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Aguilar GR, Vidal B, Ji H, Evenblij J, Ji H, Valperga G, Liao CP, Fang-Yen C, Hobert O. Functional analysis of conserved C. elegans bHLH family members uncovers lifespan control by a peptidergic hub neuron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603289. [PMID: 39071424 PMCID: PMC11275782 DOI: 10.1101/2024.07.12.603289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Throughout the animal kingdom, several members of the basic helix-loop-helix (bHLH) family act as proneural genes during early steps of nervous system development. Roles of bHLH genes in specifying terminal differentiation of postmitotic neurons have been less extensively studied. We analyze here the function of five C. elegans bHLH genes, falling into three phylogenetically conserved subfamilies, which are continuously expressed in a very small number of postmitotic neurons in the central nervous system. We show (a) that two orthologs of the vertebrate bHLHb4/b5 genes, called hlh-17 and hlh-32, function redundantly to specify the identity of a single head interneuron (AUA), as well as an individual motor neuron (VB2), (b) that the PTF1a ortholog hlh-13 acts as a terminal selector to control terminal differentiation and function of the sole octopaminergic neuron class in C. elegans , RIC, and (c) that the NHLH1/2 ortholog hlh-15 controls terminal differentiation and function of the peptidergic AVK head interneuron class, a known neuropeptidergic signaling hub in the animal. Strikingly, through null mutant analysis and cell-specific rescue experiments, we find that loss of hlh-15/NHLH in the peptidergic AVK neurons and the resulting abrogation of neuropeptide secretion causes a substantially expanded lifespan of the animal, revealing an unanticipated impact of a central, peptidergic hub neuron in regulating lifespan, which we propose to be akin to hypothalamic control of lifespan in vertebrates. Taken together, our functional analysis reveals themes of bHLH gene function during terminal differentiation that are complementary to the earlier lineage specification roles of other bHLH family members. However, such late functions are much more sparsely employed by members of the bHLH transcription factor family, compared to the function of the much more broadly employed homeodomain transcription factor family.
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2
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Hayden AN, Brandel KL, Merlau PR, Vijayakumar P, Leptich EJ, Pietryk EW, Gaytan ES, Ni CW, Chao HT, Rosenfeld JA, Arey RN. Behavioral screening of conserved RNA-binding proteins reveals CEY-1/YBX RNA-binding protein dysfunction leads to impairments in memory and cognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574402. [PMID: 38260399 PMCID: PMC10802296 DOI: 10.1101/2024.01.05.574402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
RNA-binding proteins (RBPs) regulate translation and plasticity which are required for memory. RBP dysfunction has been linked to a range of neurological disorders where cognitive impairments are a key symptom. However, of the 2,000 RBPs in the human genome, many are uncharacterized with regards to neurological phenotypes. To address this, we used the model organism C. elegans to assess the role of 20 conserved RBPs in memory. We identified eight previously uncharacterized memory regulators, three of which are in the C. elegans Y-Box (CEY) RBP family. Of these, we determined that cey-1 is the closest ortholog to the mammalian Y-Box (YBX) RBPs. We found that CEY-1 is both necessary in the nervous system for memory ability and sufficient to increase memory. Leveraging human datasets, we found both copy number variation losses and single nucleotide variants in YBX1 and YBX3 in individuals with neurological symptoms. We identified one predicted deleterious YBX3 variant of unknown significance, p.Asn127Tyr, in two individuals with neurological symptoms. Introducing this variant into endogenous cey-1 locus caused memory deficits in the worm. We further generated two humanized worm lines expressing human YBX3 or YBX1 at the cey-1 locus to test evolutionary conservation of YBXs in memory and the potential functional significance of the p.Asn127Tyr variant. Both YBX1/3 can functionally replace cey-1, and introduction of p.Asn127Tyr into the humanized YBX3 locus caused memory deficits. Our study highlights the worm as a model to reveal memory regulators and identifies YBX dysfunction as a potential new source of rare neurological disease.
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Affiliation(s)
- Ashley N Hayden
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Katie L Brandel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Paul R Merlau
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | | | - Emily J Leptich
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Edward W Pietryk
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
| | - Elizabeth S Gaytan
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Postbaccalaureate Research Education Program, Baylor College of Medicine, Houston, TX, 77030
| | - Connie W Ni
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Neuroscience, Rice University, Houston, TX 77005
| | - Hsiao-Tuan Chao
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Baylor Genetics Laboratories, Houston, TX 77021
| | - Rachel N Arey
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
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3
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Mullan TW, Felton T, Tam J, Kasem O, Yeung TJ, Memar N, Schnabel R, Poole RJ. Control of successive unequal cell divisions by neural cell fate regulators determines embryonic neuroblast cell size. Development 2024; 151:dev200981. [PMID: 38205939 PMCID: PMC10911278 DOI: 10.1242/dev.200981] [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: 05/25/2022] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
Asymmetric cell divisions often generate daughter cells of unequal size in addition to different fates. In some contexts, daughter cell size asymmetry is thought to be a key input to specific binary cell fate decisions. An alternative possibility is that unequal division is a mechanism by which a variety of cells of different sizes are generated during embryonic development. We show here that two unequal cell divisions precede neuroblast formation in the C lineage of Caenorhabditis elegans. The equalisation of these divisions in a pig-1/MELK mutant background has little effect on neuroblast specification. Instead, we demonstrate that let-19/MDT13 is a regulator of the proneural basic helix-loop-helix transcription factor hlh-14/ASCL1 and find that both are required to concomitantly regulate the acquisition of neuroblast identity and neuroblast cell size. Thus, embryonic neuroblast cell size in this lineage is progressively regulated in parallel with identity by key neural cell fate regulators. We propose that key cell fate determinants have a previously unappreciated function in regulating unequal cleavage, and therefore cell size, of the progenitor cells whose daughter cell fates they then go on to specify.
