1
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Vandenbosch M, van Hove ERA, Mohren R, Vermeulen I, Dijkman H, Heeren RMA, Leonards PEG, Hughes S. Combined matrix-assisted laser desorption/ionisation-mass spectrometry imaging with liquid chromatography-tandem mass spectrometry for observing spatial distribution of lipids in whole Caenorhabditis elegans. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9850. [PMID: 39034751 DOI: 10.1002/rcm.9850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 07/23/2024]
Abstract
RATIONALE Matrix-assisted laser desorption/ionisation-mass spectrometry imaging (MALDI-MSI) is a powerful label-free technique for biomolecule detection (e.g., lipids), within tissue sections across various biological species. However, despite its utility in many applications, the nematode Caenorhabditis elegans is not routinely used in combination with MALDI-MSI. The lack of studies exploring spatial distribution of biomolecules in nematodes is likely due to challenges with sample preparation. METHODS This study developed a sample preparation method for whole intact nematodes, evaluated using cryosectioning of nematodes embedded in a 10% gelatine solution to obtain longitudinal cross sections. The slices were then subjected to MALDI-MSI, using a RapifleX Tissuetyper in positive and negative polarities. Samples were also prepared for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis using an Exploris 480 coupled to a HPLC Vanquish system to confirm the MALDI-MSI results. RESULTS An optimised embedding method was developed for longitudinal cross-sectioning of individual worms. To obtain longitudinal cross sections, nematodes were frozen at -80°C so that all worms were rod shaped. Then, the samples were defrosted and transferred to a 10% gelatine matrix in a cryomold; the worms aligned, and the whole cryomold submerged in liquid nitrogen. Using MALDI-MSI, we were able to observe the distribution of lipids within C. elegans, with clear differences in their spatial distribution at a resolution of 5 μm. To confirm the lipids from MALDI-MSI, age-matched nematodes were subjected to LC-MS/MS. Here, 520 lipids were identified using LC-MS/MS, indicating overlap with MALDI-MSI data. CONCLUSIONS This optimised sample preparation technique enabled (un)targeted analysis of spatially distributed lipids within individual nematodes. The possibility to detect other biomolecules using this method thus laid the basis for prospective preclinical and toxicological studies on C. elegans.
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Affiliation(s)
- Michiel Vandenbosch
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Erika R Amstalden van Hove
- Amsterdam Institute for Life and Environment, Chemistry for Environment and Health, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ronny Mohren
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Isabeau Vermeulen
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Henry Dijkman
- HAN University of Applied Sciences, Nijmegen, The Netherlands
| | - Ron M A Heeren
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Pim E G Leonards
- Amsterdam Institute for Life and Environment, Chemistry for Environment and Health, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Samantha Hughes
- Amsterdam Institute for Life and Environment, Environmental Health and Toxicology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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2
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Weng Y, Murphy CT. Male-specific behavioral and transcriptomic changes in aging C. elegans neurons. iScience 2024; 27:109910. [PMID: 38783998 PMCID: PMC11111838 DOI: 10.1016/j.isci.2024.109910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/20/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Aging is a complex biological process with sexually dimorphic aspects. Although cognitive aging of Caenorhabditis elegans hermaphrodites has been studied, less is known about cognitive decline in males. We found that cognitive aging has both sex-shared and sex-dimorphic characteristics, and we identified neuron-specific age-associated sex-differential targets. In addition to sex-shared neuronal aging genes, males differentially downregulate mitochondrial metabolic genes and upregulate GPCR genes with age, while the X chromosome exhibits increased gene expression in hermaphrodites and altered dosage compensation complex expression with age, indicating possible X chromosome dysregulation that contributes to sexual dimorphism in cognitive aging. Finally, the sex-differentially expressed gene hrg-7, an aspartic-type endopeptidase, regulates male cognitive aging but does not affect hermaphrodites' behaviors. These results suggest that males and hermaphrodites exhibit different age-related neuronal changes. This study will strengthen our understanding of sex-specific vulnerability and resilience and identify pathways to target with treatments that could benefit both sexes.
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Affiliation(s)
- Yifei Weng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T. Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- LSI Genomics, Princeton University, Princeton, NJ 08544, USA
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3
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Haque R, Kurien SP, Setty H, Salzberg Y, Stelzer G, Litvak E, Gingold H, Rechavi O, Oren-Suissa M. Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans. Nat Commun 2024; 15:4273. [PMID: 38769103 PMCID: PMC11106331 DOI: 10.1038/s41467-024-48369-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Sex-specific traits and behaviors emerge during development by the acquisition of unique properties in the nervous system of each sex. However, the genetic events responsible for introducing these sex-specific features remain poorly understood. In this study, we create a comprehensive gene expression atlas of pure populations of hermaphrodites and males of the nematode Caenorhabditis elegans across development. We discover numerous differentially expressed genes, including neuronal gene families like transcription factors, neuropeptides, and G protein-coupled receptors. We identify INS-39, an insulin-like peptide, as a prominent male-biased gene expressed specifically in ciliated sensory neurons. We show that INS-39 serves as an early-stage male marker, facilitating the effective isolation of males in high-throughput experiments. Through complex and sex-specific regulation, ins-39 plays pleiotropic sexually dimorphic roles in various behaviors, while also playing a shared, dimorphic role in early life stress. This study offers a comparative sexual and developmental gene expression database for C. elegans. Furthermore, it highlights conserved genes that may underlie the sexually dimorphic manifestation of different human diseases.
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Affiliation(s)
- Rizwanul Haque
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Sonu Peedikayil Kurien
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Hagar Setty
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Salzberg
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Stelzer
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Einav Litvak
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Meital Oren-Suissa
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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4
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Fox BW, Helf MJ, Burkhardt RN, Artyukhin AB, Curtis BJ, Palomino DF, Schroeder AF, Chaturbedi A, Tauffenberger A, Wrobel CJJ, Zhang YK, Lee SS, Schroeder FC. Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans. Nat Commun 2024; 15:1520. [PMID: 38374083 PMCID: PMC10876521 DOI: 10.1038/s41467-024-45782-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, which mimics the activity of microbiota-dependent becyp#1 but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.
