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Huang X, Feng X, Yan YH, Xu D, Wang K, Zhu C, Dong MQ, Huang X, Guang S, Chen X. Compartmentalized localization of perinuclear proteins within germ granules in C. elegans. Dev Cell 2025; 60:1251-1270.e3. [PMID: 39742661 DOI: 10.1016/j.devcel.2024.12.016] [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: 03/25/2024] [Revised: 08/26/2024] [Accepted: 12/06/2024] [Indexed: 01/04/2025]
Abstract
Germ granules, or nuage, are RNA-rich condensates that are often docked on the cytoplasmic surface of germline nuclei. C. elegans perinuclear germ granules are composed of multiple subcompartments, including P granules, Mutator foci, Z granules, SIMR foci, P -bodies, and E granules. Although many perinuclear proteins have been identified, their precise localization within the subcompartments of the germ granule is still unclear. Here, we systematically labeled perinuclear proteins with fluorescent tags via CRISPR-Cas9 technology. Using this nematode strain library, we identified a series of proteins localized in Z or E granules and extended the characterization of the D granule. Finally, we found that the LOTUS domain protein MIP-1/EGGD-1 regulated the multiphase organization of the germ granule. Overall, our work identified the germ-granule architecture and redefined the compartmental localization of perinuclear proteins. Additionally, the library of genetically modified nematode strains will facilitate research on C. elegans germ granules.
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Affiliation(s)
- Xiaona Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China
| | - Xuezhu Feng
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Demin Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China
| | - Ke Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xinya Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China.
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China.
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China.
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2
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Thomas LL, Bodas DM, Seydoux G. FG repeats drive co-clustering of nuclear pores and P granules in the C. elegans germline. Development 2025; 152:dev204585. [PMID: 40067309 PMCID: PMC12050070 DOI: 10.1242/dev.204585] [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] [Received: 12/13/2024] [Accepted: 02/19/2025] [Indexed: 03/28/2025]
Abstract
Condensates that accumulate small RNA biogenesis factors (nuage) are common in germ cells and often associate with nuclei. In the Caenorhabditis elegans germline, P granules overlay large clusters of nuclear pores and this organization has been proposed to facilitate surveillance of nascent transcripts by Argonaute proteins enriched in P granules. We report that co-clustering of nuclear pores and P granules depends on FG repeat-containing nucleoporins and FG repeats in the Vasa class helicase GLH-1. Worms with mutations that prevent this co-clustering are fertile under standard growth conditions and exhibit misregulation of only a minority of genes, including replication-dependent histones. Our observations suggest that association with nuclear pores, although non-essential for genome surveillance, may serve to tune mRNA flow through P granules and other nuage condensates.
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Affiliation(s)
- Laura L. Thomas
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Devavrat M. Bodas
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Chen X, Wang K, Mufti FUD, Xu D, Zhu C, Huang X, Zeng C, Jin Q, Huang X, Yan YH, Dong MQ, Feng X, Shi Y, Kennedy S, Guang S. Germ granule compartments coordinate specialized small RNA production. Nat Commun 2024; 15:5799. [PMID: 38987544 PMCID: PMC11236994 DOI: 10.1038/s41467-024-50027-3] [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: 12/11/2023] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
Germ granules are biomolecular condensates present in most animal germ cells. One function of germ granules is to help maintain germ cell totipotency by organizing mRNA regulatory machinery, including small RNA-based gene regulatory pathways. The C. elegans germ granule is compartmentalized into multiple subcompartments whose biological functions are largely unknown. Here, we identify an uncharted subcompartment of the C. elegans germ granule, which we term the E granule. The E granule is nonrandomly positioned within the germ granule. We identify five proteins that localize to the E granule, including the RNA-dependent RNA polymerase (RdRP) EGO-1, the Dicer-related helicase DRH-3, the Tudor domain-containing protein EKL-1, and two intrinsically disordered proteins, EGC-1 and ELLI-1. Localization of EGO-1 to the E granule enables synthesis of a specialized class of 22G RNAs, which derive exclusively from 5' regions of a subset of germline-expressed mRNAs. Defects in E granule assembly elicit disordered production of endogenous siRNAs, which disturbs fertility and the RNAi response. Our results define a distinct subcompartment of the C. elegans germ granule and suggest that one function of germ granule compartmentalization is to facilitate the localized production of specialized classes of small regulatory RNAs.
