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Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024; 23:607-623. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [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: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
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Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
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2
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Guo Z, Wang S, Wang Y, Wang Z, Ou G. A machine learning enhanced EMS mutagenesis probability map for efficient identification of causal mutations in Caenorhabditis elegans. PLoS Genet 2024; 20:e1011377. [PMID: 39186782 PMCID: PMC11379379 DOI: 10.1371/journal.pgen.1011377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 09/06/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024] Open
Abstract
Chemical mutagenesis-driven forward genetic screens are pivotal in unveiling gene functions, yet identifying causal mutations behind phenotypes remains laborious, hindering their high-throughput application. Here, we reveal a non-uniform mutation rate caused by Ethyl Methane Sulfonate (EMS) mutagenesis in the C. elegans genome, indicating that mutation frequency is influenced by proximate sequence context and chromatin status. Leveraging these factors, we developed a machine learning enhanced pipeline to create a comprehensive EMS mutagenesis probability map for the C. elegans genome. This map operates on the principle that causative mutations are enriched in genetic screens targeting specific phenotypes among random mutations. Applying this map to Whole Genome Sequencing (WGS) data of genetic suppressors that rescue a C. elegans ciliary kinesin mutant, we successfully pinpointed causal mutations without generating recombinant inbred lines. This method can be adapted in other species, offering a scalable approach for identifying causal genes and revitalizing the effectiveness of forward genetic screens.
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Affiliation(s)
- Zhengyang Guo
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Shimin Wang
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Yang Wang
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Zi Wang
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
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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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Alexander KD, Ramachandran S, Biswas K, Lambert CM, Russell J, Oliver DB, Armstrong W, Rettler M, Liu S, Doitsidou M, Bénard C, Walker AK, Francis MM. The homeodomain transcriptional regulator DVE-1 directs a program for synapse elimination during circuit remodeling. Nat Commun 2023; 14:7520. [PMID: 37980357 PMCID: PMC10657367 DOI: 10.1038/s41467-023-43281-4] [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: 11/10/2022] [Accepted: 11/02/2023] [Indexed: 11/20/2023] Open
Abstract
The elimination of synapses during circuit remodeling is critical for brain maturation; however, the molecular mechanisms directing synapse elimination and its timing remain elusive. We show that the transcriptional regulator DVE-1, which shares homology with special AT-rich sequence-binding (SATB) family members previously implicated in human neurodevelopmental disorders, directs the elimination of juvenile synaptic inputs onto remodeling C. elegans GABAergic neurons. Juvenile acetylcholine receptor clusters and apposing presynaptic sites are eliminated during the maturation of wild-type GABAergic neurons but persist into adulthood in dve-1 mutants, producing heightened motor connectivity. DVE-1 localization to GABAergic nuclei is required for synapse elimination, consistent with DVE-1 regulation of transcription. Pathway analysis of putative DVE-1 target genes, proteasome inhibitor, and genetic experiments implicate the ubiquitin-proteasome system in synapse elimination. Together, our findings define a previously unappreciated role for a SATB family member in directing synapse elimination during circuit remodeling, likely through transcriptional regulation of protein degradation processes.
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Affiliation(s)
- Kellianne D Alexander
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shankar Ramachandran
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kasturi Biswas
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Christopher M Lambert
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia Russell
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Devyn B Oliver
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - William Armstrong
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Monika Rettler
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Samuel Liu
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Maria Doitsidou
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Claire Bénard
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biological Sciences, Université du Québec à Montréal, Quebec, Canada
| | - Amy K Walker
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael M Francis
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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5
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Ho J, Guerrero LA, Libuda DE, Luxton GWG, Starr DA. Actin and CDC-42 contribute to nuclear migration through constricted spaces in C. elegans. Development 2023; 150:dev202115. [PMID: 37756590 PMCID: PMC10617605 DOI: 10.1242/dev.202115] [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: 06/22/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
Successful nuclear migration through constricted spaces between cells or in the extracellular matrix relies on the ability of the nucleus to deform. Little is known about how this takes place in vivo. We have studied confined nuclear migration in Caenorhabditis elegans larval P cells, which is mediated by the LINC complex to pull nuclei towards the minus ends of microtubules. Null mutations of the LINC component unc-84 lead to a temperature-dependent phenotype, suggesting a parallel pathway for P-cell nuclear migration. A forward genetic screen for enhancers of unc-84 identified cgef-1 (CDC-42 guanine nucleotide exchange factor). Knockdown of CDC-42 in the absence of the LINC complex led to a P-cell nuclear migration defect. Expression of constitutively active CDC-42 partially rescued nuclear migration in cgef-1; unc-84 double mutants, suggesting that CDC-42 functions downstream of CGEF-1. The Arp2/3 complex and non-muscle myosin II (NMY-2) were also found to function parallel to the LINC pathway. In our model, CGEF-1 activates CDC-42, which induces actin polymerization through the Arp2/3 complex to deform the nucleus during nuclear migration, and NMY-2 helps to push the nucleus through confined spaces.
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Affiliation(s)
- Jamie Ho
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Leslie A. Guerrero
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Diana E. Libuda
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - G. W. Gant Luxton
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Daniel A. Starr
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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6
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Tomioka M, Umemura Y, Ueoka Y, Chin R, Katae K, Uchiyama C, Ike Y, Iino Y. Antagonistic regulation of salt and sugar chemotaxis plasticity by a single chemosensory neuron in Caenorhabditis elegans. PLoS Genet 2023; 19:e1010637. [PMID: 37669262 PMCID: PMC10503759 DOI: 10.1371/journal.pgen.1010637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 09/15/2023] [Accepted: 08/20/2023] [Indexed: 09/07/2023] Open
Abstract
The nematode Caenorhabditis elegans memorizes various external chemicals, such as ions and odorants, during feeding. Here we find that C. elegans is attracted to the monosaccharides glucose and fructose after exposure to these monosaccharides in the presence of food; however, it avoids them without conditioning. The attraction to glucose requires a gustatory neuron called ASEL. ASEL activity increases when glucose concentration decreases. Optogenetic ASEL stimulation promotes forward movements; however, after glucose conditioning, it promotes turning, suggesting that after glucose conditioning, the behavioral output of ASEL activation switches toward glucose. We previously reported that chemotaxis toward sodium ion (Na+), which is sensed by ASEL, increases after Na+ conditioning in the presence of food. Interestingly, glucose conditioning decreases Na+ chemotaxis, and conversely, Na+ conditioning decreases glucose chemotaxis, suggesting the reciprocal inhibition of learned chemotaxis to distinct chemicals. The activation of PKC-1, an nPKC ε/η ortholog, in ASEL promotes glucose chemotaxis and decreases Na+ chemotaxis after glucose conditioning. Furthermore, genetic screening identified ENSA-1, an ortholog of the protein phosphatase inhibitor ARPP-16/19, which functions in parallel with PKC-1 in glucose-induced chemotactic learning toward distinct chemicals. These findings suggest that kinase-phosphatase signaling regulates the balance between learned behaviors based on glucose conditioning in ASEL, which might contribute to migration toward chemical compositions where the animals were previously fed.
