rutgers Center for Lipid Research, Rutgers University, Piscataway, New Jersey, United States of America
| | - Hannes E. Bülow
- Department of Genetics Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
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3
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Abstract
Establishment of neural circuits requires reproducible and precise interactions between growing axons, dendrites and their tissue environment. Cell adhesion molecules and guidance factors are involved in the process, but how specificity is achieved remains poorly understood. Glycans are the third major class of biopolymers besides nucleic acids and proteins, and are usually covalently linked to proteins to form glycoconjugates. Common to most glycans is an extraordinary level of molecular diversity, making them attractive candidates to contribute specificity during neural development. Indeed, many genes important for neural development encode glycoproteins, or enzymes involved in synthesizing or modifying glycans. Glycoconjugates are classified based on both the types of glycans and type of attachment that link them to proteins. Here I discuss progress in understanding the function of glycans, glycan modifications and glycoconjugates during neural development in Caenorhabditis elegans. I will also highlight relevance to human disease and known roles of glycoconjugates in regeneration.
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Affiliation(s)
- Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States.
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4
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Rella L, Fernandes Póvoa EE, Mars J, Ebbing ALP, Schoppink L, Betist MC, Korswagen HC. A switch from noncanonical to canonical Wnt signaling stops neuroblast migration through a Slt-Robo and RGA-9b/ARHGAP-dependent mechanism. Proc Natl Acad Sci U S A 2021; 118:e2013239118. [PMID: 33737394 PMCID: PMC8000201 DOI: 10.1073/pnas.2013239118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Members of the Wnt family of secreted glycoproteins regulate cell migration through distinct canonical and noncanonical signaling pathways. Studies of vertebrate development and disease have shown that these pathways can have opposing effects on cell migration, but the mechanism of this functional interplay is not known. In the nematode Caenorhabditis elegans, a switch from noncanonical to canonical Wnt signaling terminates the long-range migration of the QR neuroblast descendants, providing a tractable system to study this mechanism in vivo. Here, we show that noncanonical Wnt signaling acts through PIX-1/RhoGEF, while canonical signaling directly activates the Slt-Robo pathway component EVA-1/EVA1C and the Rho GTPase-activating protein RGA-9b/ARHGAP, which are required for migration inhibition. Our results support a model in which cross-talk between noncanonical and canonical Wnt signaling occurs through antagonistic regulation of the Rho GTPases that drive cell migration.
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Affiliation(s)
- Lorenzo Rella
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Euclides E Fernandes Póvoa
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Jonas Mars
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Annabel L P Ebbing
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Luc Schoppink
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Marco C Betist
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands;
- Institute of Biodynamics and Biocomplexity, Developmental Biology, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
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Dubois C, Gupta S, Mugler A, Félix MA. Temporally regulated cell migration is sensitive to variation in body size. Development 2021; 148:dev196949. [PMID: 33593818 PMCID: PMC10683003 DOI: 10.1242/dev.196949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
Few studies have measured the robustness to perturbations of the final position of a long-range migrating cell. In the nematode Caenorhabditis elegans, the QR neuroblast migrates anteriorly, while undergoing three division rounds. We study the final position of two of its great-granddaughters, the end of migration of which was previously shown to depend on a timing mechanism. We find that the variance in their final position is similar to that of other long-range migrating neurons. As expected from the timing mechanism, the position of QR descendants depends on body size, which we varied by changing maternal age or using body size mutants. Using a mathematical model, we show that body size variation is partially compensated for. Applying environmental perturbations, we find that the variance in final position increased following starvation at hatching. The mean position is displaced upon a temperature shift. Finally, highly significant variation was found among C. elegans wild isolates. Overall, this study reveals that the final position of these neurons is quite robust to stochastic variation, shows some sensitivity to body size and to external perturbations, and varies in the species.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Clément Dubois
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
| | - Shivam Gupta
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
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Synaptic Protein Degradation Controls Sexually Dimorphic Circuits through Regulation of DCC/UNC-40. Curr Biol 2020; 30:4128-4141.e5. [PMID: 32857970 PMCID: PMC7658809 DOI: 10.1016/j.cub.2020.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/13/2020] [Accepted: 08/03/2020] [Indexed: 12/27/2022]
Abstract
Sexually dimorphic circuits underlie behavioral differences between the sexes, yet the molecular mechanisms involved in their formation are poorly understood. We show here that sexually dimorphic connectivity patterns arise in C. elegans through local ubiquitin-mediated protein degradation in selected synapses of one sex but not the other. Specifically, synaptic degradation occurs via binding of the evolutionary conserved E3 ligase SEL-10/FBW7 to a phosphodegron binding site of the netrin receptor UNC-40/DCC (Deleted in Colorectal Cancer), resulting in degradation of UNC-40. In animals carrying an undegradable unc-40 gain-of-function allele, synapses were retained in both sexes, compromising the activity of the circuit without affecting neurite guidance. Thus, by decoupling the synaptic and guidance functions of the netrin pathway, we reveal a critical role for dimorphic protein degradation in controlling neuronal connectivity and activity. Additionally, the interaction between SEL-10 and UNC-40 is necessary not only for sex-specific synapse pruning, but also for other synaptic functions. These findings provide insight into the mechanisms that generate sex-specific differences in neuronal connectivity, activity, and function. Sex-specific synapse pruning during development is regulated by the ubiquitin pathway The E3 ligase SEL-10 targets the UNC-40 netrin receptor via binding to a CPD motif UNC-40 degradation leads to synapse removal only in hermaphrodites, not males CPD mutations disrupt synaptic functions of UNC-40, leaving axon guidance intact
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The Predicted RNA-Binding Protein ETR-1/CELF1 Acts in Muscles To Regulate Neuroblast Migration in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:2365-2376. [PMID: 32398235 PMCID: PMC7341121 DOI: 10.1534/g3.120.401182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neuroblast migration is a critical aspect of nervous system development (e.g., neural crest migration). In an unbiased forward genetic screen, we identified a novel player in neuroblast migration, the ETR-1/CELF1 RNA binding protein. CELF1 RNA binding proteins are involved in multiple aspects of RNA processing including alternative splicing, stability, and translation. We find that a specific mutation in alternatively-spliced exon 8 results in migration defects of the AQR and PQR neurons, and not the embryonic lethality and body wall muscle defects of complete knockdown of the locus. Surprisingly, ETR-1 was required in body wall muscle cells for AQR/PQR migration (i.e., it acts cell non-autonomously). Genetic interactions indicate that ETR-1 acts with Wnt signaling, either in the Wnt pathway or in a parallel pathway. Possibly, ETR-1 is involved in the production of a Wnt signal or a parallel signal by the body wall muscles that controls AQR and PQR neuronal migration. In humans, CELF1 is involved in a number of neuromuscular disorders. If the role of ETR-1/CELF1 is conserved, these disorders might also involve cell or neuronal migration. Finally, we describe a technique of amplicon sequencing to detect rare, cell-specific genome edits by CRISPR/Cas9 in vivo (CRISPR-seq) as an alternative to the T7E1 assay.
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