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Affiliation(s)
- Xiangyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Ke Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Farees Ud Din Mufti
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Demin Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xinya Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Chenming Zeng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Qile Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiaona Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xuezhu Feng
- School of Basic Medicine, Anhui Medical University, Hefei, China.
| | - Yunyu Shi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China.
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA.
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, Anhui, 230027, China.
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4
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Uebel CJ, Rajeev S, Phillips CM. Caenorhabditis elegans germ granules are present in distinct configurations and assemble in a hierarchical manner. Development 2023; 150:dev202284. [PMID: 38009921 PMCID: PMC10753583 DOI: 10.1242/dev.202284] [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: 08/23/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
RNA silencing pathways are complex, highly conserved, and perform crucial regulatory roles. In Caenorhabditis elegans germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments - P granules, Z granules, SIMR foci, and Mutator foci - multiple of which form via phase separation. Although the functions of individual germ granule proteins have been extensively studied, the relationships between germ granule compartments (collectively, 'nuage') are less understood. We find that key germ granule proteins assemble into separate but adjacent condensates, and that boundaries between germ granule compartments re-establish after perturbation. We discover a toroidal P granule morphology, which encircles the other germ granule compartments in a consistent exterior-to-interior spatial organization, providing broad implications for the trajectory of an RNA as it exits the nucleus. Moreover, we quantify the stoichiometric relationships between germ granule compartments and RNA to reveal discrete populations of nuage that assemble in a hierarchical manner and differentially associate with RNAi-targeted transcripts, possibly suggesting functional differences between nuage configurations. Our work creates a more accurate model of C. elegans nuage and informs the conceptualization of RNA silencing through the germ granule compartments.
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Affiliation(s)
- Celja J. Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sanjana Rajeev
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M. Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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5
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Uebel CJ, Rajeev S, Phillips CM. Caenorhabditis elegans germ granules are present in distinct configurations that differentially associate with RNAi-targeted RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542330. [PMID: 37292702 PMCID: PMC10246010 DOI: 10.1101/2023.05.25.542330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA silencing pathways are complex, highly conserved, and perform widespread, critical regulatory roles. In C. elegans germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments-P granules, Z granules, SIMR foci, and Mutator foci-multiple of which form via phase separation and exhibit liquid-like properties. The functions of individual proteins within germ granules are well-studied, but the spatial organization, physical interaction, and coordination of biomolecule exchange between compartments within germ granule "nuage" is less understood. Here we find that key proteins are sufficient for compartment separation, and that the boundary between compartments can be reestablished after perturbation. Using super-resolution microscopy, we discover a toroidal P granule morphology which encircles the other germ granule compartments in a consistent exterior-to-interior spatial organization. Combined with findings that nuclear pores primarily interact with P granules, this nuage compartment organization has broad implications for the trajectory of an RNA as it exits the nucleus and enters small RNA pathway compartments. Furthermore, we quantify the stoichiometric relationships between germ granule compartments and RNA to reveal discrete populations of nuage that differentially associate with RNAi-targeted transcripts, possibly suggesting functional differences between nuage configurations. Together, our work creates a more spatially and compositionally accurate model of C. elegans nuage which informs the conceptualization of RNA silencing through different germ granule compartments.
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Affiliation(s)
- Celja J. Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
- Present address: Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford CA, 94305
| | - Sanjana Rajeev
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Carolyn M. Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
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6
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Cheng H, Shang D, Zhou R. Germline stem cells in human. Signal Transduct Target Ther 2022; 7:345. [PMID: 36184610 PMCID: PMC9527259 DOI: 10.1038/s41392-022-01197-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 12/02/2022] Open
Abstract
The germline cells are essential for the propagation of human beings, thus essential for the survival of mankind. The germline stem cells, as a unique cell type, generate various states of germ stem cells and then differentiate into specialized cells, spermatozoa and ova, for producing offspring, while self-renew to generate more stem cells. Abnormal development of germline stem cells often causes severe diseases in humans, including infertility and cancer. Primordial germ cells (PGCs) first emerge during early embryonic development, migrate into the gentile ridge, and then join in the formation of gonads. In males, they differentiate into spermatogonial stem cells, which give rise to spermatozoa via meiosis from the onset of puberty, while in females, the female germline stem cells (FGSCs) retain stemness in the ovary and initiate meiosis to generate oocytes. Primordial germ cell-like cells (PGCLCs) can be induced in vitro from embryonic stem cells or induced pluripotent stem cells. In this review, we focus on current advances in these embryonic and adult germline stem cells, and the induced PGCLCs in humans, provide an overview of molecular mechanisms underlying the development and differentiation of the germline stem cells and outline their physiological functions, pathological implications, and clinical applications.