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Affiliation(s)
- Thomas W. Mullan
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Terry Felton
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Janis Tam
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Osama Kasem
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Tim J. Yeung
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Nadin Memar
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Institut für Genetik, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Ralf Schnabel
- Institut für Genetik, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Richard J. Poole
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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4
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Liu J, Murray JI. Mechanisms of lineage specification in Caenorhabditis elegans. Genetics 2023; 225:iyad174. [PMID: 37847877 DOI: 10.1093/genetics/iyad174] [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: 08/26/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
The studies of cell fate and lineage specification are fundamental to our understanding of the development of multicellular organisms. Caenorhabditis elegans has been one of the premiere systems for studying cell fate specification mechanisms at single cell resolution, due to its transparent nature, the invariant cell lineage, and fixed number of somatic cells. We discuss the general themes and regulatory mechanisms that have emerged from these studies, with a focus on somatic lineages and cell fates. We next review the key factors and pathways that regulate the specification of discrete cells and lineages during embryogenesis and postembryonic development; we focus on transcription factors and include numerous lineage diagrams that depict the expression of key factors that specify embryonic founder cells and postembryonic blast cells, and the diverse somatic cell fates they generate. We end by discussing some future perspectives in cell and lineage specification.
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Affiliation(s)
- Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Reilly DK, Schwarz EM, Muirhead CS, Robidoux AN, Narayan A, Doma MK, Sternberg PW, Srinivasan J. Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in Caenorhabditis elegans. Genetics 2023; 223:iyad026. [PMID: 36801937 PMCID: PMC10319972 DOI: 10.1093/genetics/iyad026] [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: 12/22/2022] [Revised: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 02/20/2023] Open
Abstract
The nematode Caenorhabditis elegans utilizes chemosensation to navigate an ever-changing environment for its survival. A class of secreted small-molecule pheromones, termed ascarosides, play an important role in olfactory perception by affecting biological functions ranging from development to behavior. The ascaroside #8 (ascr#8) mediates sex-specific behaviors, driving avoidance in hermaphrodites and attraction in males. Males sense ascr#8 via the ciliated male-specific cephalic sensory (CEM) neurons, which exhibit radial symmetry along dorsal-ventral and left-right axes. Calcium imaging studies suggest a complex neural coding mechanism that translates stochastic physiological responses in these neurons to reliable behavioral outputs. To test the hypothesis that neurophysiological complexity arises from differential expression of genes, we performed cell-specific transcriptomic profiling; this revealed between 18 and 62 genes with at least twofold higher expression in a specific CEM neuron subtype vs both other CEM neurons and adult males. These included two G protein-coupled receptor (GPCR) genes, srw-97 and dmsr-12, that were specifically expressed in nonoverlapping subsets of CEM neurons and whose expression was confirmed by GFP reporter analysis. Single CRISPR-Cas9 knockouts of either srw-97 or dmsr-12 resulted in partial defects, while a double knockout of both srw-97 and dmsr-12 completely abolished the attractive response to ascr#8. Together, our results suggest that the evolutionarily distinct GPCRs SRW-97 and DMSR-12 act nonredundantly in discrete olfactory neurons to facilitate male-specific sensation of ascr#8.
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Affiliation(s)
- Douglas K Reilly
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Caroline S Muirhead
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Annalise N Robidoux
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Anusha Narayan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Meenakshi K Doma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01605, USA
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6
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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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7
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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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8
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Filippopoulou K, Couillault C, Bertrand V. Multiple neural bHLHs ensure the precision of a neuronal specification event in Caenorhabditis elegans. Biol Open 2021; 10:273578. [PMID: 34854469 PMCID: PMC8713986 DOI: 10.1242/bio.058976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Neural bHLH transcription factors play a key role in the early steps of neuronal specification in many animals. We have previously observed that the Achaete-Scute HLH-3, the Olig HLH-16 and their binding partner the E-protein HLH-2 activate the terminal differentiation program of a specific class of cholinergic neurons, AIY, in Caenorhabditis elegans. Here we identify a role for a fourth bHLH, the Neurogenin NGN-1, in this process, raising the question of why so many neural bHLHs are required for a single neuronal specification event. Using quantitative imaging we show that the combined action of different bHLHs is needed to activate the correct level of expression of the terminal selector transcription factors TTX-3 and CEH-10 that subsequently initiate and maintain the expression of a large battery of terminal differentiation genes. Surprisingly, the different bHLHs have an antagonistic effect on another target, the proapoptotic BH3-only factor EGL-1, normally not expressed in AIY and otherwise detrimental for its specification. We propose that the use of multiple neural bHLHs allows robust neuronal specification while, at the same time, preventing spurious activation of deleterious genes. Summary: During neuronal specification, the combined action of several neural bHLHs ensures the robust activation of terminal selector transcription factor expression and prevents the activation of deleterious genes.