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Affiliation(s)
- Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Russell N Burkhardt
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander B Artyukhin
- Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Diana Fajardo Palomino
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Allen F Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Arnaud Tauffenberger
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
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5
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Ma F, Lau CY, Zheng C. Young duplicate genes show developmental stage- and cell type-specific expression and function in Caenorhabditis elegans. CELL GENOMICS 2024; 4:100467. [PMID: 38190105 PMCID: PMC10794840 DOI: 10.1016/j.xgen.2023.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/06/2023] [Accepted: 11/23/2023] [Indexed: 01/09/2024]
Abstract
Gene duplication produces the material that fuels evolutionary innovation. The "out-of-testis" hypothesis suggests that sperm competition creates selective pressure encouraging the emergence of new genes in male germline, but the somatic expression and function of the newly evolved genes are not well understood. We systematically mapped the expression of young duplicate genes throughout development in Caenorhabditis elegans using both whole-organism and single-cell transcriptomic data. Based on the expression dynamics across developmental stages, young duplicate genes fall into three clusters that are preferentially expressed in early embryos, mid-stage embryos, and late-stage larvae. Early embryonic genes are involved in protein degradation and develop essentiality comparable to the genomic average. In mid-to-late embryos and L4-stage larvae, young genes are enriched in intestine, epidermal cells, coelomocytes, and amphid chemosensory neurons. Their molecular functions and inducible expression indicate potential roles in innate immune response and chemosensory perceptions, which may contribute to adaptation outside of the sperm.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chun Yin Lau
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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6
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Robles-Remacho A, Sanchez-Martin RM, Diaz-Mochon JJ. Spatial Transcriptomics: Emerging Technologies in Tissue Gene Expression Profiling. Anal Chem 2023; 95:15450-15460. [PMID: 37814884 PMCID: PMC10603609 DOI: 10.1021/acs.analchem.3c02029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
In this Perspective, we discuss the current status and advances in spatial transcriptomics technologies, which allow high-resolution mapping of gene expression in intact cell and tissue samples. Spatial transcriptomics enables the creation of high-resolution maps of gene expression patterns within their native spatial context, adding an extra layer of information to the bulk sequencing data. Spatial transcriptomics has expanded significantly in recent years and is making a notable impact on a range of fields, including tissue architecture, developmental biology, cancer, and neurodegenerative and infectious diseases. The latest advancements in spatial transcriptomics have resulted in the development of highly multiplexed methods, transcriptomic-wide analysis, and single-cell resolution utilizing diverse technological approaches. In this Perspective, we provide a detailed analysis of the molecular foundations behind the main spatial transcriptomics technologies, including methods based on microdissection, in situ sequencing, single-molecule FISH, spatial capturing, selection of regions of interest, and single-cell or nuclei dissociation. We contextualize the detection and capturing efficiency, strengths, limitations, tissue compatibility, and applications of these techniques as well as provide information on data analysis. In addition, this Perspective discusses future directions and potential applications of spatial transcriptomics, highlighting the importance of the continued development to promote widespread adoption of these techniques within the research community.
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Affiliation(s)
- Agustín Robles-Remacho
- GENYO.
Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion,
114. 18016 Granada, Spain
- Department
of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
| | - Rosario M. Sanchez-Martin
- GENYO.
Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion,
114. 18016 Granada, Spain
- Department
of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
| | - Juan J. Diaz-Mochon
- GENYO.
Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion,
114. 18016 Granada, Spain
- Department
of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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7
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Sounart H, Voronin D, Masarapu Y, Chung M, Saarenpää S, Ghedin E, Giacomello S. Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale. Nat Commun 2023; 14:6500. [PMID: 37838705 PMCID: PMC10576761 DOI: 10.1038/s41467-023-42237-y] [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: 11/07/2022] [Accepted: 10/03/2023] [Indexed: 10/16/2023] Open
Abstract
Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization; to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteria Wolbachia. However, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. As Wolbachia is essential for the development, reproduction, and survival of filarial worms, we spatially explored how Wolbachia interacts with the worm's reproductive system by performing a spatial characterization using Spatial Transcriptomics (ST) across a posterior region containing reproductive tissue and developing embryos of adult female Brugia malayi worms. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the method's ability to uncover nuanced tissue region expression patterns, observe the spatial localization of key B. malayi - Wolbachia pathway genes, and co-localize the B. malayi spatial transcriptome in Wolbachia tissue regions, also under antibiotic treatment. We envision our approach will open up new avenues for the study of infectious diseases caused by micro-scale parasitic worms.
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Affiliation(s)
- Hailey Sounart
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Denis Voronin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yuvarani Masarapu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sami Saarenpää
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Stefania Giacomello
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.
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8
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Lu L, Abbott AL. Male gonad-enriched microRNAs function to control sperm production in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561762. [PMID: 37873419 PMCID: PMC10592766 DOI: 10.1101/2023.10.10.561762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Germ cell development and gamete production in animals require small RNA pathways. While studies indicate that microRNAs (miRNAs) are necessary for normal sperm production and function, the specific roles for individual miRNAs are largely unknown. Here, we use small RNA sequencing of dissected gonads and functional analysis of new loss of function alleles to identify functions for miRNAs in the control of fecundity and sperm production in Caenorhabditis elegans males and hermaphrodites. We describe a set of 29 male gonad-enriched miRNAs and identify a set of 3 individual miRNAs (mir-58.1, mir-83, and mir-235) and a miRNA cluster (mir-4807-4810.1) that are required for optimal sperm production at 20°C and 5 additional miRNAs (mir-49, mir-57, mir-261, and mir-357/358) that are required for sperm production at 25°C. We observed defects in meiotic progression in mir-58.1, mir-83, mir-235, and mir-4807-4810.1 mutants that may contribute to the reduced number of sperm. Further, analysis of multiple mutants of these miRNAs suggested complex genetic interactions between these miRNAs for sperm production. This study provides insights on the regulatory roles of miRNAs that promote optimal sperm production and fecundity in males and hermaphrodites.
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Affiliation(s)
- Lu Lu
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201 USA
| | - Allison L. Abbott
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201 USA
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9
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Fox BW, Helf MJ, Burkhardt RN, Artyukhin AB, Curtis BJ, Palomino DF, Chaturbedi A, Tauffenberger A, Wrobel CJ, Zhang YK, Lee SS, Schroeder FC. Evolutionarily related host and microbial pathways regulate fat desaturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555782. [PMID: 37693574 PMCID: PMC10491262 DOI: 10.1101/2023.08.31.555782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression1-4, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, whose activity mimics that of microbiota-dependent becyp#1, but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.
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Affiliation(s)
- Bennett W. Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Maximilian J. Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Russell N. Burkhardt
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Alexander B. Artyukhin
- Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, United States
| | - Brian J. Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Diana Fajardo Palomino
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Arnaud Tauffenberger
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Chester J.J. Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ying K. Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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10
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Scott A, Willis CR, Muratani M, Higashitani A, Etheridge T, Szewczyk NJ, Deane CS. Caenorhabditis elegans in microgravity: An omics perspective. iScience 2023; 26:107189. [PMID: 37456835 PMCID: PMC10344948 DOI: 10.1016/j.isci.2023.107189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
The application of omics to study Caenorhabditis elegans (C. elegans) in the context of spaceflight is increasing, illuminating the wide-ranging biological impacts of spaceflight on physiology. In this review, we highlight the application of omics, including transcriptomics, genomics, proteomics, multi-omics, and integrated omics in the study of spaceflown C. elegans, and discuss the impact, use, and future direction of this branch of research. We highlight the variety of molecular alterations that occur in response to spaceflight, most notably changes in metabolic and neuromuscular gene regulation. These transcriptional features are reproducible and evident across many spaceflown species (e.g., mice and astronauts), supporting the use of C. elegans as a model organism to study spaceflight physiology with translational capital. Integrating tissue-specific, spatial, and multi-omics approaches, which quantitatively link molecular responses to phenotypic adaptations, will facilitate the identification of candidate regulatory molecules for therapeutic intervention and thus represents the next frontiers in C. elegans space omics research.