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Affiliation(s)
- Masahiro Tomioka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Umemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yutaro Ueoka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Risshun Chin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keita Katae
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Chihiro Uchiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yasuaki Ike
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yuichi Iino
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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7
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Lim DS, Kim J, Kim W, Kim N, Lee SH, Lee D, Lee J. daf-42 is an evolutionarily young gene essential for dauer development in Caenorhabditis elegans. Genetics 2023; 224:iyad097. [PMID: 37216205 DOI: 10.1093/genetics/iyad097] [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: 08/23/2022] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023] Open
Abstract
Under adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauer endures unfavorable environments and interacts with host animals to access favorable environments, thus playing a critical role in survival. Here, we report that in Caenorhabditis elegans, daf-42 is essential for development into the dauer stage, as the null mutant of daf-42 exhibited a "no viable dauer" phenotype in which no viable dauers were obtained in any dauer-inducing conditions. Long-term time lapse microscopy of synchronized larvae revealed that daf-42 is involved in developmental changes from the pre-dauer L2d stage to the dauer stage. daf-42 encodes large, disordered proteins of various sizes that are expressed in and secreted from the seam cells within a narrow time window shortly before the molt into dauer stage. Transcriptome analysis showed that the transcription of genes involved in larval physiology and dauer metabolism is highly affected by the daf-42 mutation. Contrary to the notion that essential genes that control the life and death of an organism may be well conserved across diverse species, daf-42 is an evolutionarily young gene conserved only in the Caenorhabditis genus. Our study shows that dauer formation is a vital process that is controlled not only by conserved genes but also by newly emerged genes, providing important insights into evolutionary mechanisms.
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Affiliation(s)
- Daisy S Lim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
- Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Wonjoo Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Nari Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Hee Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
- Korea Basic Science Institute, Ochang, Cheongju, Chungbuk 28119, Republic of Korea
| | - Daehan Lee
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
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8
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Fujii C, Wang D. Novel insights into virus-host interactions using the model organism C. elegans. Adv Virus Res 2023; 115:135-158. [PMID: 37173064 DOI: 10.1016/bs.aivir.2023.03.001] [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] [Indexed: 04/05/2023]
Abstract
Viruses continue to pose a public health threat raising the need for effective management strategies. Currently existing antiviral therapeutics are often specific to only a single viral species, and resistance to the therapeutic can often arise, and therefore new therapeutics are needed. The C. elegans-Orsay virus system offers a powerful platform for studying RNA virus-host interactions that could ultimately lead to novel targets for antiviral therapy. The relative simplicity of C. elegans, the well-established experimental tools, and its extensive evolutionary conservation of genes and pathways with mammals are key features of this model. Orsay virus, a bisegmented positive sense RNA virus, is a natural pathogen of C. elegans. Orsay virus infection can be studied in a multicellular organismal context, overcoming some of the limitations inherent to tissue culture-based systems. Moreover, compared to mice, the rapid generation time of C. elegans enables robust and facile forward genetics. This review aims to summarize studies that have laid the foundation for the C. elegans-Orsay virus experimental system, experimental tools, and key examples of C. elegans host factors that impact Orsay virus infection that have evolutionarily conserved function in mammalian virus infection.
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Affiliation(s)
- Chika Fujii
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, United States
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, United States.
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10
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Lup SD, Navarro-Quiles C, Micol JL. Versatile mapping-by-sequencing with Easymap v.2. FRONTIERS IN PLANT SCIENCE 2023; 14:1042913. [PMID: 36778692 PMCID: PMC9909543 DOI: 10.3389/fpls.2023.1042913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Mapping-by-sequencing combines Next Generation Sequencing (NGS) with classical genetic mapping by linkage analysis to establish gene-to-phenotype relationships. Although numerous tools have been developed to analyze NGS datasets, only a few are available for mapping-by-sequencing. One such tool is Easymap, a versatile, easy-to-use package that performs automated mapping of point mutations and large DNA insertions. Here, we describe Easymap v.2, which also maps small insertion/deletions (InDels), and includes workflows to perform QTL-seq and variant density mapping analyses. Each mapping workflow can accommodate different experimental designs, including outcrossing and backcrossing, F2, M2, and M3 mapping populations, chemically induced mutation and natural variant mapping, input files containing single-end or paired-end reads of genomic or complementary DNA sequences, and alternative control sample files in FASTQ and VCF formats. Easymap v.2 can also be used as a variant analyzer in the absence of a mapping algorithm and includes a multi-threading option.
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11
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Thapliyal S, Glauser DA. Neurogenetic Analysis in Caenorhabditis elegans. Neurogenetics 2023. [DOI: 10.1007/978-3-031-07793-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Li N, Hua B, Chen Q, Teng F, Ruan M, Zhu M, Zhang L, Huo Y, Liu H, Zhuang M, Shen H, Zhu H. A sphingolipid-mTORC1 nutrient-sensing pathway regulates animal development by an intestinal peroxisome relocation-based gut-brain crosstalk. Cell Rep 2022; 40:111140. [PMID: 35905721 DOI: 10.1016/j.celrep.2022.111140] [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: 08/29/2021] [Revised: 05/23/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022] Open
Abstract
The mTOR-dependent nutrient-sensing and response machinery is the central hub for animals to regulate their cellular and developmental programs. However, equivalently pivotal nutrient and metabolite signals upstream of mTOR and developmental-regulatory signals downstream of mTOR are not clear, especially at the organism level. We previously showed glucosylceramide (GlcCer) acts as a critical nutrient and metabolite signal for overall amino acid levels to promote development by activating the intestinal mTORC1 signaling pathway. Here, through a large-scale genetic screen, we find that the intestinal peroxisome is critical for antagonizing the GlcCer-mTORC1-mediated nutrient signal. Mechanistically, GlcCer deficiency, inactive mTORC1, or prolonged starvation relocates intestinal peroxisomes closer to the apical region in a kinesin- and microtubule-dependent manner. Those apical accumulated peroxisomes further release peroxisomal-β-oxidation-derived glycolipid hormones that target chemosensory neurons and downstream nuclear hormone receptor DAF-12 to arrest the animal development. Our data illustrate a sophisticated gut-brain axis that predominantly orchestrates nutrient-sensing-dependent development in animals.