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Affiliation(s)
| | - Carole Couillault
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille 13009, France
| | - Vincent Bertrand
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille 13009, France
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9
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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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10
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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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11
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Charest J, Daniele T, Wang J, Bykov A, Mandlbauer A, Asparuhova M, Röhsner J, Gutiérrez-Pérez P, Cochella L. Combinatorial Action of Temporally Segregated Transcription Factors. Dev Cell 2020; 55:483-499.e7. [PMID: 33002421 PMCID: PMC7704111 DOI: 10.1016/j.devcel.2020.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 09/01/2020] [Indexed: 01/05/2023]
Abstract
Combinatorial action of transcription factors (TFs) with partially overlapping expression is a widespread strategy to generate novel gene-expression patterns and, thus, cellular diversity. Known mechanisms underlying combinatorial activity require co-expression of TFs within the same cell. Here, we describe the mechanism by which two TFs that are never co-expressed generate a new, intersectional expression pattern in C. elegans embryos: lineage-specific priming of a gene by a transiently expressed TF generates a unique intersection with a second TF acting on the same gene four cell divisions later; the second TF is expressed in multiple cells but only activates transcription in those where priming occurred. Early induction of active transcription is necessary and sufficient to establish a competent state, maintained by broadly expressed regulators in the absence of the initial trigger. We uncover additional cells diversified through this mechanism. Our findings define a mechanism for combinatorial TF activity with important implications for generation of cell-type diversity. Lineage-specific priming enables asymmetric gene expression in L/R neuron pairs Transient, lineage-specific TFs prime a locus for later activation by a bilateral TF An early active transcriptional state is necessary and sufficient for priming Maintenance of asymmetric primed state occurs in a symmetric regulatory environment
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Affiliation(s)
- Julien Charest
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Thomas Daniele
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Aleksandr Bykov
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Ariane Mandlbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Mila Asparuhova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Josef Röhsner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Paula Gutiérrez-Pérez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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12
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Barrière A, Bertrand V. Neuronal specification in C. elegans: combining lineage inheritance with intercellular signaling. J Neurogenet 2020; 34:273-281. [PMID: 32603241 DOI: 10.1080/01677063.2020.1781850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nervous system is composed of a high diversity of neuronal types. How this diversity is generated during development is a key question in neurobiology. Addressing this question is one of the reasons that led Sydney Brenner to develop the nematode C. elegans as a model organism. While there was initially a debate on whether the neuronal specification follows a 'European' model (determined by ancestry) or an 'American' model (determined by intercellular communication), several decades of research have established that the truth lies somewhere in between. Neurons are specified by the combination of transcription factors inherited from the ancestor cells and signaling between neighboring cells (especially Wnt and Notch signaling). This converges to the activation in newly generated postmitotic neurons of a specific set of terminal selector transcription factors that initiate and maintain the differentiation of the neuron. In this review, we also discuss the evolution of these specification mechanisms in other nematodes and beyond.
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Affiliation(s)
- Antoine Barrière
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Vincent Bertrand
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
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13
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Chute CD, DiLoreto EM, Zhang YK, Reilly DK, Rayes D, Coyle VL, Choi HJ, Alkema MJ, Schroeder FC, Srinivasan J. Co-option of neurotransmitter signaling for inter-organismal communication in C. elegans. Nat Commun 2019; 10:3186. [PMID: 31320626 PMCID: PMC6639374 DOI: 10.1038/s41467-019-11240-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/28/2019] [Indexed: 12/22/2022] Open
Abstract
Biogenic amine neurotransmitters play a central role in metazoan biology, and both their chemical structures and cognate receptors are evolutionarily conserved. Their primary roles are in cell-to-cell signaling, as biogenic amines are not normally recruited for communication between separate individuals. Here, we show that in the nematode C. elegans, a neurotransmitter-sensing G protein-coupled receptor, TYRA-2, is required for avoidance responses to osas#9, an ascaroside pheromone that incorporates the neurotransmitter, octopamine. Neuronal ablation, cell-specific genetic rescue, and calcium imaging show that tyra-2 expression in the nociceptive neuron, ASH, is necessary and sufficient to induce osas#9 avoidance. Ectopic expression in the AWA neuron, which is generally associated with attractive responses, reverses the response to osas#9, resulting in attraction instead of avoidance behavior, confirming that TYRA-2 partakes in the sensing of osas#9. The TYRA-2/osas#9 signaling system represents an inter-organismal communication channel that evolved via co-option of a neurotransmitter and its cognate receptor.
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Affiliation(s)
- Christopher D Chute
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA, 01605, USA
- BioHelix Corporation, Beverly, MA, 01915, USA
| | - Elizabeth M DiLoreto
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA, 01605, USA
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas K Reilly
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA, 01605, USA
| | - Diego Rayes
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (CONICET), Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, B8000, Argentina
| | - Veronica L Coyle
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA, 01605, USA
- AbbVie, Cambridge, MA, 02139, USA
| | - Hee June Choi
- Biomedical Engineering Department, Worcester Polytechnic Institute, Worcester, MA, 01605, USA
| | - Mark J Alkema
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jagan Srinivasan
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA, 01605, USA.
