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Alicea B, Bastani S, Gordon NK, Crawford-Young S, Gordon R. The Molecular Basis of Differentiation Wave Activity in Embryogenesis. Biosystems 2024; 243:105272. [PMID: 39033973 DOI: 10.1016/j.biosystems.2024.105272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
As development varies greatly across the tree of life, it may seem difficult to suggest a model that proposes a single mechanism for understanding collective cell behaviors and the coordination of tissue formation. Here we propose a mechanism called differentiation waves, which unify many disparate results involving developmental systems from across the tree of life. We demonstrate how a relatively simple model of differentiation proceeds not from function-related molecular mechanisms, but from so-called differentiation waves. A phenotypic model of differentiation waves is introduced, and its relation to molecular mechanisms is proposed. These waves contribute to a differentiation tree, which is an alternate way of viewing cell lineage and local action of the molecular factors. We construct a model of differentiation wave-related molecular mechanisms (genome, epigenome, and proteome) based on bioinformatic data from the nematode Caenorhabditis elegans. To validate this approach across different modes of development, we evaluate protein expression across different types of development by comparing Caenorhabditis elegans with several model organisms: fruit flies (Drosophila melanogaster), yeast (Saccharomyces cerevisiae), and mouse (Mus musculus). Inspired by gene regulatory networks, two Models of Interactive Contributions (fully-connected MICs and ordered MICs) are used to suggest potential genomic contributions to differentiation wave-related proteins. This, in turn, provides a framework for understanding differentiation and development.
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Affiliation(s)
- Bradly Alicea
- Orthogonal Research and Education Lab, Champaign-Urbana, IL, USA; OpenWorm Foundation, Boston, MA, USA; University of Illinois Urbana-Champaign, USA.
| | - Suroush Bastani
- Orthogonal Research and Education Lab, Champaign-Urbana, IL, USA.
| | | | | | - Richard Gordon
- Gulf Specimen Marine Laboratory & Aquarium, Panacea, FL, USA.
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2
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Destain H, Prahlad M, Kratsios P. Maintenance of neuronal identity in C. elegans and beyond: Lessons from transcription and chromatin factors. Semin Cell Dev Biol 2024; 154:35-47. [PMID: 37438210 PMCID: PMC10592372 DOI: 10.1016/j.semcdb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023]
Abstract
Neurons are remarkably long-lived, non-dividing cells that must maintain their functional features (e.g., electrical properties, chemical signaling) for extended periods of time - decades in humans. How neurons accomplish this incredible feat is poorly understood. Here, we review recent advances, primarily in the nematode C. elegans, that have enhanced our understanding of the molecular mechanisms that enable post-mitotic neurons to maintain their functionality across different life stages. We begin with "terminal selectors" - transcription factors necessary for the establishment and maintenance of neuronal identity. We highlight new findings on five terminal selectors (CHE-1 [Glass], UNC-3 [Collier/Ebf1-4], LIN-39 [Scr/Dfd/Hox4-5], UNC-86 [Acj6/Brn3a-c], AST-1 [Etv1/ER81]) from different transcription factor families (ZNF, COE, HOX, POU, ETS). We compare the functions of these factors in specific neuron types of C. elegans with the actions of their orthologs in other invertebrate (D. melanogaster) and vertebrate (M. musculus) systems, highlighting remarkable functional conservation. Finally, we reflect on recent findings implicating chromatin-modifying proteins, such as histone methyltransferases and Polycomb proteins, in the control of neuronal terminal identity. Altogether, these new studies on transcription factors and chromatin modifiers not only shed light on the fundamental problem of neuronal identity maintenance, but also outline mechanistic principles of gene regulation that may operate in other long-lived, post-mitotic cell types.
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Affiliation(s)
- Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Manasa Prahlad
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA.
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3
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Cell context-dependent CFI-1/ARID3 functions control neuronal terminal differentiation. Cell Rep 2023; 42:112220. [PMID: 36897776 PMCID: PMC10124151 DOI: 10.1016/j.celrep.2023.112220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 12/21/2022] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
AT-rich interaction domain 3 (ARID3) transcription factors are expressed in the nervous system, but their mechanisms of action are largely unknown. Here, we provide, in vivo, a genome-wide binding map for CFI-1, the sole C. elegans ARID3 ortholog. We identify 6,396 protein-coding genes as putative direct targets of CFI-1, most of which encode neuronal terminal differentiation markers. In head sensory neurons, CFI-1 directly activates multiple terminal differentiation genes, thereby acting as a terminal selector. In motor neurons, however, CFI-1 acts as a direct repressor, continuously antagonizing three transcriptional activators. By focusing on the glr-4/GRIK4 glutamate receptor locus, we identify proximal CFI-1 binding sites and histone methyltransferase activity as necessary for glr-4 repression. Rescue assays reveal functional redundancy between core and extended DNA-binding ARID domains and a strict requirement for REKLES, the ARID3 oligomerization domain. Altogether, this study uncovers cell-context-dependent mechanisms through which a single ARID3 protein controls the terminal differentiation of distinct neuron types.