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Affiliation(s)
- Na Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Beilei Hua
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fukang Teng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Meiyu Ruan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengnan Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Li Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yinbo Huo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Hongqin Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Min Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Huali Shen
- Institutes of Biomedical Sciences, Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Huanhu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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13
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Rahman M, Ramirez‐Suarez NJ, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Rep 2022; 23:e54163. [PMID: 35586945 PMCID: PMC9253746 DOI: 10.15252/embr.202154163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 09/19/2023] Open
Abstract
N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system.
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Affiliation(s)
- Maisha Rahman
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- Dominick P. Purpura Department of NeuroscienceAlbert Einstein College of MedicineBronxNYUSA
| | - Nelson J Ramirez‐Suarez
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- Present address:
Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Carlos A Diaz‐Balzac
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- Present address:
University of RochesterRochesterNYUSA
| | - Hannes E Bülow
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- Dominick P. Purpura Department of NeuroscienceAlbert Einstein College of MedicineBronxNYUSA
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14
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Powell G, Pavlovic Djuranovic S, Djuranovic S. Gene dosage effects of poly(A) track-engineered hypomorphs. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:865-878. [PMID: 34729253 PMCID: PMC8536507 DOI: 10.1016/j.omtn.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/29/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022]
Abstract
Manipulation of gene activity through creation of hypomorphic mutants has been a long-standing tool in examining gene function. Our previous studies have indicated that hypomorphic mutants could be created by inserting cis-regulatory sequences composed of consecutive adenosine nucleotides called poly(A) tracks. Here we use poly(A) tracks to create hypomorphic mutants and functional characterization of membrane, secretory, and endogenous proteins. Insertion of poly(A) tracks into the sequences of interleukin-2 and membrane protein CD20 results in a programmable reduction of mRNA stability and attenuation of protein expression regardless of the presence of a signaling sequence. Likewise, CRISPR-Cas9 targeted insertion of poly(A) tracks into the coding sequence of the endogenous human genes AUF1 and TP53 results in a programmable reduction of targeted protein and mRNA levels. Functional analyses of AUF1-engineered hypomorphs indicate a direct correlation between AUF1 gene levels and the stability of AUF1-regulated mRNAs. Hypomorphs of TP53 affect expression of the target genes differentially depending on the severity of the hypomorphic mutation. Finally, decreases in TP53 protein affect the same cellular pathways in poly(A) track-engineered cells as in cancer cells, indicating these variants’ biological relevance. These results highlight this technology’s power to create predictable, stable hypomorphs in recombinant or endogenous genes in combination with CRISPR-Cas9 engineering tools.
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Affiliation(s)
- Geralle Powell
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
- Correspondence: Sergej Djuranovic, Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA.
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15
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Tsai CE, Yang FJ, Lee CH, Hsueh YP, Kuo CJ, Chen CS. The conserved regulator of autophagy and innate immunity hlh-30/TFEB mediates tolerance of enterohemorrhagic Escherichia coli in Caenorhabditis elegans. Genetics 2021; 217:1-17. [PMID: 33683370 DOI: 10.1093/genetics/iyaa052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/07/2020] [Indexed: 11/14/2022] Open
Abstract
Infection with antibiotic-resistant bacteria is an emerging life-threatening issue worldwide. Enterohemorrhagic Escherichia coli O157: H7 (EHEC) causes hemorrhagic colitis and hemolytic uremic syndrome via contaminated food. Treatment of EHEC infection with antibiotics is contraindicated because of the risk of worsening the syndrome through the secreted toxins. Identifying the host factors involved in bacterial infection provides information about how to combat this pathogen. In our previous study, we showed that EHEC colonizes in the intestine of Caenorhabditis elegans. However, the host factors involved in EHEC colonization remain elusive. Thus, in this study, we aimed to identify the host factors involved in EHEC colonization. We conducted forward genetic screens to isolate mutants that enhanced EHEC colonization and named this phenotype enhanced intestinal colonization (Inc). Intriguingly, four mutants with the Inc phenotype showed significantly increased EHEC-resistant survival, which contrasts with our current knowledge. Genetic mapping and whole-genome sequencing (WGS) revealed that these mutants have loss-of-function mutations in unc-89. Furthermore, we showed that the tolerance of unc-89(wf132) to EHEC relied on HLH-30/TFEB activation. These findings suggest that hlh-30 plays a key role in pathogen tolerance in C. elegans.
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Affiliation(s)
- Chia-En Tsai
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Fang-Jung Yang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ching-Han Lee
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.,Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica, Taipei 11490, Taiwan.,Taiwan International Graduate Program, National Defense Medical Center, Taipei 11490, Taiwan
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.,Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica, Taipei 11490, Taiwan.,Taiwan International Graduate Program, National Defense Medical Center, Taipei 11490, Taiwan.,Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Ju Kuo
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chang-Shi Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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16
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Hwang HY, Wang J. Fast genetic mapping using insertion-deletion polymorphisms in Caenorhabditis elegans. Sci Rep 2021; 11:11017. [PMID: 34040027 PMCID: PMC8155061 DOI: 10.1038/s41598-021-90190-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 05/07/2021] [Indexed: 11/09/2022] Open
Abstract
Genetic mapping is used in forward genetics to narrow the list of candidate mutations and genes corresponding to the mutant phenotype of interest. Even with modern advances in biology such as efficient identification of candidate mutations by whole-genome sequencing, mapping remains critical in pinpointing the responsible mutation. Here we describe a simple, fast, and affordable mapping toolkit that is particularly suitable for mapping in Caenorhabditis elegans. This mapping method uses insertion-deletion polymorphisms or indels that could be easily detected instead of single nucleotide polymorphisms in commonly used Hawaiian CB4856 mapping strain. The materials and methods were optimized so that mapping could be performed using tiny amount of genetic material without growing many large populations of mutants for DNA purification. We performed mapping of previously known and unknown mutations to show strengths and weaknesses of this method and to present examples of completed mapping. For situations where Hawaiian CB4856 is unsuitable, we provide an annotated list of indels as a basis for fast and easy mapping using other wild isolates. Finally, we provide rationale for using this mapping method over other alternatives as a part of a comprehensive strategy also involving whole-genome sequencing and other methods.
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Affiliation(s)
- Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Department of Neuroscience, Johns Hopkins University, 615 N. Wolfe Street, E8410, Baltimore, MD, 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Department of Neuroscience, Johns Hopkins University, 615 N. Wolfe Street, E8410, Baltimore, MD, 21205, USA.