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14
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Koelle MR. Neurotransmitter signaling through heterotrimeric G proteins: insights from studies in C. elegans. WORMBOOK : THE ONLINE REVIEW OF C. ELEGANS BIOLOGY 2018; 2018:1-52. [PMID: 26937633 PMCID: PMC5010795 DOI: 10.1895/wormbook.1.75.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neurotransmitters signal via G protein coupled receptors (GPCRs) to modulate activity of neurons and muscles. C. elegans has ∼150 G protein coupled neuropeptide receptor homologs and 28 additional GPCRs for small-molecule neurotransmitters. Genetic studies in C. elegans demonstrate that neurotransmitters diffuse far from their release sites to activate GPCRs on distant cells. Individual receptor types are expressed on limited numbers of cells and thus can provide very specific regulation of an individual neural circuit and behavior. G protein coupled neurotransmitter receptors signal principally via the three types of heterotrimeric G proteins defined by the G alpha subunits Gαo, Gαq, and Gαs. Each of these G alpha proteins is found in all neurons plus some muscles. Gαo and Gαq signaling inhibit and activate neurotransmitter release, respectively. Gαs signaling, like Gαq signaling, promotes neurotransmitter release. Many details of the signaling mechanisms downstream of Gαq and Gαs have been delineated and are consistent with those of their mammalian orthologs. The details of the signaling mechanism downstream of Gαo remain a mystery. Forward genetic screens in C. elegans have identified new molecular components of neural G protein signaling mechanisms, including Regulators of G protein Signaling (RGS proteins) that inhibit signaling, a new Gαq effector (the Trio RhoGEF domain), and the RIC-8 protein that is required for neuronal Gα signaling. A model is presented in which G proteins sum up the variety of neuromodulator signals that impinge on a neuron to calculate its appropriate output level.
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Affiliation(s)
- Michael R Koelle
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven CT 06520 USA
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15
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Zheng C, Jin FQ, Trippe BL, Wu J, Chalfie M. Inhibition of cell fate repressors secures the differentiation of the touch receptor neurons of Caenorhabditis elegans. Development 2018; 145:dev.168096. [PMID: 30291162 DOI: 10.1242/dev.168096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
Abstract
Terminal differentiation generates the specialized features and functions that allow postmitotic cells to acquire their distinguishing characteristics. This process is thought to be controlled by transcription factors called 'terminal selectors' that directly activate a set of downstream effector genes. In Caenorhabditis elegans, the differentiation of both the mechanosensory touch receptor neurons (TRNs) and the multidendritic nociceptor FLP neurons uses the terminal selectors UNC-86 and MEC-3. The FLP neurons fail to activate TRN genes, however, because a complex of two transcriptional repressors (EGL-44/EGL-46) prevents their expression. Here, we show that the ZEB family transcriptional factor ZAG-1 promotes TRN differentiation not by activating TRN genes but by preventing the expression of EGL-44/EGL-46. As EGL-44/EGL-46 also inhibits the production of ZAG-1, these proteins form a bistable, negative-feedback loop that regulates the choice between the two neuronal fates.
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Affiliation(s)
- Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Felix Qiaochu Jin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brian Loeber Trippe
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ji Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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16
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Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity. PLoS Biol 2018; 16:e2004979. [PMID: 29672507 PMCID: PMC5908064 DOI: 10.1371/journal.pbio.2004979] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/12/2018] [Indexed: 11/19/2022] Open
Abstract
Proneural genes are among the most early-acting genes in nervous system development, instructing blast cells to commit to a neuronal fate. Drosophila Atonal and Achaete-Scute complex (AS-C) genes, as well as their vertebrate orthologs, are basic helix-loop-helix (bHLH) transcription factors with such proneural activity. We show here that a C. elegans AS-C homolog, hlh-4, functions in a fundamentally different manner. In the embryonic, larval, and adult nervous systems, hlh-4 is expressed exclusively in a single nociceptive neuron class, ADL, and its expression in ADL is maintained via transcriptional autoregulation throughout the life of the animal. However, in hlh-4 null mutants, the ADL neuron is generated and still appears neuronal in overall morphology and expression of panneuronal and pansensory features. Rather than acting as a proneural gene, we find that hlh-4 is required for the ADL neuron to function properly, to adopt its correct morphology, to express its unusually large repertoire of olfactory receptor-encoding genes, and to express other known features of terminal ADL identity, including neurotransmitter phenotype, neuropeptides, ion channels, and electrical synapse proteins. hlh-4 is sufficient to induce ADL identity features upon ectopic expression in other neuron types. The expression of ADL terminal identity features is directly controlled by HLH-4 via a phylogenetically conserved E-box motif, which, through bioinformatic analysis, we find to constitute a predictive feature of ADL-expressed terminal identity markers. The lineage that produces the ADL neuron was previously shown to require the conventional, transient proneural activity of another AS-C homolog, hlh-14, demonstrating sequential activities of distinct AS-C-type bHLH genes in neuronal specification. Taken together, we have defined here an unconventional function of an AS-C-type bHLH gene as a terminal selector of neuronal identity and we speculate that such function could be reflective of an ancestral function of an "ur-" bHLH gene.
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17
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Shear force-based genetic screen reveals negative regulators of cell adhesion and protrusive activity. Proc Natl Acad Sci U S A 2017; 114:E7727-E7736. [PMID: 28847951 DOI: 10.1073/pnas.1616600114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The model organism Dictyostelium discoideum has greatly facilitated our understanding of the signal transduction and cytoskeletal pathways that govern cell motility. Cell-substrate adhesion is downstream of many migratory and chemotaxis signaling events. Dictyostelium cells lacking the tumor suppressor PTEN show strongly impaired migratory activity and adhere strongly to their substrates. We reasoned that other regulators of migration could be obtained through a screen for overly adhesive mutants. A screen of restriction enzyme-mediated integration mutagenized cells yielded numerous mutants with the desired phenotypes, and the insertion sites in 18 of the strains were mapped. These regulators of adhesion and motility mutants have increased adhesion and decreased motility. Characterization of seven strains demonstrated decreased directed migration, flatness, increased filamentous actin-based protrusions, and increased signal transduction network activity. Many of the genes share homology to human genes and demonstrate the diverse array of cellular networks that function in adhesion and migration.