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Affiliation(s)
- Amanda Scott
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Craig R.G. Willis
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
| | - Masafumi Muratani
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | | | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Nathaniel J. Szewczyk
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
- Ohio Musculoskeletal and Neurological Institute, Ohio University, Athens, OH, USA
| | - Colleen S. Deane
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
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11
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Angeles-Albores D, Aprison EZ, Dzitoyeva S, Ruvinsky I. A Caenorhabditis elegans Male Pheromone Feminizes Germline Gene Expression in Hermaphrodites and Imposes Life-History Costs. Mol Biol Evol 2023; 40:msad119. [PMID: 37210586 PMCID: PMC10244002 DOI: 10.1093/molbev/msad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/14/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Sex pheromones not only improve the reproductive success of the recipients, but also impose costs, such as a reduced life span. The underlying mechanisms largely remain to be elucidated. Here, we show that even a brief exposure to physiological amounts of the dominant Caenorhabditis elegans male pheromone, ascr#10, alters the expression of thousands of genes in hermaphrodites. The most dramatic effect on the transcriptome is the upregulation of genes expressed during oogenesis and the downregulation of genes associated with male gametogenesis. This result reveals a way in which social signals help to resolve the inherent conflict between spermatogenesis and oogenesis in a simultaneous hermaphrodite, presumably to optimally align reproductive function with the presence of potential mating partners. We also found that exposure to ascr#10 increased the risk of persistent intestinal infections in hermaphrodites due to pathological pharyngeal hypertrophy. Thus, our study reveals ways in which the male pheromone can not only have beneficial effects on the recipients' reproduction, but also cause harmful consequences that reduce life span.
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Affiliation(s)
| | - Erin Z Aprison
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Svetlana Dzitoyeva
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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12
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Angeles-Albores D, Aprison EZ, Dzitoyeva S, Ruvinsky I. A C. elegans male pheromone feminizes germline gene expression in hermaphrodites and imposes life-history costs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528976. [PMID: 36824927 PMCID: PMC9949107 DOI: 10.1101/2023.02.17.528976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Sex pheromones improve reproductive success, but also impose costs. Here we show that even brief exposure to physiological amounts of the dominant C. elegans male pheromone, ascr#10, alters the expression of thousands of genes in hermaphrodites. The most dramatic effect on the transcriptome was the upregulation of genes expressed during oogenesis and downregulation of genes associated with male gametogenesis. Among the detrimental effects of ascr#10 on hermaphrodites is the increased risk of persistent infections caused by pathological pharyngeal hypertrophy. Our results reveal a way in which social signals help to resolve the inherent conflict between spermatogenesis and oogenesis in a simultaneous hermaphrodite, presumably to optimally align reproductive function to the presence of potential mating partners. They also show that the beneficial effects of the pheromone are accompanied by harmful consequences that reduce lifespan.
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Affiliation(s)
- David Angeles-Albores
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Current address: Altos Labs, Bay Area Institute of Science, Redwood Shores, CA 94065, USA
| | - Erin Z. Aprison
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Svetlana Dzitoyeva
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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Crittenden SL, Seidel HS, Kimble J. Analysis of the C. elegans Germline Stem Cell Pool. Methods Mol Biol 2023; 2677:1-36. [PMID: 37464233 DOI: 10.1007/978-1-0716-3259-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The Caenorhabditis elegans germline is an excellent model for studying the genetic and molecular regulation of stem cell self-renewal and progression of cells from a stem cell state to a differentiated state. The germline tissue is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated gametes at the other. A simple mesenchymal niche caps the GSC pool and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Notch signaling activates transcription of the key GSC regulators lst-1 and sygl-1 proteins in a gradient through the GSC pool. LST-1 and SYGL-1 proteins work with PUF RNA regulators in a self-renewal hub to maintain the GSC pool. In this chapter, we present methods for characterizing the C. elegans GSC pool and early stages of germ cell differentiation. The methods include examination of germlines in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutant phenotypes that affect the stem cell vs. differentiation decision from those that affect germ cell processes more generally.
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Affiliation(s)
- Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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14
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Erven I, Abraham E, Hermanns T, Baumann U, Hofmann K. A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins. Nat Commun 2022; 13:7643. [PMID: 36496440 PMCID: PMC9741609 DOI: 10.1038/s41467-022-35244-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Distinct families of eukaryotic deubiquitinases (DUBs) are regulators of ubiquitin signaling. Here, we report on the presence of an additional DUB class broadly distributed in eukaryotes and several bacteria. The only described members of this family are the large tegument proteins of herpesviruses, which are attached to the outside of the viral capsid. By using a bioinformatics screen, we have identified distant homologs of this VTD (Viral tegument-like DUB) family in vertebrate transposons, fungi, insects, nematodes, cnidaria, protists and bacteria. While some VTD activities resemble viral tegument DUBs in that they favor K48-linked ubiquitin chains, other members are highly specific for K6- or K63-linked ubiquitin chains. The crystal structures of K48- and K6-specific members reveal considerable differences in ubiquitin recognition. The VTD family likely evolved from non-DUB proteases and spread through transposons, many of which became 'domesticated', giving rise to the Drosophila male sterile (3)76Ca gene and several nematode genes with male-specific expression.
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Affiliation(s)
- Ilka Erven
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Elena Abraham
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, D-50674 Cologne, Germany
| | - Thomas Hermanns
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Ulrich Baumann
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, D-50674 Cologne, Germany
| | - Kay Hofmann
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
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15
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Niu B, Nguyen Bach T, Chen X, Raghunath Chandratre K, Isaac Murray J, Zhao Z, Zhang M. Computational modeling and analysis of the morphogenetic domain signaling networks regulating C. elegans embryogenesis. Comput Struct Biotechnol J 2022; 20:3653-3666. [PMID: 35891777 PMCID: PMC9289785 DOI: 10.1016/j.csbj.2022.05.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/03/2022] Open
Abstract
Caenorhabditis elegans, often referred to as the ‘roundworm’, provides a powerful model for studying cell autonomous and cell–cell interactions through the direct observation of embryonic development in vivo. By leveraging the precisely mapped cell lineage at single cell resolution, we are able to study at a systems level how early embryonic cells communicate across morphogenetic domains for the coordinated processes of gene expressions and collective cellular behaviors that regulate tissue morphogenesis. In this study, we developed a computational framework for the exploration of the morphogenetic domain cell signaling networks that may regulate C. elegans gastrulation and embryonic organogenesis. We demonstrated its utility by producing the following results, i) established a virtual reference model of developing C. elegans embryos through the spatiotemporal alignment of individual embryo cell nuclear imaging samples; ii) integrated the single cell spatiotemporal gene expression profile with the established virtual embryo model by data pooling; iii) trained a Machine Learning model (Random Forest Regression), which predicts accurately the spatial positions of the cells given their gene expression profiles for a given developmental time (e.g. total cell number of the embryo); iv) enabled virtual 4-dimensional tomographic graphical modeling of single cell data; v) inferred the biology signaling pathways that act in each of morphogenetic domains by meta-data analysis. It is intriguing that the morphogenetic domain cell signaling network seems to involve some crosstalk of multiple biology signaling pathways during the formation of tissue boundary pattern. Lastly, we developed the Software tool ‘Embryo aligner version 1.0’ and provided it as an Open Source program to the research community for virtual embryo modeling, and phenotype perturbation analyses (https://github.com/csniuben/embryo_aligner/wiki and https://bioinfo89.github.io/C.elegansEmbryonicOrganogenesisweb/).