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4
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol 2022; 23:623-640. [PMID: 35562425 PMCID: PMC9099300 DOI: 10.1038/s41580-022-00483-w] [Citation(s) in RCA: 135] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/14/2022]
Abstract
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, G9A and G9A-like protein (GLP) — and the ‘readers’ of H3K9me2 or H3K9me3 are highly conserved and show considerable redundancy. Despite their redundancy, genetic ablation or mistargeting of an individual H3K9 methyltransferase can correlate with impaired cell differentiation, loss of tissue identity, premature aging and/or cancer. In this Review, we discuss recent advances in understanding the roles of the known H3K9-specific HMTs in ensuring transcriptional homeostasis during tissue differentiation in mammals. We examine the effects of H3K9-methylation-dependent gene repression in haematopoiesis, muscle differentiation and neurogenesis in mammals, and compare them with mechanistic insights obtained from the study of model organisms, notably Caenorhabditis elegans and Drosophila melanogaster. In all these organisms, H3K9-specific HMTs have both unique and redundant roles that ensure the maintenance of tissue integrity by restricting the binding of transcription factors to lineage-specific promoters and enhancer elements. Histone H3 Lys9 (H3K9)-methylated heterochromatin ensures transcriptional silencing of repetitive elements and genes, and its deregulation leads to impaired cell and tissue identity, premature aging and cancer. Recent studies in mammals clarified the roles H3K9-specific histone methyltransferases in ensuring transcriptional homeostasis during tissue differentiation.
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5
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Wang C, Zheng C. Using Caenorhabditis elegans to Model Therapeutic Interventions of Neurodegenerative Diseases Targeting Microbe-Host Interactions. Front Pharmacol 2022; 13:875349. [PMID: 35571084 PMCID: PMC9096141 DOI: 10.3389/fphar.2022.875349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
Emerging evidence from both clinical studies and animal models indicates the importance of the interaction between the gut microbiome and the brain in the pathogenesis of neurodegenerative diseases (NDs). Although how microbes modulate neurodegeneration is still mostly unclear, recent studies have started to probe into the mechanisms for the communication between microbes and hosts in NDs. In this review, we highlight the advantages of using Caenorhabditis elegans (C. elegans) to disentangle the microbe-host interaction that regulates neurodegeneration. We summarize the microbial pro- and anti-neurodegenerative factors identified using the C. elegans ND models and the effects of many are confirmed in mouse models. Specifically, we focused on the role of bacterial amyloid proteins, such as curli, in promoting proteotoxicity and neurodegeneration by cross-seeding the aggregation of endogenous ND-related proteins, such as α-synuclein. Targeting bacterial amyloid production may serve as a novel therapeutic strategy for treating NDs, and several compounds, such as epigallocatechin-3-gallate (EGCG), were shown to suppress neurodegeneration at least partly by inhibiting curli production. Because bacterial amyloid fibrils contribute to biofilm formation, inhibition of amyloid production often leads to the disruption of biofilms. Interestingly, from a list of 59 compounds that showed neuroprotective effects in C. elegans and mouse ND models, we found that about half of them are known to inhibit bacterial growth or biofilm formation, suggesting a strong correlation between the neuroprotective and antibiofilm activities. Whether these potential therapeutics indeed protect neurons from proteotoxicity by inhibiting the cross-seeding between bacterial and human amyloid proteins awaits further investigations. Finally, we propose to screen the long list of antibiofilm agents, both FDA-approved drugs and novel compounds, for their neuroprotective effects and develop new pharmaceuticals that target the gut microbiome for the treatment of NDs. To this end, the C. elegans ND models can serve as a platform for fast, high-throughput, and low-cost drug screens that target the microbe-host interaction in NDs.