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18
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Schmeisser K, Parker JA. Worms on the spectrum - C. elegans models in autism research. Exp Neurol 2017; 299:199-206. [PMID: 28434869 DOI: 10.1016/j.expneurol.2017.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/10/2017] [Accepted: 04/18/2017] [Indexed: 12/13/2022]
Abstract
The small non-parasitic nematode Caenorhabditis elegans is widely used in neuroscience thanks to its well-understood development and lineage of the nervous system. Furthermore, C. elegans has been used to model many human developmental and neurological conditions to better understand disease mechanisms and identify potential therapeutic strategies. Autism spectrum disorder (ASD) is the most prevalent of all neurodevelopmental disorders, and the C. elegans system may provide opportunities to learn more about this complex disorder. Since basic cell biology and biochemistry of the C. elegans nervous system is generally very similar to mammals, cellular or molecular phenotypes can be investigated, along with a repertoire of behaviours. For instance, worms have contributed greatly to the understanding of mechanisms underlying mutations in genes coding for synaptic proteins such as neuroligin and neurexin. Using worms to model neurodevelopmental disorders like ASD is an emerging topic that harbours great, untapped potential. This review summarizes the numerous contributions of C. elegans to the field of neurodevelopment and introduces the nematode system as a potential research tool to study essential roles of genes associated with ASD.
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Affiliation(s)
- Kathrin Schmeisser
- Centre de Recherche du Centre Hospitalier de l'Université de Montreál (CRCHUM), 900 St-Denis Street, Montreál, Queb́ec H2X 0A9, Canada
| | - J Alex Parker
- Centre de Recherche du Centre Hospitalier de l'Université de Montreál (CRCHUM), 900 St-Denis Street, Montreál, Queb́ec H2X 0A9, Canada; Department of Neuroscience, Université de Montreál, 2960 Chemin de la Tour, Montreál, Queb́ec H3T 1J4, Canada.
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19
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Hobert O. A map of terminal regulators of neuronal identity in Caenorhabditis elegans. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:474-98. [PMID: 27136279 PMCID: PMC4911249 DOI: 10.1002/wdev.233] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/07/2016] [Accepted: 02/21/2016] [Indexed: 12/31/2022]
Abstract
Our present day understanding of nervous system development is an amalgam of insights gained from studying different aspects and stages of nervous system development in a variety of invertebrate and vertebrate model systems, with each model system making its own distinctive set of contributions. One aspect of nervous system development that has been among the most extensively studied in the nematode Caenorhabditis elegans is the nature of the gene regulatory programs that specify hardwired, terminal cellular identities. I first summarize a number of maps (anatomical, functional, and molecular) that describe the terminal identity of individual neurons in the C. elegans nervous system. I then provide a comprehensive summary of regulatory factors that specify terminal identities in the nervous system, synthesizing these past studies into a regulatory map of cellular identities in the C. elegans nervous system. This map shows that for three quarters of all neurons in the C. elegans nervous system, regulatory factors that control terminal identity features are known. In-depth studies of specific neuron types have revealed that regulatory factors rarely act alone, but rather act cooperatively in neuron-type specific combinations. In most cases examined so far, distinct, biochemically unlinked terminal identity features are coregulated via cooperatively acting transcription factors, termed terminal selectors, but there are also cases in which distinct identity features are controlled in a piecemeal fashion by independent regulatory inputs. The regulatory map also illustrates that identity-defining transcription factors are reemployed in distinct combinations in different neuron types. However, the same transcription factor can drive terminal differentiation in neurons that are unrelated by lineage, unrelated by function, connectivity and neurotransmitter deployment. Lastly, the regulatory map illustrates the preponderance of homeodomain transcription factors in the control of terminal identities, suggesting that these factors have ancient, phylogenetically conserved roles in controlling terminal neuronal differentiation in the nervous system. WIREs Dev Biol 2016, 5:474-498. doi: 10.1002/wdev.233 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY, USA
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20
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Dobi KC, Schulman VK, Baylies MK. Specification of the somatic musculature in Drosophila. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:357-75. [PMID: 25728002 PMCID: PMC4456285 DOI: 10.1002/wdev.182] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/16/2015] [Accepted: 02/04/2015] [Indexed: 11/09/2022]
Abstract
The somatic muscle system formed during Drosophila embryogenesis is required for larvae to hatch, feed, and crawl. This system is replaced in the pupa by a new adult muscle set, responsible for activities such as feeding, walking, and flight. Both the larval and adult muscle systems are comprised of distinct muscle fibers to serve these specific motor functions. In this way, the Drosophila musculature is a valuable model for patterning within a single tissue: while all muscle cells share properties such as the contractile apparatus, properties such as size, position, and number of nuclei are unique for a particular muscle. In the embryo, diversification of muscle fibers relies first on signaling cascades that pattern the mesoderm. Subsequently, the combinatorial expression of specific transcription factors leads muscle fibers to adopt particular sizes, shapes, and orientations. Adult muscle precursors (AMPs), set aside during embryonic development, proliferate during the larval phases and seed the formation of the abdominal, leg, and flight muscles in the adult fly. Adult muscle fibers may either be formed de novo from the fusion of the AMPs, or are created by the binding of AMPs to an existing larval muscle. While less is known about adult muscle specification compared to the larva, expression of specific transcription factors is also important for its diversification. Increasingly, the mechanisms required for the diversification of fly muscle have found parallels in vertebrate systems and mark Drosophila as a robust model system to examine questions about how diverse cell types are generated within an organism.