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Nikonorova IA, Wang J, Cope AL, Tilton PE, Power KM, Walsh JD, Akella JS, Krauchunas AR, Shah P, Barr MM. Isolation, profiling, and tracking of extracellular vesicle cargo in Caenorhabditis elegans. Curr Biol 2022; 32:1924-1936.e6. [PMID: 35334227 PMCID: PMC9491618 DOI: 10.1016/j.cub.2022.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 01/04/2023]
Abstract
Extracellular vesicles (EVs) may mediate intercellular communication by carrying protein and RNA cargo. The composition, biology, and roles of EVs in physiology and pathology have been primarily studied in the context of biofluids and in cultured mammalian cells. The experimental tractability of C. elegans makes for a powerful in vivo animal system to identify and study EV cargo from its cellular source. We developed an innovative method to label, track, and profile EVs using genetically encoded, fluorescent-tagged EV cargo and conducted a large-scale isolation and proteomic profiling. Nucleic acid binding proteins (∼200) are overrepresented in our dataset. By integrating our EV proteomic dataset with single-cell transcriptomic data, we identified and validated ciliary EV cargo: CD9-like tetraspanin (TSP-6), ectonucleotide pyrophosphatase/phosphodiesterase (ENPP-1), minichromosome maintenance protein (MCM-3), and double-stranded RNA transporter SID-2. C. elegans EVs also harbor RNA, suggesting that EVs may play a role in extracellular RNA-based communication.
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Affiliation(s)
- Inna A Nikonorova
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA.
| | - Juan Wang
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Alexander L Cope
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Peter E Tilton
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Kaiden M Power
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Jonathon D Walsh
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Jyothi S Akella
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Amber R Krauchunas
- University of Delaware, Department of Biological Sciences, 105 The Green, Newark, DE 19716, USA
| | - Premal Shah
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Maureen M Barr
- Rutgers, The State University of New Jersey, Department of Genetics and Human Genetics Institute of New Jersey Piscataway, 145 Bevier Road, Piscataway, NJ 08854, USA.
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Airs PM, Vaccaro K, Gallo KJ, Dinguirard N, Heimark ZW, Wheeler NJ, He J, Weiss KR, Schroeder NE, Huisken J, Zamanian M. Spatial transcriptomics reveals antiparasitic targets associated with essential behaviors in the human parasite Brugia malayi. PLoS Pathog 2022; 18:e1010399. [PMID: 35390105 PMCID: PMC9017939 DOI: 10.1371/journal.ppat.1010399] [Citation(s) in RCA: 7] [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: 10/14/2021] [Revised: 04/19/2022] [Accepted: 02/25/2022] [Indexed: 01/24/2023] Open
Abstract
Lymphatic filariasis (LF) is a chronic debilitating neglected tropical disease (NTD) caused by mosquito-transmitted nematodes that afflicts over 60 million people. Control of LF relies on routine mass drug administration with antiparasitics that clear circulating larval parasites but are ineffective against adults. The development of effective adulticides is hampered by a poor understanding of the processes and tissues driving parasite survival in the host. The adult filariae head region contains essential tissues that control parasite feeding, sensory, secretory, and reproductive behaviors, which express promising molecular substrates for the development of antifilarial drugs, vaccines, and diagnostics. We have adapted spatial transcriptomic approaches to map gene expression patterns across these prioritized but historically intractable head tissues. Spatial and tissue-resolved data reveal distinct biases in the origins of known drug targets and secreted antigens. These data were used to identify potential new drug and vaccine targets, including putative hidden antigens expressed in the alimentary canal, and to spatially associate receptor subunits belonging to druggable families. Spatial transcriptomic approaches provide a powerful resource to aid gene function inference and seed antiparasitic discovery pipelines across helminths of relevance to human and animal health.
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Affiliation(s)
- Paul M. Airs
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kathy Vaccaro
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kendra J. Gallo
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nathalie Dinguirard
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zachary W. Heimark
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicolas J. Wheeler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jiaye He
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Kurt R. Weiss
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Nathan E. Schroeder
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jan Huisken
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Integrative Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Mustapha UF, Assan D, Huang YQ, Li GL, Jiang DN. High Polymorphism in the Dmrt2a Gene Is Incompletely Sex-Linked in Spotted Scat, Scatophagus argus. Animals (Basel) 2022; 12:ani12050613. [PMID: 35268179 PMCID: PMC8909180 DOI: 10.3390/ani12050613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 12/10/2022] Open
Abstract
Unlike mammals and birds, many fishes have young sex chromosomes, providing excellent models to study sex chromosome differentiation at early stages. Previous studies showed that spotted scat possesses an XX-XY sex determination system. The X has a complete Dmrt3 copy (termed normal) and a truncated copy of Dmrt1 (called Dmrt1b), while the Y has the opposite (normal Dmrt1, which is male-specific, and a truncated Dmrt3 called Dmrt3△-Y). Dmrt1 is the candidate sex determination gene, while the differentiation of other sex-linked genes remains unknown. The spotted scat has proven to be a good model to study the evolution of sex chromosomes in vertebrates. Herein, we sequenced a neighbor gene of this family, Dmrt2, positioned farther from Dmrt1 and closer to Dmrt3 in the spotted scat, and analyzed its sequence variation and expression profiles. The physical locations of the three genes span across an estimated size of >40 kb. The open reading frames of Dmrt2a and its paralog Dmrt2b are 1578 bp and 1311 bp, encoding peptides of 525 and 436 amino acid residues, respectively. Dmrt2a is positioned close to Dmrt3 but farther from Dmrt1 on the same chromosome, while Dmrt2b is not. Sequence analysis revealed several mutations; insertions, and deletions (indels) on Dmrt2a non-coding regions and single-nucleotide polymorphisms (SNPs) on the Dmrt2a transcript. These indels and SNPs are sex-linked and showed high male heterogeneity but do not affect gene translation. The markers designed to span the mutation sites tested on four different populations showed varied concordance with the genetic sexes. Dmrt2a is transcribed solely in the gonads and gills, while Dmrt2b exists in the gonads, hypothalamus, gills, heart, and spleen. The Dmrt2a and Dmrt2b transcripts are profoundly expressed in the male gonads. Analyses of the transcriptome data from five other fish species (Hainan medaka (Oryzias curvinotus), silver sillago (Sillago sihama), Nile tilapia (Oreochromis niloticus), Hong Kong catfish (Clarias fuscus), and spot-fin porcupine fish (Diodon hystrix)) revealed testes-biased expression of Dmrt1 in all, similar to spotted scat. Additionally, the expression of Dmrt2a is higher in the testes than the ovaries in spotted scat and Hainan medaka. The Dmrt2a transcript was not altered in the coding regions as found in Dmrt1 and Dmrt3 in spotted scat. This could be due to the functional importance of Dmrt2a in development. Another possibility is that because Dmrt2a is positioned farther from Dmrt1 and the chromosome is still young, meaning it is only a matter of time before it differentiates. This study undeniably will aid in understanding the functional divergence of the sex-linked genes in fish.