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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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7
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Zheng C, Lee HMT, Pham K. Nervous system-wide analysis of Hox regulation of terminal neuronal fate specification in Caenorhabditis elegans. PLoS Genet 2022; 18:e1010092. [PMID: 35226663 PMCID: PMC8912897 DOI: 10.1371/journal.pgen.1010092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/10/2022] [Accepted: 02/12/2022] [Indexed: 12/01/2022] Open
Abstract
Hox genes encode evolutionarily conserved transcription factors that specify regional identities along the anterior-posterior (A-P) axis. Although some Hox genes are known to regulate the differentiation of certain neurons, to what extent Hox genes are involved in the terminal specification of the entire nervous system is unclear. Here, we systematically mapped the expression of all six Hox genes in C. elegans nervous system and found Hox expression in 97 (32%) of the 302 neurons in adult hermaphrodites. Our results are generally consistent with previous high-throughput expression mapping and single-cell transcriptomic studies. Detailed analysis of the fate markers for these neurons revealed that Hox genes regulate the differentiation of 29 (25%) of the 118 classes of C. elegans neurons. Hox genes not only regulate the specification of terminal neuronal fates through multiple mechanisms but also control subtype diversification along the A-P axis. The widespread involvement of Hox genes in neuronal differentiation indicates their roles in establishing complex nervous systems. The nervous system contains an extraordinary array of neuron types. How this neuronal diversity arises during development and what genes regulate the differentiation of each neuron type are among the major questions of neurobiology. Hox genes are a set of transcription factors highly conserved in the animal kingdom and are involved in setting up the body plan in the embryos. Hox genes are known to regulate the differentiation of some neurons, but their contribution to the overall development of a nervous system is unclear. In this study, we analyzed the activity of the Hox genes in the differentiation of the 302 neurons of the C. elegans nervous system in its entirety. We found that the six Hox genes are expressed in 32% of all neurons and five Hox genes regulate the differentiation of 25% of all neuron types through multiple mechanisms and act at various stages of cellular development. Thus, our results suggest that a small number of Hox genes could control the development of a significant portion of the nervous system. Given the conserved functions of Hox genes across species, we suspect that the increasing number of Hox genes may have allowed increased complexity in the nervous system in animal evolution.
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Affiliation(s)
- Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- * E-mail:
| | - Ho Ming Terence Lee
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Kenneth Pham
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
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8
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Zhang Y, Zhao C, Zhang H, Lu Q, Zhou J, Liu R, Wang S, Pu Y, Yin L. Trans-generational effects of copper on nerve damage in Caenorhabditis elegans. CHEMOSPHERE 2021; 284:131324. [PMID: 34225113 DOI: 10.1016/j.chemosphere.2021.131324] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 05/15/2023]
Abstract
The potential toxicity of copper has received great attention for a long time, however, trans-generational effects of copper have not been extensively investigated. Caenorhabditis elegans (C. elegans) was used to evaluate the trans-generational toxicities of copper several physiological endpoints: growth, head thrashes and body bends and degree of neuronal damage. Copper significantly inhibited growth, body bends, head thrashes and caused degeneration of dopaminergic neurons in a concentration-dependent manner in parental worms. Further we found oxidative damage was to underlying the onset of neuron degeneration. In our study copper promoted ROS accumulation, and led to an increased expression of the oxidative stress response-related genes sod-3 and a decreased expression of metal detoxification genes mtl-1 and mtl-2. Moreover, copper increased the fluorescence intensity of the transgenic strain that encodes the antioxidant enzyme SOD-3. Gradually decline in copper-induced impairments were observed in the filial generations without exposure. No growth impairment was shown in F3, the trend of head thrashes recovery gradually appeared in F2 and no growth impairment was shown in F3, the body bends impairment caused by the parental copper exposure was recovery until F4 and no growth impairment was shown in F5. Besides, dopamine neurons revealed damage related to neurobehavioral endpoints, with hereditary effects in the progeny together. In addition, sequencing results suggested that copper exposure could cause epigenetic changes. QRT-PCR results showed that differentially expressed genes can also be passed on to offspring.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Chao Zhao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Hu Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Qiang Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Jingjing Zhou
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
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9
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Willis CRG, Szewczyk NJ, Costes SV, Udranszky IA, Reinsch SS, Etheridge T, Conley CA. Comparative Transcriptomics Identifies Neuronal and Metabolic Adaptations to Hypergravity and Microgravity in Caenorhabditis elegans. iScience 2020; 23:101734. [PMID: 33376968 PMCID: PMC7756135 DOI: 10.1016/j.isci.2020.101734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Deep space exploration is firmly within reach, but health decline during extended spaceflight remains a key challenge. In this study, we performed comparative transcriptomic analysis of Caenorhabditis elegans responses to varying degrees of hypergravity and to two spaceflight experiments (ICE-FIRST and CERISE). We found that progressive hypergravitational load concomitantly increases the extent of differential gene regulation and that subtle changes in ∼1,000 genes are reproducibly observed during spaceflight-induced microgravity. Consequently, we deduce those genes that are concordantly regulated by altered gravity per se or that display inverted expression profiles during hypergravity versus microgravity. Through doing so, we identify several candidate targets with terrestrial roles in neuronal function and/or cellular metabolism, which are linked to regulation by daf-16/FOXO signaling. These data offer a strong foundation from which to expedite mechanistic understanding of spaceflight-induced maladaptation in higher organisms and, ultimately, promote future targeted therapeutic development. Comparative transcriptomics in C. elegans exposed to hypergravity and spaceflight Bioinformatics identifies novel putative regulators of altered gravitational load Candidate molecules infer a close gravity > daf-16/FOXO > neuronal link