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Affiliation(s)
- Krista C. Dobi
- Program in Developmental Biology, Sloan Kettering Institute, New York, NY, USA
| | - Victoria K. Schulman
- Program in Developmental Biology, Sloan Kettering Institute, New York, NY, USA
- Cell and Developmental Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Mary K. Baylies
- Program in Developmental Biology, Sloan Kettering Institute, New York, NY, USA
- Cell and Developmental Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
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21
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Lin L, Li Y, Yan L, Zhang G, Zhao Y, Zhang H. LSY-2 is essential for maintaining the germ-soma distinction in C. elegans. Protein Cell 2015; 6:599-609. [PMID: 26050091 PMCID: PMC4506282 DOI: 10.1007/s13238-015-0173-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/14/2015] [Indexed: 11/28/2022] Open
Abstract
The mechanisms that specify and maintain the characteristics of germ cells during animal development are poorly understood. In this study, we demonstrated that loss of function of the zinc-finger gene lsy-2 results in various somatic cells adopting germ cells characteristics, including expression of germline-specific P granules, enhanced RNAi activity and transgene silencing. The soma to germ transformation in lsy-2 mutants requires the activities of multiple chromatin remodeling complexes, including the MES-4 complex and the ISW-1 complex. The distinct germline-specific features in somatic cells and the gene expression profile indicate that LSY-2 acts in the Mec complex in this process. Our study demonstrated that lsy-2 functions in the maintenance of the soma-germ distinction.
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Affiliation(s)
- Long Lin
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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22
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Samuel TK, Sinclair JW, Pinter KL, Hamza I. Culturing Caenorhabditis elegans in axenic liquid media and creation of transgenic worms by microparticle bombardment. J Vis Exp 2014:e51796. [PMID: 25145601 DOI: 10.3791/51796] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this protocol, we present the required materials, and the procedure for making modified C. elegans Habituation and Reproduction media (mCeHR). Additionally, the steps for exposing and acclimatizing C. elegans grown on E. coli to axenic liquid media are described. Finally, downstream experiments that utilize axenic C. elegans illustrate the benefits of this procedure. The ability to analyze and determine C. elegans nutrient requirement was illustrated by growing N2 wild type worms in axenic liquid media with varying heme concentrations. This procedure can be replicated with other nutrients to determine the optimal concentration for worm growth and development or, to determine the toxicological effects of drug treatments. The effects of varied heme concentrations on the growth of wild type worms were determined through qualitative microscopic observation and by quantitating the number of worms that grew in each heme concentration. In addition, the effect of varied nutrient concentrations can be assayed by utilizing worms that express fluorescent sensors that respond to changes in the nutrient of interest. Furthermore, a large number of worms were easily produced for the generation of transgenic C. elegans using microparticle bombardment.
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Affiliation(s)
- Tamika K Samuel
- Department of Animal and Avian Sciences, University of Maryland
| | | | | | - Iqbal Hamza
- Department of Animal and Avian Sciences, University of Maryland; Department of Cell Biology and Molecular Genetics, University of Maryland;
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23
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Whole-genome analysis of muscle founder cells implicates the chromatin regulator Sin3A in muscle identity. Cell Rep 2014; 8:858-70. [PMID: 25088419 DOI: 10.1016/j.celrep.2014.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/21/2013] [Accepted: 07/01/2014] [Indexed: 10/25/2022] Open
Abstract
Skeletal muscles are formed in numerous shapes and sizes, and this diversity impacts function and disease susceptibility. To understand how muscle diversity is generated, we performed gene expression profiling of two muscle subsets from Drosophila embryos. By comparing the transcriptional profiles of these subsets, we identified a core group of founder cell-enriched genes. We screened mutants for muscle defects and identified functions for Sin3A and 10 other transcription and chromatin regulators in the Drosophila embryonic somatic musculature. Sin3A is required for the morphogenesis of a muscle subset, and Sin3A mutants display muscle loss and misattachment. Additionally, misexpression of identity gene transcription factors in Sin3A heterozygous embryos leads to direct transformations of one muscle into another, whereas overexpression of Sin3A results in the reverse transformation. Our data implicate Sin3A as a key buffer controlling muscle responsiveness to transcription factors in the formation of muscle identity, thereby generating tissue diversity.