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van Sluijs L, Bosman KJ, Pankok F, Blokhina T, Wilten JIHA, te Molder DM, Riksen JAG, Snoek BL, Pijlman GP, Kammenga JE, Sterken MG. Balancing Selection of the Intracellular Pathogen Response in Natural Caenorhabditis elegans Populations. Front Cell Infect Microbiol 2022; 11:758331. [PMID: 35174100 PMCID: PMC8841876 DOI: 10.3389/fcimb.2021.758331] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.
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Affiliation(s)
- Lisa van Sluijs
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Kobus J. Bosman
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Frederik Pankok
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Tatiana Blokhina
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Jop I. H. A. Wilten
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Dennie M. te Molder
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Mark G. Sterken
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mark G. Sterken,
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20
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Cornes E, Bourdon L, Singh M, Mueller F, Quarato P, Wernersson E, Bienko M, Li B, Cecere G. piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development. Dev Cell 2022; 57:180-196.e7. [PMID: 34921763 PMCID: PMC8796119 DOI: 10.1016/j.devcel.2021.11.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/02/2021] [Accepted: 11/26/2021] [Indexed: 12/22/2022]
Abstract
Eukaryotic genomes harbor invading transposable elements that are silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatogenic genes during spermatogenesis, promoting sperm differentiation and function. This silencing signal requires piRNA-dependent small RNA biogenesis and loading into downstream nuclear effectors, which correlates with the dynamic reorganization of two distinct perinuclear biomolecular condensates present in germ cells. In addition, the silencing capacity of piRNAs is temporally counteracted by the Argonaute CSR-1, which targets and licenses spermatogenic gene transcription. The spatial and temporal overlap between these opposing small RNA pathways contributes to setting up the timing of the spermatogenic differentiation program. Thus, our work identifies a prominent role for piRNAs as direct regulators of endogenous transcriptional programs during germline development and gamete differentiation.
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Affiliation(s)
- Eric Cornes
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris 75015, France
| | - Loan Bourdon
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris 75015, France
| | - Meetali Singh
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris 75015, France
| | - Florian Mueller
- Imaging and Modeling Unit, Institut Pasteur, UMR 3691 CNRS, C3BI USR 3756 IP CNRS, Paris, France
| | - Piergiuseppe Quarato
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris 75015, France
| | - Erik Wernersson
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17165, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, Stockholm 17165, Sweden
| | - Magda Bienko
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17165, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, Stockholm 17165, Sweden
| | - Blaise Li
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris 75015, France; Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756, CNRS, Paris 75015, France
| | - Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris 75015, France.
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21
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Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo AF, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett SW, Kienberger H, Kleigrewe K, de Bono M, Wakelam MJO, Casanueva O. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biol 2021; 19:e3001431. [PMID: 34723964 PMCID: PMC8585009 DOI: 10.1371/journal.pbio.3001431] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 11/11/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane's phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal.
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Affiliation(s)
- Laetitia Chauve
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Francesca Hodge
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Sharlene Murdoch
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | | | | | | | | | - Greg West
- Babraham Institute, Cambridge, United Kingdom
| | | | | | - Cheryl Li
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | | | | | - Karin Kleigrewe
- Bavarian Centre for Biomolecular Mass Spectrometry, Freising, Germany
| | - Mario de Bono
- Institute of Science and Technology, Klosterneuburg, Austria
| | | | - Olivia Casanueva
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
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22
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Rappaport Y, Achache H, Falk R, Murik O, Ram O, Tzur YB. Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans. Nat Commun 2021; 12:4802. [PMID: 34376665 PMCID: PMC8355143 DOI: 10.1038/s41467-021-24815-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.
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Affiliation(s)
- Yisrael Rappaport
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanna Achache
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roni Falk
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omer Murik
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Oren Ram
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonatan B Tzur
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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23
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Schede HH, Schneider CG, Stergiadou J, Borm LE, Ranjak A, Yamawaki TM, David FPA, Lönnerberg P, Tosches MA, Codeluppi S, La Manno G. Spatial tissue profiling by imaging-free molecular tomography. Nat Biotechnol 2021; 39:968-977. [PMID: 33875865 DOI: 10.1038/s41587-021-00879-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 03/05/2021] [Indexed: 02/02/2023]
Abstract
Several techniques are currently being developed for spatially resolved omics profiling, but each new method requires the setup of specific detection strategies or specialized instrumentation. Here we describe an imaging-free framework to localize high-throughput readouts within a tissue by cutting the sample into thin strips in a way that allows subsequent image reconstruction. We implemented this framework to transform a low-input RNA sequencing protocol into an imaging-free spatial transcriptomics technique (called STRP-seq) and validated it by profiling the spatial transcriptome of the mouse brain. We applied the technique to the brain of the Australian bearded dragon, Pogona vitticeps. Our results reveal the molecular anatomy of the telencephalon of this lizard, providing evidence for a marked regionalization of the reptilian pallium and subpallium. We expect that STRP-seq can be used to derive spatially resolved data from a range of other omics techniques.
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Affiliation(s)
- Halima Hannah Schede
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christian G Schneider
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Charité-Universitätsmedizin Berlin, corporate member of the Freie Universität Berlin and Humboldt-Universität zu Berlin: NeuroCure Clinical Research Center, Berlin, Germany
| | - Johanna Stergiadou
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,10x Genomics, Stockholm, Sweden
| | - Lars E Borm
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Anurag Ranjak
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tracy M Yamawaki
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Amgen, Inc., South San Francisco, CA, USA
| | - Fabrice P A David
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,BioInformatics Competence Center, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Peter Lönnerberg
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Maria Antonietta Tosches
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Simone Codeluppi
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Gioele La Manno
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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24
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Schild ES, Mars J, Ebbing A, Vivié J, Betist M, Korswagen HC. Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography. STAR Protoc 2021; 2:100411. [PMID: 33870220 PMCID: PMC8044689 DOI: 10.1016/j.xpro.2021.100411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RNA tomography or tomo-seq combines mRNA sequencing and cryo-sectioning to spatially resolve gene expression. We have adapted this method for the nematode Caenorhabditis elegans to generate anteroposterior gene expression maps at near-cellular resolution. Here, we provide a detailed overview of the method and present two approaches: one that includes RNA isolation for maximum sensitivity and one that is suitable for partial automatization and is therefore less time-consuming. For complete details on the use and execution of this protocol, please refer to Ebbing et al. (2018).