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Affiliation(s)
- Craig R G Willis
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX1 2LU, UK
| | - Nathaniel J Szewczyk
- MRC-ARUK Centre for Musculoskeletal Ageing Research and National Institute of Health Research, Biomedical Research Centre, School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, DE22 3DT, UK.,Ohio Musculoskeletal and Neurological Institute (OMNI) and Department of Biomedical Sciences, Ohio University, Athens, OH 43147, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Sigrid S Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX1 2LU, UK
| | - Catharine A Conley
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
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The Conserved ASCL1/MASH-1 Ortholog HLH-3 Specifies Sex-Specific Ventral Cord Motor Neuron Fate in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:4201-4213. [PMID: 32973001 PMCID: PMC7642948 DOI: 10.1534/g3.120.401458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neural specification is regulated by one or many transcription factors that control expression of effector genes that mediate function and determine neuronal type. Here we identify a novel role for one conserved proneural factor, the bHLH protein HLH-3, implicated in the specification of sex-specific ventral cord motor neurons in C. elegans. Proneural genes act in early stages of neurogenesis in early progenitors, but here, we demonstrate a later role for hlh-3. First, we document that differentiation of the ventral cord type C motor neuron class (VC) within their neuron class, is dynamic in time and space. Expression of VC class-specific and subclass-specific identity genes is distinct through development and is dependent on the VC position along the A-P axis and their proximity to the vulva. Our characterization of the expression of VC class and VC subclass-specific differentiation markers in the absence of hlh-3 function reveals that VC fate specification, differentiation, and morphology requires hlh-3 function. Finally, we conclude that hlh-3 cell-autonomously specifies VC cell fate.
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11
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DasGupta A, Lee TL, Li C, Saltzman AL. Emerging Roles for Chromo Domain Proteins in Genome Organization and Cell Fate in C. elegans. Front Cell Dev Biol 2020; 8:590195. [PMID: 33195254 PMCID: PMC7649781 DOI: 10.3389/fcell.2020.590195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022] Open
Abstract
In most eukaryotes, the genome is packaged with histones and other proteins to form chromatin. One of the major mechanisms for chromatin regulation is through post-translational modification of histone proteins. Recognition of these modifications by effector proteins, often dubbed histone “readers,” provides a link between the chromatin landscape and gene regulation. The diversity of histone reader proteins for each modification provides an added layer of regulatory complexity. In this review, we will focus on the roles of chromatin organization modifier (chromo) domain containing proteins in the model nematode, Caenorhabditis elegans. An amenability to genetic and cell biological approaches, well-studied development and a short life cycle make C. elegans a powerful system to investigate the diversity of chromo domain protein functions in metazoans. We will highlight recent insights into the roles of chromo domain proteins in the regulation of heterochromatin and the spatial conformation of the genome as well as their functions in cell fate, fertility, small RNA pathways and transgenerational epigenetic inheritance. The spectrum of different chromatin readers may represent a layer of regulation that integrates chromatin landscape, genome organization and gene expression.
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Affiliation(s)
- Abhimanyu DasGupta
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Tammy L Lee
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Chengyin Li
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Arneet L Saltzman
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
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12
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Mutlu B, Chen HM, Gutnik S, Hall DH, Keppler-Ross S, Mango SE. Distinct functions and temporal regulation of methylated histone H3 during early embryogenesis. Development 2019; 146:dev174516. [PMID: 31540912 PMCID: PMC6803369 DOI: 10.1242/dev.174516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 09/09/2019] [Indexed: 01/25/2023]
Abstract
During the first hours of embryogenesis, formation of higher-order heterochromatin coincides with the loss of developmental potential. Here, we examine the relationship between these two events, and we probe the processes that contribute to the timing of their onset. Mutations that disrupt histone H3 lysine 9 (H3K9) methyltransferases reveal that the methyltransferase MET-2 helps terminate developmental plasticity, through mono- and di-methylation of H3K9 (me1/me2), and promotes heterochromatin formation, through H3K9me3. Although loss of H3K9me3 perturbs formation of higher-order heterochromatin, embryos are still able to terminate plasticity, indicating that the two processes can be uncoupled. Methylated H3K9 appears gradually in developing C. elegans embryos and depends on nuclear localization of MET-2. We find that the timing of H3K9me2 and nuclear MET-2 is sensitive to rapid cell cycles, but not to zygotic genome activation or cell counting. These data reveal distinct roles for different H3K9 methylation states in the generation of heterochromatin and loss of developmental plasticity by MET-2, and identify the cell cycle as a crucial parameter of MET-2 regulation.