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24
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Dopamine signaling in C. elegans is mediated in part by HLH-17-dependent regulation of extracellular dopamine levels. G3-GENES GENOMES GENETICS 2014; 4:1081-9. [PMID: 24709946 PMCID: PMC4065251 DOI: 10.1534/g3.114.010819] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Caenorhabditis elegans, the dopamine transporter DAT-1 regulates synaptic dopamine (DA) signaling by controlling extracellular DA levels. In dat-1(ok157) animals, DA is not taken back up presynaptically but instead reaches extrasynpatic sites, where it activates the dopamine receptor DOP-3 on choligeneric motor neurons and causes animals to become paralyzed in water. This phenotype is called swimming-induced paralysis (SWIP) and is dependent on dat-1 and dop-3. Upstream regulators of dat-1 and dop-3 have yet to be described in C. elegans. In our previous studies, we defined a role for HLH-17 during dopamine response through its regulation of the dopamine receptors. Here we continue our characterization of the effects of HLH-17 on dopamine signaling. Our results suggest that HLH-17 acts downstream of dopamine synthesis to regulate the expression of dop-3 and dat-1. First, we show that hlh-17 animals display a SWIP phenotype that is consistent with its regulation of dop-3 and dat-1. Second, we show that this behavior is enhanced by treatment with the dopamine reuptake inhibitor, bupropion, in both hlh-17 and dat-1 animals, a result suggesting that SWIP behavior is regulated via a mechanism that is both dependent on and independent of DAT-1. Third, and finally, we show that although the SWIP phenotype of hlh-17 animals is unresponsive to the dopamine agonist, reserpine, and to the antidepressant, fluoxetine, hlh-17 animals are not defective in acetylcholine signaling. Taken together, our work suggests that HLH-17 is required to maintain normal levels of dopamine in the synaptic cleft through its regulation of dop-3 and dat-1.
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25
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Hobert O. Development of left/right asymmetry in the Caenorhabditis elegans nervous system: From zygote to postmitotic neuron. Genesis 2014; 52:528-43. [DOI: 10.1002/dvg.22747] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/23/2014] [Accepted: 01/28/2014] [Indexed: 01/23/2023]
Affiliation(s)
- Oliver Hobert
- Department of Biochemistry and Molecular Biophysics; Howard Hughes Medical Institute, Columbia University Medical Center; New York New York
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26
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Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. ACTA ACUST UNITED AC 2013:1-34. [PMID: 23801596 DOI: 10.1895/wormbook.1.45.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.
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Affiliation(s)
- Valerie Reinke
- Department of Genetics, Yale University, New Haven, CT 06520, USA.
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27
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Smith MA, Zhang Y, Polli JR, Wu H, Zhang B, Xiao P, Farwell MA, Pan X. Impacts of chronic low-level nicotine exposure on Caenorhabditis elegans reproduction: identification of novel gene targets. Reprod Toxicol 2013; 40:69-75. [PMID: 23735997 DOI: 10.1016/j.reprotox.2013.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/25/2013] [Accepted: 05/24/2013] [Indexed: 12/17/2022]
Abstract
Effects and mechanisms of chronic exposure to low levels of nicotine is an area fundamentally important however less investigated. We employed the model organism Caenorhabditis elegans to investigate potential impacts of chronic (24h) and low nicotine exposure (6.17-194.5 μM) on stimulus-response, reproduction, and gene expressions. Nicotine significantly affects the organism's response to touch stimulus (p=0.031), which follows a dose-dependent pattern. Chronic nicotine exposure promotes early egg-laying events and slightly increased egg productions during the first 72 h of adulthood. The expressions of 10 (egl-10, egl-44, hlh-14, ric-3, unc-103, unc-50, unc-68, sod-1, oxi-1, and old-1) out of 18 selected genes were affected significantly. Other tested genes were cat-4, egl-19, egl-47, egl-5, lin-39, unc-43, pink-1, and age-1. Changes in gene expression were more evident at low dosages than at relatively high levels. Genes implicated in reproduction, cholinergic signaling, and stress response were regulated by nicotine, suggesting widespread physiological impacts of nicotine.
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Affiliation(s)
- Michael A Smith
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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28
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The conserved PHD1-PHD2 domain of ZFP-1/AF10 is a discrete functional module essential for viability in Caenorhabditis elegans. Mol Cell Biol 2012; 33:999-1015. [PMID: 23263989 DOI: 10.1128/mcb.01462-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant homeodomain (PHD)-type zinc fingers play an important role in recognizing chromatin modifications and recruiting regulatory proteins to specific genes. A specific module containing a conventional PHD finger followed by an extended PHD finger exists in the mammalian AF10 protein, among a few others. AF10 has mostly been studied in the context of the leukemic MLL-AF10 fusion protein, which lacks the N-terminal PHD fingers of AF10. Although this domain of AF10 is the most conserved region of the protein, its biological significance has not been elucidated. In this study, we used genetic and biochemical approaches to examine the PHD1-PHD2 region of the Caenorhabditis elegans ortholog of AF10, zinc finger protein 1 (ZFP-1). We demonstrate that the PHD1-PHD2 region is essential for viability and that the first PHD finger contributes to the preferred binding of PHD1-PHD2 to lysine 4-methylated histone H3 tails. Moreover, we show that ZFP-1 localization peaks overlap with H3K4 methylation-enriched promoters of actively expressed genes genomewide and that H3K4 methylation is important for ZFP-1 localization to promoters in the embryo. We predict that the essential biological role of the PHD1-PHD2 module of ZFP-1/AF10 is connected to the regulation of actively expressed genes during early development.
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29
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Cochella L, Hobert O. Embryonic priming of a miRNA locus predetermines postmitotic neuronal left/right asymmetry in C. elegans. Cell 2012. [PMID: 23201143 DOI: 10.1016/j.cell.2012.10.049] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mechanisms by which functional left/right asymmetry arises in morphologically symmetric nervous systems are poorly understood. Here, we provide a mechanistic framework for how functional asymmetry in a postmitotic neuron pair is specified in C. elegans. A key feature of this mechanism is a temporally separated, two-step activation of the lsy-6 miRNA locus. The lsy-6 locus is first "primed" by chromatin decompaction in the precursor for the left neuron, but not the right neuron, several divisions before the neurons are born. lsy-6 expression is then "boosted" to functionally relevant levels several divisions later in the mother of the left neuron, through the activity of a bilaterally expressed transcription factor that can only activate lsy-6 in the primed neuron. This study shows how cells can become committed during early developmental stages to execute a specific fate much later in development and provides a conceptual framework for understanding the generation of neuronal diversity.