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17
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Hintze M, Katsanos D, Shahrezaei V, Barkoulas M. Phenotypic Robustness of Epidermal Stem Cell Number in C. elegans Is Modulated by the Activity of the Conserved N-acetyltransferase nath-10/NAT10. Front Cell Dev Biol 2021; 9:640856. [PMID: 34084768 PMCID: PMC8168469 DOI: 10.3389/fcell.2021.640856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
Individual cells and organisms experience perturbations from internal and external sources, yet manage to buffer these to produce consistent phenotypes, a property known as robustness. While phenotypic robustness has often been examined in unicellular organisms, it has not been sufficiently studied in multicellular animals. Here, we investigate phenotypic robustness in Caenorhabditis elegans seam cells. Seam cells are stem cell-like epithelial cells along the lateral edges of the animal, which go through asymmetric and symmetric divisions contributing cells to the hypodermis and neurons, while replenishing the stem cell reservoir. The terminal number of seam cells is almost invariant in the wild-type population, allowing the investigation of how developmental precision is achieved. We report here that a loss-of-function mutation in the highly conserved N-acetyltransferase nath-10/NAT10 increases seam cell number variance in the isogenic population. RNA-seq analysis revealed increased levels of mRNA transcript variability in nath-10 mutant populations, which may have an impact on the phenotypic variability observed. Furthermore, we found disruption of Wnt signaling upon perturbing nath-10 function, as evidenced by changes in POP-1/TCF nuclear distribution and ectopic activation of its GATA transcription factor target egl-18. These results highlight that NATH-10/NAT-10 can influence phenotypic variability partly through modulation of the Wnt signaling pathway.
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Affiliation(s)
- Mark Hintze
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Dimitris Katsanos
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College, London, United Kingdom
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18
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Giunti S, Andersen N, Rayes D, De Rosa MJ. Drug discovery: Insights from the invertebrate Caenorhabditis elegans. Pharmacol Res Perspect 2021; 9:e00721. [PMID: 33641258 PMCID: PMC7916527 DOI: 10.1002/prp2.721] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/06/2021] [Indexed: 12/18/2022] Open
Abstract
Therapeutic drug development is a long, expensive, and complex process that usually takes 12-15 years. In the early phases of drug discovery, in particular, there is a growing need for animal models that ensure the reduction in both cost and time. Caenorhabditis elegans has been traditionally used to address fundamental aspects of key biological processes, such as apoptosis, aging, and gene expression regulation. During the last decade, with the advent of large-scale platforms for screenings, this invertebrate has also emerged as an essential tool in the pharmaceutical research industry to identify novel drugs and drug targets. In this review, we discuss the reasons why C. elegans has been positioned as an outstanding cost-effective option for drug discovery, highlighting both the advantages and drawbacks of this model. Particular attention is paid to the suitability of this nematode in large-scale genetic and pharmacological screenings. High-throughput screenings in C. elegans have indeed contributed to the breakthrough of a wide variety of candidate compounds involved in extensive fields including neurodegeneration, pathogen infections and metabolic disorders. The versatility of this nematode, which enables its instrumentation as a model of human diseases, is another attribute also herein underscored. As illustrative examples, we discuss the utility of C. elegans models of both human neurodegenerative diseases and parasitic nematodes in the drug discovery industry. Summing up, this review aims to demonstrate the impact of C. elegans models on the drug discovery pipeline.
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Affiliation(s)
- Sebastián Giunti
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Natalia Andersen
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Diego Rayes
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - María José De Rosa
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
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19
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Guo Y, Tocchini C, Ciosk R. CLK-2/TEL2 is a conserved component of the nonsense-mediated mRNA decay pathway. PLoS One 2021; 16:e0244505. [PMID: 33444416 PMCID: PMC7808604 DOI: 10.1371/journal.pone.0244505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) controls eukaryotic mRNA quality, inducing the degradation of faulty transcripts. Key players in the NMD pathway were originally identified, through genetics, in Caenorhabditis elegans as smg (suppressor with morphological effect on genitalia) genes. Using forward genetics and fluorescence-based NMD reporters, we reexamined the genetic landscape underlying NMD. Employing a novel strategy for mapping sterile mutations, Het-Map, we identified clk-2, a conserved gene previously implicated in DNA damage signaling, as a player in the nematode NMD. We find that CLK-2 is expressed predominantly in the germline, highlighting the importance of auxiliary factors in tissue-specific mRNA decay. Importantly, the human counterpart of CLK-2/TEL2, TELO2, has been also implicated in the NMD, suggesting a conserved role of CLK-2/TEL2 proteins in mRNA surveillance. Recently, variants of TELO2 have been linked to an intellectual disability disorder, the You-Hoover-Fong syndrome, which could be related to its function in the NMD.
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Affiliation(s)
- Yanwu Guo
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Rafal Ciosk
- Department of Biosciences, University of Oslo, Oslo, Norway
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- * E-mail:
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20
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Sahu PK, Sao R, Mondal S, Vishwakarma G, Gupta SK, Kumar V, Singh S, Sharma D, Das BK. Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review. PLANTS 2020; 9:plants9101355. [PMID: 33066352 PMCID: PMC7602136 DOI: 10.3390/plants9101355] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022]
Abstract
The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sudhir Kumar Gupta
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India;
| | - Sudhir Singh
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
- Correspondence: (D.S.); (B.K.D.)
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
- Correspondence: (D.S.); (B.K.D.)
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21
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Power KM, Akella JS, Gu A, Walsh JD, Bellotti S, Morash M, Zhang W, Ramadan YH, Ross N, Golden A, Smith HE, Barr MM, O’Hagan R. Mutation of NEKL-4/NEK10 and TTLL genes suppress neuronal ciliary degeneration caused by loss of CCPP-1 deglutamylase function. PLoS Genet 2020; 16:e1009052. [PMID: 33064774 PMCID: PMC7592914 DOI: 10.1371/journal.pgen.1009052] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/28/2020] [Accepted: 08/14/2020] [Indexed: 12/29/2022] Open
Abstract
Ciliary microtubules are subject to post-translational modifications that act as a "Tubulin Code" to regulate motor traffic, binding proteins and stability. In humans, loss of CCP1, a cytosolic carboxypeptidase and tubulin deglutamylating enzyme, causes infantile-onset neurodegeneration. In C. elegans, mutations in ccpp-1, the homolog of CCP1, result in progressive degeneration of neuronal cilia and loss of neuronal function. To identify genes that regulate microtubule glutamylation and ciliary integrity, we performed a forward genetic screen for suppressors of ciliary degeneration in ccpp-1 mutants. We isolated the ttll-5(my38) suppressor, a mutation in a tubulin tyrosine ligase-like glutamylase gene. We show that mutation in the ttll-4, ttll-5, or ttll-11 gene suppressed the hyperglutamylation-induced loss of ciliary dye filling and kinesin-2 mislocalization in ccpp-1 cilia. We also identified the nekl-4(my31) suppressor, an allele affecting the NIMA (Never in Mitosis A)-related kinase NEKL-4/NEK10. In humans, NEK10 mutation causes bronchiectasis, an airway and mucociliary transport disorder caused by defective motile cilia. C. elegans NEKL-4 localizes to the ciliary base but does not localize to cilia, suggesting an indirect role in ciliary processes. This work defines a pathway in which glutamylation, a component of the Tubulin Code, is written by TTLL-4, TTLL-5, and TTLL-11; is erased by CCPP-1; is read by ciliary kinesins; and its downstream effects are modulated by NEKL-4 activity. Identification of regulators of microtubule glutamylation in diverse cellular contexts is important to the development of effective therapies for disorders characterized by changes in microtubule glutamylation. By identifying C. elegans genes important for neuronal and ciliary stability, our work may inform research into the roles of the tubulin code in human ciliopathies and neurodegenerative diseases.