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Affiliation(s)
- Beste Mutlu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Huei-Mei Chen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Silvia Gutnik
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Susan E Mango
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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13
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Characterization of paralogous uncx transcription factor encoding genes in zebrafish. Gene X 2019; 721S:100011. [PMID: 31193955 PMCID: PMC6543554 DOI: 10.1016/j.gene.2019.100011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/12/2019] [Accepted: 02/15/2019] [Indexed: 12/23/2022] Open
Abstract
The paired-type homeodomain transcription factor Uncx is involved in multiple processes of embryogenesis in vertebrates. Reasoning that zebrafish genes uncx4.1 and uncx are orthologs of mouse Uncx, we studied their genomic environment and developmental expression. Evolutionary analyses indicate the zebrafish uncx genes as being paralogs deriving from teleost-specific whole-genome duplication. Whole-mount in situ mRNA hybridization of uncx transcripts in zebrafish embryos reveals novel expression domains, confirms those previously known, and suggests sub-functionalization of paralogs. Using genetic mutants and pharmacological inhibitors, we investigate the role of signaling pathways on the expression of zebrafish uncx genes in developing somites. In identifying putative functional role(s) of zebrafish uncx genes, we hypothesized that they encode transcription factors that coordinate growth and innervation of somitic muscles. The Uncx4.1 and Uncx genes derive from the teleost-specific whole-genome duplication. Uncx genes are expressed during embryogenesis in unique and overlapping domains. Uncx gene expression during somite differentiation is regulated by FGF signaling. Synteny and expression profiles correlate Uncx genes with axon guidance.
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Key Words
- AP, antero-posterior
- Ace, acerebellar
- CAMP, conserved ancestral microsyntenic pairs
- CNE, conserved non-coding elements
- CRM, cis-regulatory module
- CS, Corpuscle of Stannius
- CaP, caudal primary motor neuron axons
- Ce, cerebellum
- Development
- Di, diencephalon
- Elfn1, Extracellular Leucine Rich Repeat And Fibronectin Type III Domain Containing 1
- Ey, eye
- FB, forebrain
- FGF, fibroblast growth factor
- Flh, floating head
- HB, hindbrain
- HM, hybridization mix
- Hy, hypothalamus
- MO, morpholino
- Mical, molecule interacting with CasL
- No, notochord
- OP, olfactory placode
- OT, optic tectum
- PA, pharyngeal arches
- PSM, presomitic mesoderm
- SC, spinal cord
- Shh, sonic hedgehog
- Signaling pathway
- So, somites
- Synteny
- TSGD
- TSGD, teleost-specific genome duplication
- Te, telencephalon
- Th, thalamus
- Uncx
- VLP, ventro-lateral-posterior
- WIHC, whole-mount immunohistochemistry
- WISH, whole-mount in situ hybridization
- YE, yolk extension
- Yo, yolk
- Zebrafish
- cyc, cyclops
- fss, fused-somites
- hpf, hours post fertilization
- ptc, patched
- smu, slow-muscle-omitted
- syu, sonic-you
- yot, you-too
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14
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Saltzman AL, Soo MW, Aram R, Lee JT. Multiple Histone Methyl-Lysine Readers Ensure Robust Development and Germline Immortality in Caenorhabditis elegans. Genetics 2018; 210:907-923. [PMID: 30185429 PMCID: PMC6218232 DOI: 10.1534/genetics.118.301518] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022] Open
Abstract
Chromatin modifications, including methylation of histone H3 at lysine 27 (H3K27me) by the Polycomb group proteins, play a broadly conserved role in the maintenance of cell fate. Diverse chromatin organization modifier (chromo) domain proteins act as "readers" of histone methylation states. However, understanding the functional relationships among chromo domains and their roles in the inheritance of gene expression patterns remains challenging. Here, we identify two chromo-domain proteins, CEC-1 and CEC-6, as potential readers of H3K27me in Caenorhabditis elegans, where they have divergent expression patterns and contribute to distinct phenotypes. Both cec-1 and cec-6 genetically interact with another chromo-domain gene, cec-3, a reader of H3K9 methylation. Combined loss of cec-1 and cec-3 leads to developmental defects in the adult that result in decreased fitness. Furthermore, loss of cec-6 and cec-3 surprisingly leads to a progressive loss of fertility across generations, a "mortal germline" phenotype. Our results provide evidence of functional compensation between H3K27me and H3K9me heterochromatin pathways, and show that histone methylation readers contribute to both somatic development and transgenerational fitness.