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Affiliation(s)
- Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, 430072, Wuhan, China.
| | - Dantong Shang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, 430072, Wuhan, China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, 430072, Wuhan, China.
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7
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Somers HM, Fuqua JH, Bonnet FX, Rollins JA. Quantification of tissue-specific protein translation in whole C. elegans using O-propargyl-puromycin labeling and fluorescence microscopy. CELL REPORTS METHODS 2022; 2:100203. [PMID: 35497499 PMCID: PMC9046455 DOI: 10.1016/j.crmeth.2022.100203] [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] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 01/23/2023]
Abstract
The regulation of gene expression via protein translation is critical for growth, development, and stress response. While puromycin-based techniques have been used to quantify protein translation in C. elegans, they have been limited to using lysate from whole worms. To achieve tissue-specific quantification of ribosome activity in intact C. elegans, we report the application of O-propargyl-puromycin in a cuticle defective mutant followed by conjugation of an azide fluorophore for detection using fluorescent confocal microscopy. We apply this technique to quantify translation in response to heat shock, cycloheximide, or knockdown of translation factors. Furthermore, we demonstrate that O-propargyl-puromycin can be used to quantify translation between tissues or within a tissue like the germline. This technique is expected to have a broad range of applications in determining how protein translation is altered in different tissues in response to stress or gene knockdowns or with age.
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Affiliation(s)
- Hannah M. Somers
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
| | - Jeremy H. Fuqua
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
| | - Frédéric X.A. Bonnet
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
| | - Jarod A. Rollins
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
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8
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Phillips CM, Updike DL. Germ granules and gene regulation in the Caenorhabditis elegans germline. Genetics 2022; 220:6541922. [PMID: 35239965 PMCID: PMC8893257 DOI: 10.1093/genetics/iyab195] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/10/2021] [Indexed: 01/27/2023] Open
Abstract
The transparency of Caenorhabditis elegans provides a unique window to observe and study the function of germ granules. Germ granules are specialized ribonucleoprotein (RNP) assemblies specific to the germline cytoplasm, and they are largely conserved across Metazoa. Within the germline cytoplasm, they are positioned to regulate mRNA abundance, translation, small RNA production, and cytoplasmic inheritance to help specify and maintain germline identity across generations. Here we provide an overview of germ granules and focus on the significance of more recent observations that describe how they further demix into sub-granules, each with unique compositions and functions.
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Affiliation(s)
- Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA,Corresponding author: (C.M.P.); (D.L.U.)
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA,Corresponding author: (C.M.P.); (D.L.U.)
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9
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Fry AL, Webster AK, Burnett J, Chitrakar R, Baugh LR, Hubbard EJA. DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence. PLoS Genet 2021; 17:e1009650. [PMID: 34288923 PMCID: PMC8294487 DOI: 10.1371/journal.pgen.1009650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Quiescence, an actively-maintained reversible state of cell cycle arrest, is not well understood. PTEN is one of the most frequently lost tumor suppressors in human cancers and regulates quiescence of stem cells and cancer cells. The sole PTEN ortholog in Caenorhabditis elegans is daf-18. In a C. elegans loss-of-function mutant for daf-18, primordial germ cells (PGCs) divide inappropriately in L1 larvae hatched into starvation conditions, in a TOR-dependent manner. Here, we further investigated the role of daf-18 in maintaining PGC quiescence in L1 starvation. We found that maternal or zygotic daf-18 is sufficient to maintain cell cycle quiescence, that daf-18 acts in the germ line and soma, and that daf-18 affects timing of PGC divisions in fed animals. Importantly, our results also implicate daf-18 in repression of germline zygotic gene activation, though not in germline fate specification. However, TOR is less important to germline zygotic gene expression, suggesting that in the absence of food, daf-18/PTEN prevents inappropriate germline zygotic gene activation and cell division by distinct mechanisms.