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Affiliation(s)
- Kade M. Power
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Jyothi S. Akella
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Amanda Gu
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Jonathon D. Walsh
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Sebastian Bellotti
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Margaret Morash
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Winnie Zhang
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Yasmin H. Ramadan
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Nicole Ross
- Biology Department, Montclair State University, Montclair, NJ, United States of America
| | - Andy Golden
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Harold E. Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maureen M. Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Robert O’Hagan
- Biology Department, Montclair State University, Montclair, NJ, United States of America
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22
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Wang Y, Bu L, Cao X, Qu H, Zhang C, Ren J, Huang Z, Zhao Y, Luo C, Hu X, Shu D, Li N. Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line. Front Genet 2020; 11:894. [PMID: 33033489 PMCID: PMC7509424 DOI: 10.3389/fgene.2020.00894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F2 generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F0, F2, F8, and F9 generations of AIL and demonstrate that the population of the F9 generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F2 generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth.
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Affiliation(s)
- Yuzhe Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lina Bu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuemin Cao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hao Qu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunyuan Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangli Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhuolin Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Harnessing the power of genetics: fast forward genetics in Caenorhabditis elegans. Mol Genet Genomics 2020; 296:1-20. [PMID: 32888055 DOI: 10.1007/s00438-020-01721-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022]
Abstract
Forward genetics is a powerful tool to unravel molecular mechanisms of diverse biological processes. The success of genetic screens primarily relies on the ease of genetic manipulation of an organism and the availability of a plethora of genetic tools. The roundworm Caenorhabditis elegans has been one of the favorite models for genetic studies due to its hermaphroditic lifestyle, ease of maintenance, and availability of various genetic manipulation tools. The strength of C. elegans genetics is highlighted by the leading role of this organism in the discovery of several conserved biological processes. In this review, the principles and strategies for forward genetics in C. elegans are discussed. Further, the recent advancements that have drastically accelerated the otherwise time-consuming process of mutation identification, making forward genetic screens a method of choice for understanding biological functions, are discussed. The emphasis of the review has been on providing practical and conceptual pointers for designing genetic screens that will identify mutations, specifically disrupting the biological processes of interest.
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Zhou X, St Pierre CL, Gonzales NM, Zou J, Cheng R, Chitre AS, Sokoloff G, Palmer AA. Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity. G3 (BETHESDA, MD.) 2020; 10:951-965. [PMID: 31974095 PMCID: PMC7056977 DOI: 10.1534/g3.119.400763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
There has been extensive discussion of the "Replication Crisis" in many fields, including genome-wide association studies (GWAS). We explored replication in a mouse model using an advanced intercross line (AIL), which is a multigenerational intercross between two inbred strains. We re-genotyped a previously published cohort of LG/J x SM/J AIL mice (F34; n = 428) using a denser marker set and genotyped a new cohort of AIL mice (F39-43; n = 600) for the first time. We identified 36 novel genome-wide significant loci in the F34 and 25 novel loci in the F39-43 cohort. The subset of traits that were measured in both cohorts (locomotor activity, body weight, and coat color) showed high genetic correlations, although the SNP heritabilities were slightly lower in the F39-43 cohort. For this subset of traits, we attempted to replicate loci identified in either F34 or F39-43 in the other cohort. Coat color was robustly replicated; locomotor activity and body weight were only partially replicated, which was inconsistent with our power simulations. We used a random effects model to show that the partial replications could not be explained by Winner's Curse but could be explained by study-specific heterogeneity. Despite this heterogeneity, we performed a mega-analysis by combining F34 and F39-43 cohorts (n = 1,028), which identified four novel loci associated with locomotor activity and body weight. These results illustrate that even with the high degree of genetic and environmental control possible in our experimental system, replication was hindered by study-specific heterogeneity, which has broad implications for ongoing concerns about reproducibility.
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Affiliation(s)
- Xinzhu Zhou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92092
| | - Celine L St Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110
| | | | - Jennifer Zou
- Department of Computer Science, University of California, Los Angeles, CA, 90095
| | | | | | - Greta Sokoloff
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, IO, 52242
| | - Abraham A Palmer
- Department of Psychiatry,
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92037 and
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Zhan Q, Wang L, Xu X, Sun Y, Li L, Qi X, Chen F, Wei X, Raff ML, Yu P, Jin F. An APC Mutation in a Large Chinese Kindred With Familial Adenomatous Polyposis Was Identified Using Both Next Generation Sequencing and Simple STR Marker Haplotypes. Front Genet 2020; 11:191. [PMID: 32194643 PMCID: PMC7064715 DOI: 10.3389/fgene.2020.00191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 02/18/2020] [Indexed: 12/30/2022] Open
Abstract
Background Familial adenomatous polyposis (FAP) is an autosomal dominant disorder characterized primarily by the development of numerous adenomatous polyps in the colon and a high risk for colorectal cancer. FAP is caused by germline mutations of the adenomatous polyposis coli (APC) gene. The proband in this family was a 39-year-old female patient with the pathologic diagnosis of adenomatous polyps, and then a five-generation kindred with FAP was characterized in the following years. This article identified an APC mutation, and demonstrated the practical use of APC-linked STR markers, which could be used to reduce misdiagnosis of prenatal diagnosis or preimplantation genetic diagnosis resulted from contamination or allele drop-out. Methods Next-generation sequencing (NGS) was used to identify the possible APC mutations in an affected individual from a family with autosomal dominant colon cancer. Targeted sequencing then used to identify additional related individuals with the mutation. Three short tandem repeat (STR) loci, D5S299, D5S134, and D5S346, were used for PCR-based microsatellite analysis of the APC gene in the extended family. Results We identified an APC: p.W553X mutation. The STR haplotype at the APC locus, A1B4C1, was shared by all clinically affected individuals with the APC: p.W553X mutation. In addition, the APC: p.D1822V variant was observed in 40% affected individuals and in two unaffected individuals. Conclusion We described a protein truncation mutation, APC: p.W553X; demonstrated the value of APC-linked STR markers (D5S299, D5S134, and D5S346) haplotypes; and suggested the potential role of these haplotypes in detecting loss of heterozygosity of the APC gene.