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Affiliation(s)
- Luisa Cochella
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA.
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Patel T, Tursun B, Rahe DP, Hobert O. Removal of Polycomb repressive complex 2 makes C. elegans germ cells susceptible to direct conversion into specific somatic cell types. Cell Rep 2012; 2:1178-86. [PMID: 23103163 DOI: 10.1016/j.celrep.2012.09.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/18/2012] [Accepted: 09/14/2012] [Indexed: 01/10/2023] Open
Abstract
How specific cell types can be directly converted into other distinct cell types is a matter of intense investigation with wide-ranging basic and biomedical implications. Here, we show that removal of the histone 3 lysine 27 (H3K27) methyltransferase Polycomb repressor complex 2 (PRC2) permits ectopically expressed, neuron-type-specific transcription factors ("terminal selectors") to convert Caenorhabditis elegans germ cells directly into specific neuron types. Terminal-selector-induced germ-cell-to-neuron conversion can be observed not only upon genome-wide loss of H3K27 methylation in PRC2(-) animals but also upon genome-wide redistribution of H3K27 methylation patterns in animals that lack the H3K36 methyltransferase MES-4. Manipulation of the H3K27 methylation status not only permits conversion of germ cells into neurons but also permits hlh-1/MyoD-dependent conversion of germ cells into muscle cells, indicating that PRC2 protects the germline from the aberrant execution of multiple distinct somatic differentiation programs. Taken together, our findings demonstrate that the normally multistep process of development from a germ cell via a zygote to a terminally differentiated somatic cell type can be short-cut by providing an appropriate terminal selector transcription factor and manipulating histone methylation patterns.
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Affiliation(s)
- Tulsi Patel
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
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Simpson KJ, Davis GM, Boag PR. Comparative high-throughput RNAi screening methodologies in C. elegans and mammalian cells. N Biotechnol 2012; 29:459-70. [PMID: 22306616 DOI: 10.1016/j.nbt.2012.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/16/2012] [Accepted: 01/18/2012] [Indexed: 01/05/2023]
Abstract
The discovery of RNAi in Caenorhabditis elegans has generated a paradigm shift in how research is performed. Targeted gene knockdown using high throughput screening approaches is becoming a routine feature of the scientific landscape, and researchers can now evaluate the function of each gene in the genome in a relatively short period of time. This review compares and contrasts high throughput screening methodologies in C. elegans and mammalian cells and highlights the breadth of applications of this technology.
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Affiliation(s)
- Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Australia.
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Shilatifard A. The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu Rev Biochem 2012; 81:65-95. [PMID: 22663077 PMCID: PMC4010150 DOI: 10.1146/annurev-biochem-051710-134100] [Citation(s) in RCA: 777] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Saccharomyces cerevisiae Set1/COMPASS was the first histone H3 lysine 4 (H3K4) methylase identified over 10 years ago. Since then, it has been demonstrated that Set1/COMPASS and its enzymatic product, H3K4 methylation, is highly conserved across the evolutionary tree. Although there is only one COMPASS in yeast, Drosophila possesses three and humans bear six COMPASS family members, each capable of methylating H3K4 with nonredundant functions. In yeast, the histone H2B monoubiquitinase Rad6/Bre1 is required for proper H3K4 and H3K79 trimethylations. The machineries involved in this process are also highly conserved from yeast to human. In this review, the process of histone H2B monoubiquitination-dependent and -independent histone H3K4 methylation as a mark of active transcription, enhancer signatures, and developmentally poised genes is discussed. The misregulation of histone H2B monoubiquitination and H3K4 methylation result in the pathogenesis of human diseases, including cancer. Recent findings in this regard are also examined.
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Affiliation(s)
- Ali Shilatifard
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.
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Rechavi O, Minevich G, Hobert O. Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans. Cell 2011; 147:1248-56. [PMID: 22119442 PMCID: PMC3250924 DOI: 10.1016/j.cell.2011.10.042] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/13/2011] [Accepted: 10/25/2011] [Indexed: 11/29/2022]
Abstract
Induced expression of the Flock House virus in the soma of C. elegans results in the RNAi-dependent production of virus-derived, small-interfering RNAs (viRNAs), which in turn silence the viral genome. We show here that the viRNA-mediated viral silencing effect is transmitted in a non-Mendelian manner to many ensuing generations. We show that the viral silencing agents, viRNAs, are transgenerationally transmitted in a template-independent manner and work in trans to silence viral genomes present in animals that are deficient in producing their own viRNAs. These results provide evidence for the transgenerational inheritance of an acquired trait, induced by the exposure of animals to a specific, biologically relevant physiological challenge. The ability to inherit such extragenic information may provide adaptive benefits to an animal.
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Affiliation(s)
- Oded Rechavi
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA.
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Mohr SE, Perrimon N. RNAi screening: new approaches, understandings, and organisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:145-58. [PMID: 21953743 DOI: 10.1002/wrna.110] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA, USA
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