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Affiliation(s)
- Arneet L Saltzman
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Mark W Soo
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Reta Aram
- Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3G5, Canada
| | - Jeannie T Lee
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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15
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Mondal S, Hegarty E, Sahn JJ, Scott LL, Gökçe SK, Martin C, Ghorashian N, Satarasinghe PN, Iyer S, Sae-Lee W, Hodges TR, Pierce JT, Martin SF, Ben-Yakar A. High-Content Microfluidic Screening Platform Used To Identify σ2R/Tmem97 Binding Ligands that Reduce Age-Dependent Neurodegeneration in C. elegans SC_APP Model. ACS Chem Neurosci 2018; 9:1014-1026. [PMID: 29426225 DOI: 10.1021/acschemneuro.7b00428] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The nematode Caenorhabditis elegans, with tractable genetics and a well-defined nervous system, provides a unique whole-animal model system to identify novel drug targets and therapies for neurodegenerative diseases. Large-scale drug or target screens in models that recapitulate the subtle age- and cell-specific aspects of neurodegenerative diseases are limited by a technological requirement for high-throughput analysis of neuronal morphology. Recently, we developed a single-copy model of amyloid precursor protein (SC_APP) induced neurodegeneration that exhibits progressive degeneration of select cholinergic neurons. Our previous work with this model suggests that small molecule ligands of the sigma 2 receptor (σ2R), which was recently cloned and identified as transmembrane protein 97 (TMEM97), are neuroprotective. To determine structure-activity relationships for unexplored chemical space in our σ2R/Tmem97 ligand collection, we developed an in vivo high-content screening (HCS) assay to identify potential drug leads. The HCS assay uses our recently developed large-scale microfluidic immobilization chip and automated imaging platform. We discovered norbenzomorphans that reduced neurodegeneration in our C. elegans model, including two compounds that demonstrated significant neuroprotective activity at multiple doses. These findings provide further evidence that σ2R/Tmem97-binding norbenzomorphans may represent a new drug class for treating neurodegenerative diseases.
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16
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Ahringer J, Gasser SM. Repressive Chromatin in Caenorhabditis elegans: Establishment, Composition, and Function. Genetics 2018; 208:491-511. [PMID: 29378810 PMCID: PMC5788517 DOI: 10.1534/genetics.117.300386] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/18/2017] [Indexed: 01/08/2023] Open
Abstract
Chromatin is organized and compacted in the nucleus through the association of histones and other proteins, which together control genomic activity. Two broad types of chromatin can be distinguished: euchromatin, which is generally transcriptionally active, and heterochromatin, which is repressed. Here we examine the current state of our understanding of repressed chromatin in Caenorhabditis elegans, focusing on roles of histone modifications associated with repression, such as methylation of histone H3 lysine 9 (H3K9me2/3) or the Polycomb Repressive Complex 2 (MES-2/3/6)-deposited modification H3K27me3, and on proteins that recognize these modifications. Proteins involved in chromatin repression are important for development, and have demonstrated roles in nuclear organization, repetitive element silencing, genome integrity, and the regulation of euchromatin. Additionally, chromatin factors participate in repression with small RNA pathways. Recent findings shed light on heterochromatin function and regulation in C. elegans, and should inform our understanding of repressed chromatin in other animals.
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Affiliation(s)
- Julie Ahringer
- The Gurdon Institute, University of Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge CB2 1QN, United Kingdom
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland, and
- Faculty of Natural Sciences, University of Basel, 4056, Switzerland
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17
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Zheng C, Diaz-Cuadros M, Nguyen KCQ, Hall DH, Chalfie M. Distinct effects of tubulin isotype mutations on neurite growth in Caenorhabditis elegans. Mol Biol Cell 2017; 28:2786-2801. [PMID: 28835377 PMCID: PMC5638583 DOI: 10.1091/mbc.e17-06-0424] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/20/2022] Open
Abstract
Different tubulin isotypes perform different functions in the regulation of microtubule (MT) structure and neurite growth, and missense mutations of tubulin genes have three types of distinct effects on MT stability and neurite growth. One α-tubulin isotype appears to induce relative instability due to the lack of potential posttranslational modification sites. Tubulins, the building block of microtubules (MTs), play a critical role in both supporting and regulating neurite growth. Eukaryotic genomes contain multiple tubulin isotypes, and their missense mutations cause a range of neurodevelopmental defects. Using the Caenorhabditis elegans touch receptor neurons, we analyzed the effects of 67 tubulin missense mutations on neurite growth. Three types of mutations emerged: 1) loss-of-function mutations, which cause mild defects in neurite growth; 2) antimorphic mutations, which map to the GTP binding site and intradimer and interdimer interfaces, significantly reduce MT stability, and cause severe neurite growth defects; and 3) neomorphic mutations, which map to the exterior surface, increase MT stability, and cause ectopic neurite growth. Structure-function analysis reveals a causal relationship between tubulin structure and MT stability. This stability affects neuronal morphogenesis. As part of this analysis, we engineered several disease-associated human tubulin mutations into C. elegans genes and examined their impact on neuronal development at the cellular level. We also discovered an α-tubulin (TBA-7) that appears to destabilize MTs. Loss of TBA-7 led to the formation of hyperstable MTs and the generation of ectopic neurites; the lack of potential sites for polyamination and polyglutamination on TBA-7 may be responsible for this destabilization.