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Affiliation(s)
- Qitao Zhan
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liya Wang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangrong Xu
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Sun
- Department of Obstetrics and Gynecology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lejun Li
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuchen Qi
- Department of Neurosurgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feng Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Michael L Raff
- Genomics Institute, MultiCare Health System, Tacoma, WA, United States
| | - Ping Yu
- Department of Cell Biology and Medical Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Fan Jin
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Romanelli-Credrez L, Doitsidou M, Alkema MJ, Salinas G. HIF-1 Has a Central Role in Caenorhabditis elegans Organismal Response to Selenium. Front Genet 2020; 11:63. [PMID: 32161616 PMCID: PMC7052493 DOI: 10.3389/fgene.2020.00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 11/13/2022] Open
Abstract
Selenium is a trace element for most organisms; its deficiency and excess are detrimental. Selenium beneficial effects are mainly due to the role of the 21st genetically encoded amino acid selenocysteine (Sec). Selenium also exerts Sec-independent beneficial effects. Its harmful effects are thought to be mainly due to non-specific incorporation in protein synthesis. Yet the selenium response in animals is poorly understood. In Caenorhabditis elegans, Sec is genetically incorporated into a single selenoprotein. Similar to mammals, a 20-fold excess of the optimal selenium requirement is harmful. Sodium selenite (Na2SeO3) excess causes development retardation, impaired growth, and neurodegeneration of motor neurons. To study the organismal response to selenium we performed a genetic screen for C. elegans mutants that are resistant to selenite. We isolated non-sense and missense egl-9/EGLN mutants that confer robust resistance to selenium. In contrast, hif-1/HIF null mutant was highly sensitive to selenium, establishing a role for this transcription factor in the selenium response. We showed that EGL-9 regulates HIF-1 activity through VHL-1, and identified CYSL-1 as a key sensor that transduces the selenium signal. Finally, we showed that the key enzymes involved in sulfide and sulfite stress (sulfide quinone oxidoreductase and sulfite oxidase) are not required for selenium resistance. In contrast, knockout strains in the persulfide dioxygenase ETHE-1 and the sulfurtransferase MPST-7 affect the organismal response to selenium. In sum, our results identified a transcriptional pathway as well as enzymes possibly involved in the organismal selenium response.
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Affiliation(s)
- Laura Romanelli-Credrez
- Laboratorio de Biología de Gusanos. Unidad Mixta, Departamento de Biociencias, Facultad de Química, Universidad de la República-Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Maria Doitsidou
- Centre for Discovery Brain Sciences (CDBS), University of Edinburgh, Edinburgh, United Kingdom
| | - Mark J Alkema
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA, United States
| | - Gustavo Salinas
- Laboratorio de Biología de Gusanos. Unidad Mixta, Departamento de Biociencias, Facultad de Química, Universidad de la República-Institut Pasteur de Montevideo, Montevideo, Uruguay
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27
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Marques F, Saro G, Lia AS, Poole RJ, Falquet L, Glauser DA. Identification of avoidance genes through neural pathway-specific forward optogenetics. PLoS Genet 2019; 15:e1008509. [PMID: 31891575 PMCID: PMC6938339 DOI: 10.1371/journal.pgen.1008509] [Citation(s) in RCA: 10] [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: 06/19/2019] [Accepted: 11/05/2019] [Indexed: 11/19/2022] Open
Abstract
Understanding how the nervous system bridges sensation and behavior requires the elucidation of complex neural and molecular networks. Forward genetic approaches, such as screens conducted in C. elegans, have successfully identified genes required to process natural sensory stimuli. However, functional redundancy within the underlying neural circuits, which are often organized with multiple parallel neural pathways, limits our ability to identify 'neural pathway-specific genes', i.e. genes that are essential for the function of some, but not all of these redundant neural pathways. To overcome this limitation, we developed a 'forward optogenetics' screening strategy in which natural stimuli are initially replaced by the selective optogenetic activation of a specific neural pathway. We used this strategy to address the function of the polymodal FLP nociceptors mediating avoidance of noxious thermal and mechanical stimuli. According to our expectations, we identified both mutations in 'general' avoidance genes that broadly impact avoidance responses to a variety of natural noxious stimuli (unc-4, unc-83, and eat-4) and mutations that produce a narrower impact, more restricted to the FLP pathway (syd-2, unc-14 and unc-68). Through a detailed follow-up analysis, we further showed that the Ryanodine receptor UNC-68 acts cell-autonomously in FLP to adjust heat-evoked calcium signals and aversive behaviors. As a whole, our work (i) reveals the importance of properly regulated ER calcium release for FLP function, (ii) provides new entry points for new nociception research and (iii) demonstrates the utility of our forward optogenetic strategy, which can easily be transposed to analyze other neural pathways.
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Affiliation(s)
- Filipe Marques
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gabriella Saro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andrei-Stefan Lia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Richard J. Poole
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
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28
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Delaney K, Strobino M, Wenda JM, Pankowski A, Steiner FA. H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans. Nat Commun 2019; 10:2529. [PMID: 31175278 PMCID: PMC6555832 DOI: 10.1038/s41467-019-10404-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/10/2019] [Indexed: 12/20/2022] Open
Abstract
Substitution of lysine 27 with methionine in histone H3.3 is a recently discovered driver mutation of pediatric high-grade gliomas. Mutant cells show decreased levels and altered distribution of H3K27 trimethylation (H3K27me3). How these chromatin changes are established genome-wide and lead to tumorigenesis remains unclear. Here we show that H3.3K27M-mediated alterations in H3K27me3 distribution result in ectopic DNA replication and cell cycle progression of germ cells in Caenorhabditis elegans. By genetically inducing changes in the H3.3 distribution, we demonstrate that both H3.3K27M and pre-existing H3K27me3 act locally and antagonistically on Polycomb Repressive Complex 2 (PRC2) in a concentration-dependent manner. The heterochromatin changes result in extensive gene misregulation, and genetic screening identified upregulation of JNK as an underlying cause of the germcell aberrations. Moreover, JNK inhibition suppresses the replicative fate in human tumor-derived H3.3K27M cells, thus establishing C. elegans as a powerful model for the identification of potential drug targets for treatment of H3.3K27M tumors. Substitution of lysine 27 with methionine in histone H3.3 (H3.3K27M) is a driver mutation of pediatric high-grade gliomas. Here the authors show that H3.3K27M-mediated alterations in H3K27me3 distribution result in ectopic DNA replication and cell cycle progression of germ cells in Caenorhabditis elegans, through JNK pathway misregulation.
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Affiliation(s)
- Kamila Delaney
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Maude Strobino
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Andrzej Pankowski
- Team of Mathematics and Physics, Faculty of Civil Engineering, Mechanics and Petrochemistry, Warsaw University of Technology, 09-400, Płock, Poland
| | - Florian A Steiner
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland.