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Affiliation(s)
- Erik S Schild
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jonas Mars
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Annabel Ebbing
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Judith Vivié
- Single Cell Discoveries B.V., Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Marco Betist
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.,Institute of Biodynamics and Biocomplexity, Developmental Biology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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25
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Kasimatis KR, Sánchez-Ramírez S, Stevenson ZC. Sexual Dimorphism through the Lens of Genome Manipulation, Forward Genetics, and Spatiotemporal Sequencing. Genome Biol Evol 2021; 13:evaa243. [PMID: 33587127 PMCID: PMC7883666 DOI: 10.1093/gbe/evaa243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2020] [Indexed: 11/14/2022] Open
Abstract
Sexual reproduction often leads to selection that favors the evolution of sex-limited traits or sex-specific variation for shared traits. These sexual dimorphisms manifest due to sex-specific genetic architectures and sex-biased gene expression across development, yet the molecular mechanisms underlying these patterns are largely unknown. The first step is to understand how sexual dimorphisms arise across the genotype-phenotype-fitness map. The emergence of "4D genome technologies" allows for efficient, high-throughput, and cost-effective manipulation and observations of this process. Studies of sexual dimorphism will benefit from combining these technological advances (e.g., precision genome editing, inducible transgenic systems, and single-cell RNA sequencing) with clever experiments inspired by classic designs (e.g., bulked segregant analysis, experimental evolution, and pedigree tracing). This perspective poses a synthetic view of how manipulative approaches coupled with cutting-edge observational methods and evolutionary theory are poised to uncover the molecular genetic basis of sexual dimorphism with unprecedented resolution. We outline hypothesis-driven experimental paradigms for identifying genetic mechanisms of sexual dimorphism among tissues, across development, and over evolutionary time.
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Affiliation(s)
- Katja R Kasimatis
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, USA
| | | | - Zachary C Stevenson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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26
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Rödelsperger C, Ebbing A, Sharma DR, Okumura M, Sommer RJ, Korswagen HC. Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution. Mol Biol Evol 2021; 38:229-243. [PMID: 32785688 PMCID: PMC8480184 DOI: 10.1093/molbev/msaa207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Divergence of gene function and expression during development can give rise to phenotypic differences at the level of cells, tissues, organs, and ultimately whole organisms. To gain insights into the evolution of gene expression and novel genes at spatial resolution, we compared the spatially resolved transcriptomes of two distantly related nematodes, Caenorhabditis elegans and Pristionchus pacificus, that diverged 60-90 Ma. The spatial transcriptomes of adult worms show little evidence for strong conservation at the level of single genes. Instead, regional expression is largely driven by recent duplication and emergence of novel genes. Estimation of gene ages across anatomical structures revealed an enrichment of novel genes in sperm-related regions. This provides first evidence in nematodes for the "out of testis" hypothesis that has been previously postulated based on studies in Drosophila and mammals. "Out of testis" genes represent a mix of products of pervasive transcription as well as fast evolving members of ancient gene families. Strikingly, numerous novel genes have known functions during meiosis in Caenorhabditis elegans indicating that even universal processes such as meiosis may be targets of rapid evolution. Our study highlights the importance of novel genes in generating phenotypic diversity and explicitly characterizes gene origination in sperm-related regions. Furthermore, it proposes new functions for previously uncharacterized genes and establishes the spatial transcriptome of Pristionchus pacificus as a catalog for future studies on the evolution of gene expression and function.
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Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Annabel Ebbing
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht,
The Netherlands
| | - Devansh Raj Sharma
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht,
The Netherlands
- Developmental Biology, Department of Biology, Institute of Biodynamics and Biocomplexity, Utrecht University, Utrecht,
The Netherlands
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27
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Ragle JM, Aita AL, Morrison KN, Martinez-Mendez R, Saeger HN, Ashley GA, Johnson LC, Schubert KA, Shakes DC, Ward JD. The conserved molting/circadian rhythm regulator NHR-23/NR1F1 serves as an essential co-regulator of C. elegans spermatogenesis. Development 2020; 147:dev193862. [PMID: 33060131 PMCID: PMC7710015 DOI: 10.1242/dev.193862] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/12/2020] [Indexed: 12/21/2022]
Abstract
In sexually reproducing metazoans, spermatogenesis is the process by which uncommitted germ cells give rise to haploid sperm. Work in model systems has revealed mechanisms controlling commitment to the sperm fate, but how this fate is subsequently executed remains less clear. While studying the well-established role of the conserved nuclear hormone receptor transcription factor, NHR-23/NR1F1, in regulating C. elegans molting, we discovered that NHR-23/NR1F1 is also constitutively expressed in developing primary spermatocytes and is a critical regulator of spermatogenesis. In this novel role, NHR-23/NR1F1 functions downstream of the canonical sex-determination pathway. Degron-mediated depletion of NHR-23/NR1F1 within hermaphrodite or male germlines causes sterility due to an absence of functional sperm, as depleted animals produce arrested primary spermatocytes rather than haploid sperm. These spermatocytes arrest in prometaphase I and fail to either progress to anaphase or attempt spermatid-residual body partitioning. They make sperm-specific membranous organelles but fail to assemble their major sperm protein into fibrous bodies. NHR-23/NR1F1 appears to function independently of the known SPE-44 gene regulatory network, revealing the existence of an NHR-23/NR1F1-mediated module that regulates the spermatogenesis program.
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Affiliation(s)
- James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Abigail L Aita
- Department of Biology, William & Mary, Williamsburg, VA 23187, USA
| | | | - Raquel Martinez-Mendez
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hannah N Saeger
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guinevere A Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Londen C Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katherine A Schubert
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Diane C Shakes
- Department of Biology, William & Mary, Williamsburg, VA 23187, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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28
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Mei X, Singson AW. The molecular underpinnings of fertility: Genetic approaches in Caenorhabditis elegans. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 2:e10034. [PMID: 34322672 PMCID: PMC8315475 DOI: 10.1002/ggn2.10034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The study of mutations that impact fertility has a catch-22. Fertility mutants are often lost since they cannot simply be propagated and maintained. This has hindered progress in understanding the genetics of fertility. In mice, several molecules are found to be required for the interactions between the sperm and egg, with JUNO and IZUMO1 being the only known receptor pair on the egg and sperm surface, respectively. In Caenorhabditis elegans, a total of 12 proteins on the sperm or oocyte have been identified to mediate gamete interactions. Majority of these genes were identified through mutants isolated from genetic screens. In this review, we summarize the several key screening strategies that led to the identification of fertility mutants in C. elegans and provide a perspective about future research using genetic approaches. Recently, advancements in new technologies such as high-throughput sequencing and Crispr-based genome editing tools have accelerated the molecular, cell biological, and mechanistic analysis of fertility genes. We review how these valuable tools advance our understanding of the molecular underpinnings of fertilization. We draw parallels of the molecular mechanisms of fertilization between worms and mammals and argue that our work in C. elegans complements fertility research in humans and other species.
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Affiliation(s)
- Xue Mei
- Department of GeneticsWaksman Institute, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Andrew W. Singson
- Department of GeneticsWaksman Institute, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
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29
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Roles for the RNA polymerase III regulator MAFR-1 in regulating sperm quality in Caenorhabditis elegans. Sci Rep 2020; 10:19367. [PMID: 33168938 PMCID: PMC7652826 DOI: 10.1038/s41598-020-76423-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/27/2020] [Indexed: 11/08/2022] Open
Abstract
The negative regulator of RNA polymerase (pol) III mafr-1 has been shown to affect RNA pol III transcript abundance, lipid biosynthesis and storage, progeny output, and lifespan. We deleted mafr-1 from the Caenorhabditis elegans genome and found that animals lacking mafr-1 replicated many phenotypes from previous RNAi-based studies and discovered a new sperm-specific role. Utilizing a yeast two-hybrid assay, we discovered several novel interactors of MAFR-1 that are expressed in a sperm- and germline-enriched manner. In support of a role for MAFR-1 in the male germline, we found mafr-1 null males have smaller spermatids that are less capable in competition for fertilization; a phenotype that was dependent on RNA pol III activity. Restoration of MAFR-1 expression specifically in the germline rescued the spermatid-related phenotypes, suggesting a cell autonomous role for MAFR-1 in nematode male fertility. Based on the high degree of conservation of Maf1 activity across species, our study may inform similar roles for Maf1 and RNA pol III in mammalian male fertility.