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Affiliation(s)
- Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | - Ken C Q Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027
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18
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Riveiro AR, Mariani L, Malmberg E, Amendola PG, Peltonen J, Wong G, Salcini AE. JMJD-1.2/PHF8 controls axon guidance by regulating Hedgehog-like signaling. Development 2017; 144:856-865. [PMID: 28126843 DOI: 10.1242/dev.142695] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/09/2017] [Indexed: 01/10/2023]
Abstract
Components of the KDM7 family of histone demethylases are implicated in neuronal development and one member, PHF8, is often found to be mutated in cases of X-linked mental retardation. However, how PHF8 regulates neurodevelopmental processes and contributes to the disease is still largely unknown. Here, we show that the catalytic activity of a PHF8 homolog in Caenorhabditis elegans, JMJD-1.2, is required non-cell-autonomously for proper axon guidance. Loss of JMJD-1.2 dysregulates transcription of the Hedgehog-related genes wrt-8 and grl-16, the overexpression of which is sufficient to induce the axonal defects. Deficiency of either wrt-8 or grl-16, or reduced expression of homologs of genes promoting Hedgehog signaling, restores correct axon guidance in jmjd-1.2 mutants. Genetic and overexpression data indicate that Hedgehog-related genes act on axon guidance through actin remodelers. Thus, our study highlights a novel function of jmjd-1.2 in axon guidance that might be relevant for the onset of X-linked mental retardation and provides compelling evidence of a conserved function of the Hedgehog pathway in C. elegans axon migration.
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Affiliation(s)
- Alba Redo Riveiro
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.,Centre for Epigenetics, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.,Centre for Epigenetics, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Emily Malmberg
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.,Centre for Epigenetics, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Pier Giorgio Amendola
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.,Centre for Epigenetics, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Juhani Peltonen
- A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, 70211, Kuopio, Finland
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark .,Centre for Epigenetics, University of Copenhagen, 2200, Copenhagen, Denmark
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19
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Zheng C, Diaz-Cuadros M, Chalfie M. Hox Genes Promote Neuronal Subtype Diversification through Posterior Induction in Caenorhabditis elegans. Neuron 2016; 88:514-27. [PMID: 26539892 DOI: 10.1016/j.neuron.2015.09.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/05/2015] [Accepted: 09/19/2015] [Indexed: 10/22/2022]
Abstract
Although Hox genes specify the differentiation of neuronal subtypes along the anterior-posterior axis, their mode of action is not entirely understood. Using two subtypes of the touch receptor neurons (TRNs) in C. elegans, we found that a "posterior induction" mechanism underlies the Hox control of terminal neuronal differentiation. The anterior subtype maintains a default TRN state, whereas the posterior subtype undergoes further morphological and transcriptional specification induced by the posterior Hox proteins, mainly EGL-5/Abd-B. Misexpression of the posterior Hox proteins transformed the anterior TRN subtype toward a posterior identity both morphologically and genetically. The specification of the posterior subtype requires EGL-5-induced repression of TALE cofactors, which antagonize EGL-5 functions, and the activation of rfip-1, a component of recycling endosomes, which mediates Hox activities by promoting subtype-specific neurite outgrowth. Finally, EGL-5 is required for subtype-specific circuit formation by acting in both the sensory neuron and downstream interneuron to promote functional connectivity.
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Affiliation(s)
- Chaogu Zheng
- 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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20
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Abstract
Transcription factors control neuronal differentiation by acting as "terminal selectors" that determine the specific cell fates of different types of neurons. The specification of cell fate, however, requires high fidelity, which relies on stable and robust expression of the terminal selectors. Our recent studies in C. elegans suggest that a second set of transcription factors function as reinforcing or protecting factors to stabilize the expression and activity of terminal selectors. Some serve as "guarantors" to ensure the activation and continuous expression of the selectors by reducing stochastic fluctuations in gene expression; others safeguard the protein function of selectors by repressing inhibitors that would block their activity. These transcription factors, unlike the terminal selectors, do not induce specification but secure neuronal cell fate and provide reliability in differentiation.