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29
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Yoshimura J, Ichikawa K, Shoura MJ, Artiles KL, Gabdank I, Wahba L, Smith CL, Edgley ML, Rougvie AE, Fire AZ, Morishita S, Schwarz EM. Recompleting the Caenorhabditis elegans genome. Genome Res 2019; 29:1009-1022. [PMID: 31123080 PMCID: PMC6581061 DOI: 10.1101/gr.244830.118] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. elegans available today. To provide a more accurate C. elegans genome, we performed long-read assembly of VC2010, a modern strain derived from N2. Our VC2010 assembly has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and genome duplications. For 116 structural discrepancies between N2 and VC2010, 97 structures matching VC2010 (84%) were also found in two outgroup strains, implying deficiencies in N2. Over 98% of N2 genes encoded unchanged products in VC2010; moreover, we predicted ≥53 new genes in VC2010. The recompleted genome of C. elegans should be a valuable resource for genetics, genomics, and systems biology.
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Affiliation(s)
- Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Massa J Shoura
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Karen L Artiles
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Lamia Wahba
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Cheryl L Smith
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Mark L Edgley
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z3, British Columbia, Canada
| | - Ann E Rougvie
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55454, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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30
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Turner KJ, Hoyle J, Valdivia LE, Cerveny KL, Hart W, Mangoli M, Geisler R, Rees M, Houart C, Poole RJ, Wilson SW, Gestri G. Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits. PLoS One 2019; 14:e0211073. [PMID: 30695021 PMCID: PMC6350959 DOI: 10.1371/journal.pone.0211073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/07/2019] [Indexed: 12/26/2022] Open
Abstract
Through forward genetic screening for mutations affecting visual system development, we identified prominent coloboma and cell-autonomous retinal neuron differentiation, lamination and retinal axon projection defects in eisspalte (ele) mutant zebrafish. Additional axonal deficits were present, most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp, which encodes a conserved RNA stem-loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when, and locations where, post-mitotic cells have differentiated in wild-type siblings. Indeed, RNAseq analysis showed down-regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated, for instance, in axon guidance, that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise, or promote transitions in, cell state and require the correct function of Slbp-dependent histone and chromatin regulatory genes.
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Affiliation(s)
- Katherine J. Turner
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Jacqueline Hoyle
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- Department of Paediatrics and Child Health, University College London, London, United Kingdom
| | - Leonardo E. Valdivia
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Kara L. Cerveny
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Wendy Hart
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Maryam Mangoli
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Robert Geisler
- Karlsruhe Institute of Technology (KIT) Institute of Toxicology and Genetics, Eggenstein-Leopoldshafen, Germany
| | - Michele Rees
- Department of Paediatrics and Child Health, University College London, London, United Kingdom
| | - Corinne Houart
- Department of Developmental Neurobiology and MRC Centre for Developmental Disorders, Kings College London, London, United Kingdom
| | - Richard J. Poole
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Stephen W. Wilson
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- * E-mail: (GG); (SWW)
| | - Gaia Gestri
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- * E-mail: (GG); (SWW)
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31
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Kegel L, Rubio M, Almeida RG, Benito S, Klingseisen A, Lyons DA. Forward Genetic Screen Using Zebrafish to Identify New Genes Involved in Myelination. Methods Mol Biol 2019; 1936:185-209. [PMID: 30820900 DOI: 10.1007/978-1-4939-9072-6_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zebrafish are now well established as the preeminent vertebrate model with which to carry out gene discovery/forward genetic screens to identify the molecular genetic basis of biological processes. Gene discovery screens in zebrafish have already provided novel insight into mechanisms of glial cell development and function. The vast majority of genetic screens in zebrafish are based around a three generation screen that starts with the random induction of mutations in adult males using the chemical mutagen ENU. Here we outline the methods that underlie this type of screen, detailing each step, from ENU mutagenesis, through the breeding schemes required to recover homozygous mutant animals in subsequent generations, the screening procedure itself, with a focus on the analysis of myelinating glia, and the subsequent confirmation of mutant phenotypes.
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Affiliation(s)
- Linde Kegel
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Maria Rubio
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rafael G Almeida
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Silvia Benito
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Anna Klingseisen
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - David A Lyons
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK.
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32
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Use of a Sibling Subtraction Method for Identifying Causal Mutations in Caenorhabditis elegans by Whole-Genome Sequencing. G3-GENES GENOMES GENETICS 2018; 8:669-678. [PMID: 29237702 PMCID: PMC5919755 DOI: 10.1534/g3.117.300135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome sequencing (WGS) is an indispensable tool for identifying causal mutations obtained from genetic screens. To reduce the number of causal mutation candidates typically uncovered by WGS, Caenorhabditis elegans researchers have developed several strategies. One involves crossing N2-background mutants to the polymorphic Hawaiian (HA) strain, which can be used to simultaneously identify mutant strain variants and obtain high-density mapping information. This approach, however, is not well suited for uncovering mutations in complex genetic backgrounds, and HA polymorphisms can alter phenotypes. Other approaches make use of DNA variants present in the initial background or introduced by mutagenesis. This information is used to implicate genomic regions with high densities of DNA lesions that persist after backcrossing, but these methods can provide lower resolution than HA mapping. To identify suppressor mutations using WGS, we developed an approach termed the sibling subtraction method (SSM). This method works by eliminating variants present in both mutants and their nonmutant siblings, thus greatly reducing the number of candidates. We used this method with two members of the C. elegans NimA-related kinase family, nekl-2 and nekl-3. Combining weak aphenotypic alleles of nekl-2 and nekl-3 leads to penetrant molting defects and larval arrest. We isolated ∼50 suppressors of nekl-2; nekl-3 synthetic lethality using F1 clonal screening methods and a peel-1–based counterselection strategy. When applied to five of the suppressors, SSM led to only one to four suppressor candidates per strain. Thus SSM is a powerful approach for identifying causal mutations in any genetic background and provides an alternative to current methods.
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Abstract
The free-living nematode Caenorhabditis elegans is the simplest animal model organism to work with. Substantial knowledge and tools have accumulated over 50 years of C. elegans research. The use of C. elegans relating to parasitic nematodes from a basic biology standpoint or an applied perspective has increased in recent years. The wealth of information gained on the model organism, the use of the powerful approaches and technologies that have advanced C. elegans research to parasitic nematodes and the enormous success of the omics fields have contributed to bridge the divide between C. elegans and parasite nematode researchers. We review key fields, such as genomics, drug discovery and genetics, where C. elegans and nematode parasite research have convened. We advocate the use of C. elegans as a model to study helminth metabolism, a neglected area ready to advance. How emerging technologies being used in C. elegans can pave the way for parasitic nematode research is discussed.