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30
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Abstract
New species arise as the genomes of populations diverge. The developmental 'alarm clock' of speciation sounds off when sufficient divergence in genetic control of development leads hybrid individuals to infertility or inviability, the world awoken to the dawn of new species with intrinsic post-zygotic reproductive isolation. Some developmental stages will be more prone to hybrid dysfunction due to how molecular evolution interacts with the ontogenetic timing of gene expression. Considering the ontogeny of hybrid incompatibilities provides a profitable connection between 'evo-devo' and speciation genetics to better link macroevolutionary pattern, microevolutionary process, and molecular mechanisms. Here, we explore speciation alongside development, emphasizing their mutual dependence on genetic network features, fitness landscapes, and developmental system drift. We assess models for how ontogenetic timing of reproductive isolation can be predictable. Experiments and theory within this synthetic perspective can help identify new rules of speciation as well as rules in the molecular evolution of development.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of TorontoTorontoCanada
| | - Joanna D Bundus
- Department of Integrative Biology, University of Wisconsin – MadisonMadisonUnited States
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31
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Systematic analysis of long intergenic non-coding RNAs in C. elegans germline uncovers roles in somatic growth. RNA Biol 2020; 18:435-445. [PMID: 32892705 DOI: 10.1080/15476286.2020.1814549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides that are transcribed from non-coding loci yet undergo biosynthesis similar to coding mRNAs. The disproportional number of lincRNAs expressed in testes suggests that lincRNAs are important during gametogenesis, but experimental evidence has implicated very few lincRNAs in this process. We took advantage of the relatively limited number of lincRNAs in the genome of the nematode Caenorhabditis elegans to systematically analyse the functions of lincRNAs during meiosis. We deleted six lincRNA genes that are highly and dynamically expressed in the C. elegans gonad and tested the effects on central meiotic processes. Surprisingly, whereas the lincRNA deletions did not strongly impact fertility, germline apoptosis, crossovers, or synapsis, linc-4 was required for somatic growth. Slower growth was observed in linc-4-deletion mutants and in worms depleted of linc-4 using RNAi, indicating that linc-4 transcripts are required for this post-embryonic process. Unexpectedly, analysis of worms depleted of linc-4 in soma versus germline showed that the somatic role stems from linc-4 expression in germline cells. This unique feature suggests that some lincRNAs, like some small non-coding RNAs, are required for germ-soma interactions.
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32
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Fan Z, Chen R, Chen X. SpatialDB: a database for spatially resolved transcriptomes. Nucleic Acids Res 2020; 48:D233-D237. [PMID: 31713629 PMCID: PMC7145543 DOI: 10.1093/nar/gkz934] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
Spatially resolved transcriptomic techniques allow the characterization of spatial organization of cells in tissues, which revolutionize the studies of tissue function and disease pathology. New strategies for detecting spatial gene expression patterns are emerging, and spatially resolved transcriptomic data are accumulating rapidly. However, it is not convenient for biologists to exploit these data due to the diversity of strategies and complexity in data analysis. Here, we present SpatialDB, the first manually curated database for spatially resolved transcriptomic techniques and datasets. The current version of SpatialDB contains 24 datasets (305 sub-datasets) from 5 species generated by 8 spatially resolved transcriptomic techniques. SpatialDB provides a user-friendly web interface for visualization and comparison of spatially resolved transcriptomic data. To further explore these data, SpatialDB also provides spatially variable genes and their functional enrichment annotation. SpatialDB offers a repository for research community to investigate the spatial cellular structure of tissues, and may bring new insights into understanding the cellular microenvironment in disease. SpatialDB is freely available at https://www.spatialomics.org/SpatialDB.
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Affiliation(s)
- Zhen Fan
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Runsheng Chen
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Chen
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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33
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Serrano-Saiz E, Vogt MC, Levy S, Wang Y, Kaczmarczyk KK, Mei X, Bai G, Singson A, Grant BD, Hobert O. SLC17A6/7/8 Vesicular Glutamate Transporter Homologs in Nematodes. Genetics 2020; 214:163-178. [PMID: 31776169 PMCID: PMC6944403 DOI: 10.1534/genetics.119.302855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/24/2019] [Indexed: 01/04/2023] Open
Abstract
Members of the superfamily of solute carrier (SLC) transmembrane proteins transport diverse substrates across distinct cellular membranes. Three SLC protein families transport distinct neurotransmitters into synaptic vesicles to enable synaptic transmission in the nervous system. Among them is the SLC17A6/7/8 family of vesicular glutamate transporters, which endows specific neuronal cell types with the ability to use glutamate as a neurotransmitter. The genome of the nematode Caenorhabditis elegans encodes three SLC17A6/7/8 family members, one of which, eat-4/VGLUT, has been shown to be involved in glutamatergic neurotransmission. Here, we describe our analysis of the two remaining, previously uncharacterized SLC17A6/7/8 family members, vglu-2 and vglu-3 These two genes directly neighbor one another and are the result of a recent gene duplication event in C. elegans, but not in other Caenorhabditis species. Compared to EAT-4, the VGLU-2 and VGLU-3 protein sequences display a more distant similarity to canonical, vertebrate VGLUT proteins. We tagged both genomic loci with gfp and detected no expression of vglu-3 at any stage of development in any cell type of both C. elegans sexes. In contrast, vglu-2::gfp is dynamically expressed in a restricted set of distinct cell types. Within the nervous system, vglu-2::gfp is exclusively expressed in a single interneuron class, AIA, where it localizes to vesicular structures in the soma, but not along the axon, suggesting that VGLU-2 may not be involved in synaptic transport of glutamate. Nevertheless, vglu-2 mutants are partly defective in the function of the AIA neuron in olfactory behavior. Outside the nervous system, VGLU-2 is expressed in collagen secreting skin cells where VGLU-2 most prominently localizes to early endosomes, and to a lesser degree to apical clathrin-coated pits, the trans-Golgi network, and late endosomes. On early endosomes, VGLU-2 colocalizes most strongly with the recycling promoting factor SNX-1, a retromer component. Loss of vglu-2 affects the permeability of the collagen-containing cuticle of the worm, and based on the function of a vertebrate VGLUT1 protein in osteoclasts, we speculate that vglu-2 may have a role in collagen trafficking in the skin. We conclude that C. elegans SLC17A6/7/8 family members have diverse functions within and outside the nervous system.