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21
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Pereira L, Kratsios P, Serrano-Saiz E, Sheftel H, Mayo AE, Hall DH, White JG, LeBoeuf B, Garcia LR, Alon U, Hobert O. A cellular and regulatory map of the cholinergic nervous system of C. elegans. eLife 2015; 4. [PMID: 26705699 PMCID: PMC4769160 DOI: 10.7554/elife.12432] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/22/2015] [Indexed: 12/18/2022] Open
Abstract
Nervous system maps are of critical importance for understanding how nervous systems develop and function. We systematically map here all cholinergic neuron types in the male and hermaphrodite C. elegans nervous system. We find that acetylcholine (ACh) is the most broadly used neurotransmitter and we analyze its usage relative to other neurotransmitters within the context of the entire connectome and within specific network motifs embedded in the connectome. We reveal several dynamic aspects of cholinergic neurotransmitter identity, including a sexually dimorphic glutamatergic to cholinergic neurotransmitter switch in a sex-shared interneuron. An expression pattern analysis of ACh-gated anion channels furthermore suggests that ACh may also operate very broadly as an inhibitory neurotransmitter. As a first application of this comprehensive neurotransmitter map, we identify transcriptional regulatory mechanisms that control cholinergic neurotransmitter identity and cholinergic circuit assembly. DOI:http://dx.doi.org/10.7554/eLife.12432.001 To better understand the nervous system—the most complex of all the body’s organs—scientists have begun to painstakingly map its many features. These maps can then be used as a basis for understanding how the nervous system develops and works. Researchers have mapped the connections – called synapses – between all the nerve cells in the nervous system of a simple worm called Caenorhabditis elegans. Cells communicate by releasing chemicals called neurotransmitters across the synapses, but it is not fully known which types of neurotransmitters are released across each of the synapses in C. elegans. Now, Pereira et al. have mapped all worm nerve cells that use a neurotransmitter called acetylcholine by fluorescently marking proteins that synthesize and transport the neurotransmitter. This map revealed that 52 of the 118 types of nerve cells in the worm use acetylcholine, making it the most widely used neurotransmitter. This information was then combined with the findings of previous work that investigated which nerve cells release some other types of neurotransmitters. The combined data mean that it is now known which neurotransmitter is used for signaling by over 90% of the nerve cells in C. elegans. Using the map, Pereira et al. found that some neurons release different neurotransmitters in the different sexes of the worm. Additionally, the experiments revealed a set of proteins that cause the nerve cells to produce acetylcholine. Some of these proteins affect the fates of connected nerve cells. Overall, this information will allow scientists to more precisely manipulate specific cells or groups of cells in the worm nervous system to investigate how the nervous system develops and is regulated. DOI:http://dx.doi.org/10.7554/eLife.12432.002
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Affiliation(s)
- Laura Pereira
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Paschalis Kratsios
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Esther Serrano-Saiz
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Hila Sheftel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi E Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, New York, United States
| | - John G White
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Brigitte LeBoeuf
- Department of Biology, Texas A&M University, College Station, United States
| | - L Rene Garcia
- Department of Biology, Texas A&M University, College Station, United States.,Howard Hughes Medical Institute, Texas A&M University, College Station, United States
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
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22
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Perinuclear Anchoring of H3K9-Methylated Chromatin Stabilizes Induced Cell Fate in C. elegans Embryos. Cell 2015; 163:1333-47. [PMID: 26607792 DOI: 10.1016/j.cell.2015.10.066] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/07/2015] [Accepted: 10/27/2015] [Indexed: 01/24/2023]
Abstract
Interphase chromatin is organized in distinct nuclear sub-compartments, reflecting its degree of compaction and transcriptional status. In Caenorhabditis elegans embryos, H3K9 methylation is necessary to silence and to anchor repeat-rich heterochromatin at the nuclear periphery. In a screen for perinuclear anchors of heterochromatin, we identified a previously uncharacterized C. elegans chromodomain protein, CEC-4. CEC-4 binds preferentially mono-, di-, or tri-methylated H3K9 and localizes at the nuclear envelope independently of H3K9 methylation and nuclear lamin. CEC-4 is necessary for endogenous heterochromatin anchoring, but not for transcriptional repression, in contrast to other known H3K9 methyl-binders in worms, which mediate gene repression but not perinuclear anchoring. When we ectopically induce a muscle differentiation program in embryos, cec-4 mutants fail to commit fully to muscle cell fate. This suggests that perinuclear sequestration of chromatin during development helps restrict cell differentiation programs by stabilizing commitment to a specific cell fate. PAPERCLIP.
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23
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Hu PJ. Whole genome sequencing and the transformation of C. elegans forward genetics. Methods 2014; 68:437-40. [PMID: 24874788 DOI: 10.1016/j.ymeth.2014.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 11/16/2022] Open
Abstract
Forward genetics has been an undeniably powerful approach in Caenorhabditis elegans and other model organisms. However, the trek from mutant isolation to identification of the causative molecular lesion can be time-consuming and fraught with obstacles. This has changed with the advent of whole genome sequencing (WGS). The widespread availability of high-throughput sequencing technology, coupled with the increasing affordability of WGS, has enabled the routine use of WGS in the analysis of forward genetic screens. The noteworthy development of one-step mapping/sequencing approaches has largely eliminated the bottleneck of conventional high-resolution mapping, greatly accelerating the journey from mutagenesis to gene discovery. By enabling the use of increasingly complex and diverse genetic backgrounds as substrates for mutagenesis, WGS is expanding the landscape of biological problems that can be interrogated using forward genetic approaches in C. elegans and other organisms.
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Affiliation(s)
- Patrick J Hu
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, United States; Institute of Gerontology, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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