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34
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Katsanos D, Koneru SL, Mestek Boukhibar L, Gritti N, Ghose R, Appleford PJ, Doitsidou M, Woollard A, van Zon JS, Poole RJ, Barkoulas M. Stochastic loss and gain of symmetric divisions in the C. elegans epidermis perturbs robustness of stem cell number. PLoS Biol 2017; 15:e2002429. [PMID: 29108019 PMCID: PMC5690688 DOI: 10.1371/journal.pbio.2002429] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 11/16/2017] [Accepted: 10/20/2017] [Indexed: 11/19/2022] Open
Abstract
Biological systems are subject to inherent stochasticity. Nevertheless, development is remarkably robust, ensuring the consistency of key phenotypic traits such as correct cell numbers in a certain tissue. It is currently unclear which genes modulate phenotypic variability, what their relationship is to core components of developmental gene networks, and what is the developmental basis of variable phenotypes. Here, we start addressing these questions using the robust number of Caenorhabditis elegans epidermal stem cells, known as seam cells, as a readout. We employ genetics, cell lineage tracing, and single molecule imaging to show that mutations in lin-22, a Hes-related basic helix-loop-helix (bHLH) transcription factor, increase seam cell number variability. We show that the increase in phenotypic variability is due to stochastic conversion of normally symmetric cell divisions to asymmetric and vice versa during development, which affect the terminal seam cell number in opposing directions. We demonstrate that LIN-22 acts within the epidermal gene network to antagonise the Wnt signalling pathway. However, lin-22 mutants exhibit cell-to-cell variability in Wnt pathway activation, which correlates with and may drive phenotypic variability. Our study demonstrates the feasibility to study phenotypic trait variance in tractable model organisms using unbiased mutagenesis screens.
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Affiliation(s)
- Dimitris Katsanos
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Sneha L. Koneru
- Department of Life Sciences, Imperial College, London, United Kingdom
| | | | - Nicola Gritti
- Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, The Netherlands
| | - Ritobrata Ghose
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Peter J. Appleford
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Maria Doitsidou
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Woollard
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jeroen S. van Zon
- Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, The Netherlands
| | - Richard J. Poole
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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Smith HE, Yun S. Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing. PLoS One 2017; 12:e0174446. [PMID: 28333980 PMCID: PMC5363872 DOI: 10.1371/journal.pone.0174446] [Citation(s) in RCA: 14] [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: 01/15/2017] [Accepted: 03/09/2017] [Indexed: 12/30/2022] Open
Abstract
Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification have been targeted to C. elegans, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria. Although success is predicated upon the sensitive and accurate detection of candidate alleles, relatively little effort has been invested in evaluating the underlying software components that are required for mutation identification. Therefore, we have benchmarked a number of commonly used tools for sequence alignment and variant calling, in all pair-wise combinations, against both simulated and actual datasets. We compared the accuracy of those pipelines for mutation identification in C. elegans, and found that the combination of BBMap for alignment plus FreeBayes for variant calling offers the most robust performance.
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Affiliation(s)
- Harold E. Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Sijung Yun
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Xue H, Shi T, Wang F, Zhou H, Yang J, Wang L, Wang S, Su Y, Zhang Z, Qiao Y, Li X. Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method. HORTICULTURE RESEARCH 2017; 4:17053. [PMID: 29118994 PMCID: PMC5674137 DOI: 10.1038/hortres.2017.53] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 05/16/2023]
Abstract
Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars. The 'Dangshansuli' cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit.
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Affiliation(s)
- Huabai Xue
- College of Horticulture, Nanjing Agricultural
University, Nanjing
210095, China
- Zhengzhou Fruit Research Institute, Chinese
Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of
Ministry of Agriculture, Zhengzhou
450009, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural
University, Nanjing
210095, China
| | - Fangfang Wang
- Zhengzhou Fruit Research Institute, Chinese
Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of
Ministry of Agriculture, Zhengzhou
450009, China
| | - Huangkai Zhou
- Guangzhou Gene Denovo Biotechnology Co.
Ltd, Guangzhou
510006, China
| | - Jian Yang
- Zhengzhou Fruit Research Institute, Chinese
Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of
Ministry of Agriculture, Zhengzhou
450009, China
| | - Long Wang
- Zhengzhou Fruit Research Institute, Chinese
Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of
Ministry of Agriculture, Zhengzhou
450009, China
| | - Suke Wang
- Zhengzhou Fruit Research Institute, Chinese
Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of
Ministry of Agriculture, Zhengzhou
450009, China
| | - Yanli Su
- Zhengzhou Fruit Research Institute, Chinese
Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of
Ministry of Agriculture, Zhengzhou
450009, China
| | - Zhen Zhang
- College of Horticulture, Nanjing Agricultural
University, Nanjing
210095, China
| | - Yushan Qiao
- College of Horticulture, Nanjing Agricultural
University, Nanjing
210095, China
| | - Xiugen Li
- Zhengzhou Fruit Research Institute, Chinese
Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of
Ministry of Agriculture, Zhengzhou
450009, China
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MITANI S. Comprehensive functional genomics using Caenorhabditis elegans as a model organism. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:561-577. [PMID: 29021508 PMCID: PMC5743858 DOI: 10.2183/pjab.93.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
We have been working on functional genomics using C. elegans as a model organism. We first used cell-type specific markers and preexisting mutants to investigate how genotype-phenotype causal relationships are regulated. With the aid of transgenic methods, we analyzed various biological processes in C. elegans. We have developed efficient methods to isolate gene knockout strains. Thousands of strains isolated this way are used by many researchers and have revealed many biological mechanisms. We have also developed methods to examine the functions of genes in a comprehensive manner by integrating transgenes into chromosomes, designing conditional knockouts, and creating balancers for lethal mutations. A combination of these biological resources and techniques will be useful to understand the functions of genes in C. elegans, which has many genes that are orthologous to those of higher organisms including humans.
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Affiliation(s)
- Shohei MITANI
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, Tokyo, Japan
- Tokyo Women’s Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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Miranda-Vizuete A, Veal EA. Caenorhabditis elegans as a model for understanding ROS function in physiology and disease. Redox Biol 2016; 11:708-714. [PMID: 28193593 PMCID: PMC5304259 DOI: 10.1016/j.redox.2016.12.020] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/19/2016] [Indexed: 01/05/2023] Open
Abstract
ROS (reactive oxygen species) are potentially damaging by-products of aerobic metabolism which, unchecked, can have detrimental effects on cell function. However, it is now widely accepted that, at physiological levels, certain ROS play important roles in cell signaling, acting as second messengers to regulate cell choices that contribute to the development, adaptation and survival of plants and animals. Despite important recent advances in the biochemical tools available to study redox-signaling, the molecular mechanisms underlying most of these responses remain poorly understood, particularly in multicellular organisms. As we will review here, C. elegans has emerged as a powerful animal model to elucidate these and other aspects of redox biology.
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Affiliation(s)
- Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain.
| | - Elizabeth A Veal
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; Institute for Ageing, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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