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Affiliation(s)
- Esther Serrano-Saiz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
- Centro de Biologia Molecular Severo Ochoa/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
| | - Sagi Levy
- Rockefeller University, New York, New York 10065
| | - Yu Wang
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Karolina K Kaczmarczyk
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
| | - Xue Mei
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
| | - Ge Bai
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Andrew Singson
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
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34
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Nett EM, Sepulveda NB, Petrella LN. Defects in mating behavior and tail morphology are the primary cause of sterility in Caenorhabditis elegans males at high temperature. ACTA ACUST UNITED AC 2019; 222:jeb.208041. [PMID: 31672732 DOI: 10.1242/jeb.208041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022]
Abstract
Reproduction is a fundamental imperative of all forms of life. For all the advantages sexual reproduction confers, it has a deeply conserved flaw: it is temperature sensitive. As temperatures rise, fertility decreases. Across species, male fertility is particularly sensitive to elevated temperature. Previously, we have shown in the model nematode Caenorhabditis elegans that all males are fertile at 20°C, but almost all males have lost fertility at 27°C. Male fertility is dependent on the production of functional sperm, successful mating and transfer of sperm, and successful fertilization post-mating. To determine how male fertility is impacted by elevated temperature, we analyzed these aspects of male reproduction at 27°C in three wild-type strains of C. elegans: JU1171, LKC34 and N2. We found no effect of elevated temperature on the number of immature non-motile spermatids formed. There was only a weak effect of elevated temperature on sperm activation. In stark contrast, there was a strong effect of elevated temperature on male mating behavior, male tail morphology and sperm transfer such that males very rarely completed mating successfully when exposed to 27°C. Therefore, we propose a model where elevated temperature reduces male fertility as a result of the negative impacts of temperature on the somatic tissues necessary for mating. Loss of successful mating at elevated temperature overrides any effects that temperature may have on the germline or sperm cells.
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Affiliation(s)
- Emily M Nett
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Nicholas B Sepulveda
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Lisa N Petrella
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
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Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science 2019; 365:eaax1971. [PMID: 31488706 PMCID: PMC7428862 DOI: 10.1126/science.aax1971] [Citation(s) in RCA: 254] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/21/2019] [Indexed: 12/18/2022]
Abstract
Caenorhabditis elegans is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in C. elegans' invariant lineage. Using these annotations, we find that (i) the correlation between a cell's lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adopt their terminal fates; (ii) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and (iii) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.
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Affiliation(s)
- Jonathan S Packer
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Qin Zhu
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Chau Huynh
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Priya Sivaramakrishnan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elicia Preston
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hannah Dueck
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Derek Stefanik
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kai Tan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert H Waterston
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - John I Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Cutter AD, Morran LT, Phillips PC. Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes. Genetics 2019; 213:27-57. [PMID: 31488593 PMCID: PMC6727802 DOI: 10.1534/genetics.119.300244] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022] Open
Abstract
Males of Caenorhabditis elegans provide a crucial practical tool in the laboratory, but, as the rarer and more finicky sex, have not enjoyed the same depth of research attention as hermaphrodites. Males, however, have attracted the attention of evolutionary biologists who are exploiting the C. elegans system to test longstanding hypotheses about sexual selection, sexual conflict, transitions in reproductive mode, and genome evolution, as well as to make new discoveries about Caenorhabditis organismal biology. Here, we review the evolutionary concepts and data informed by study of males of C. elegans and other Caenorhabditis We give special attention to the important role of sperm cells as a mediator of inter-male competition and male-female conflict that has led to drastic trait divergence across species, despite exceptional phenotypic conservation in many other morphological features. We discuss the evolutionary forces important in the origins of reproductive mode transitions from males being common (gonochorism: females and males) to rare (androdioecy: hermaphrodites and males) and the factors that modulate male frequency in extant androdioecious populations, including the potential influence of selective interference, host-pathogen coevolution, and mutation accumulation. Further, we summarize the consequences of males being common vs rare for adaptation and for trait divergence, trait degradation, and trait dimorphism between the sexes, as well as for molecular evolution of the genome, at both micro-evolutionary and macro-evolutionary timescales. We conclude that C. elegans male biology remains underexploited and that future studies leveraging its extensive experimental resources are poised to discover novel biology and to inform profound questions about animal function and evolution.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario M5S3B2, Canada
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, Georgia 30322, and
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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Shi C, Booth LN, Murphy CT. Insulin-like peptides and the mTOR-TFEB pathway protect Caenorhabditis elegans hermaphrodites from mating-induced death. eLife 2019; 8:46413. [PMID: 31282862 PMCID: PMC6697448 DOI: 10.7554/elife.46413] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/07/2019] [Indexed: 01/01/2023] Open
Abstract
Lifespan is shortened by mating, but these deleterious effects must be delayed long enough for successful reproduction. Susceptibility to brief mating-induced death is caused by the loss of protection upon self-sperm depletion. Self-sperm maintains the expression of a DAF-2 insulin-like antagonist, INS-37, which promotes the nuclear localization of intestinal HLH-30/TFEB, a key pro-longevity regulator. Mating induces the agonist INS-8, promoting HLH-30 nuclear exit and subsequent death. In opposition to the protective role of HLH-30 and DAF-16/FOXO, TOR/LET-363 and the IIS-regulated Zn-finger transcription factor PQM-1 promote seminal-fluid-induced killing. Self-sperm maintenance of nuclear HLH-30/TFEB allows hermaphrodites to resist mating-induced death until self-sperm are exhausted, increasing the chances that mothers will survive through reproduction. Mothers combat males' hijacking of their IIS pathway by expressing an insulin antagonist that keeps her healthy through the activity of pro-longevity factors, as long as she has her own sperm to utilize.
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Affiliation(s)
- Cheng Shi
- Department of Molecular Biology, Princeton University, Princeton, United States.,LSI Genomics, Princeton University, Princeton, United States
| | - Lauren N Booth
- Department of Genetics, Stanford University, Stanford, United States
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, United States.,LSI Genomics, Princeton University, Princeton, United States
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Breimann L, Preusser F, Preibisch S. Light-microscopy methods in C. elegans research. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2018.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Spatiotemporal m(i)RNA Architecture and 3' UTR Regulation in the C. elegans Germline. Dev Cell 2018; 47:785-800.e8. [PMID: 30416012 DOI: 10.1016/j.devcel.2018.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/31/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
In animal germlines, regulation of cell proliferation and differentiation is particularly important but poorly understood. Here, using a cryo-cut approach, we mapped RNA expression along the Caenorhabditis elegans germline and, using mutants, dissected gene regulatory mechanisms that control spatiotemporal expression. We detected, at near single-cell resolution, >10,000 mRNAs, >300 miRNAs, and numerous unannotated miRNAs. Most RNAs were organized in distinct spatial patterns. Germline-specific miRNAs and their targets were co-localized. Moreover, we observed differential 3' UTR isoform usage for hundreds of mRNAs. In tumorous gld-2 gld-1 mutants, gene expression was strongly perturbed. In particular, differential 3' UTR usage was significantly impaired. We propose that PIE-1, a transcriptional repressor, functions to maintain spatial gene expression. Our data also suggest that cpsf-4 and fipp-1 control differential 3' UTR usage for hundreds of genes. Finally, we constructed a "virtual gonad" enabling "virtual in situ hybridizations" and access to all data (https://shiny.mdc-berlin.de/spacegerm/).
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