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Affiliation(s)
- Amanda L. Fry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Amy K. Webster
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Julia Burnett
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Rojin Chitrakar
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - L. Ryan Baugh
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - E. Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
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10
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Uebel CJ, Agbede D, Wallis DC, Phillips CM. Mutator Foci Are Regulated by Developmental Stage, RNA, and the Germline Cell Cycle in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2020; 10:3719-3728. [PMID: 32763952 PMCID: PMC7534428 DOI: 10.1534/g3.120.401514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/03/2020] [Indexed: 02/02/2023]
Abstract
RNA interference is a crucial gene regulatory mechanism in Caenorhabditis elegans Phase-separated perinuclear germline compartments called Mutator foci are a key element of RNAi, ensuring robust gene silencing and transgenerational epigenetic inheritance. Despite their importance, Mutator foci regulation is not well understood, and observations of Mutator foci have been largely limited to adult hermaphrodite germlines. Here we reveal that punctate Mutator foci arise in the progenitor germ cells of early embryos and persist throughout all larval stages. They are additionally present throughout the male germline and in the cytoplasm of post-meiotic spermatids, suggestive of a role in paternal epigenetic inheritance. In the adult germline, transcriptional inhibition results in a pachytene-specific loss of Mutator foci, indicating that Mutator foci are partially reliant on RNA for their stability. Finally, we demonstrate that Mutator foci intensity is modulated by the stage of the germline cell cycle and specifically, that Mutator foci are brightest and most robust in the mitotic cells, transition zone, and late pachytene of adult germlines. Thus, our data defines several new factors that modulate Mutator foci morphology which may ultimately have implications for efficacy of RNAi in certain cell stages or environments.
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Affiliation(s)
- Celja J Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Dana Agbede
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Dylan C Wallis
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
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11
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Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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12
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Svendsen JM, Reed KJ, Vijayasarathy T, Montgomery BE, Tucci RM, Brown KC, Marks TN, Nguyen DAH, Phillips CM, Montgomery TA. henn-1/HEN1 Promotes Germline Immortality in Caenorhabditis elegans. Cell Rep 2020; 29:3187-3199.e4. [PMID: 31801082 PMCID: PMC6922003 DOI: 10.1016/j.celrep.2019.10.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/28/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
The germline contains an immortal cell lineage that ensures the faithful transmission of genetic and, in some instances, epigenetic information from one generation to the next. Here, we show that in Caenorhabditis elegans, the small RNA 3′-2′-O-methyltransferase henn-1/HEN1 is required for sustained fertility across generations. In the absence of henn-1, animals become progressively less fertile, becoming sterile after ~30 generations at 25°C. Sterility in henn-1 mutants is accompanied by severe defects in germline proliferation and maintenance. The requirement for henn-1 in transgenerational fertility is likely due to its role in methylating and, thereby, stabilizing Piwi-interacting RNAs (piRNAs). However, despite being essential for piRNA stability in embryos, henn-1 is not required for piRNA stability in adults. Thus, we propose that methylation is important for the role of piRNAs in establishing proper gene silencing during early stages of development but is dispensable for their role in the proliferated germline. Svendsen et al. identify a requirement for the small RNA methyltransferase HENN-1 in germline immortality. HENN-1 is required for piRNA stability during embryogenesis but is dispensable in the adult germline, pointing to a role for piRNAs in establishing a gene regulatory network in embryos that protects the germline throughout development.
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Affiliation(s)
- Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Kailee J Reed
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Tarah Vijayasarathy
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Brooke E Montgomery
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Rachel M Tucci
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kristen C Brown
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Taylor N Marks
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Dieu An H Nguyen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
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13
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Huggins HP, Keiper BD. Regulation of Germ Cell mRNPs by eIF4E:4EIP Complexes: Multiple Mechanisms, One Goal. Front Cell Dev Biol 2020; 8:562. [PMID: 32733883 PMCID: PMC7358283 DOI: 10.3389/fcell.2020.00562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Translational regulation of mRNAs is critically important for proper gene expression in germ cells, gametes, and embryos. The ability of the nucleus to control gene expression in these systems may be limited due to spatial or temporal constraints, as well as the breadth of gene products they express to prepare for the rapid animal development that follows. During development germ granules are hubs of post-transcriptional regulation of mRNAs. They assemble and remodel messenger ribonucleoprotein (mRNP) complexes for translational repression or activation. Recently, mRNPs have been appreciated as discrete regulatory units, whose function is dictated by the many positive and negative acting factors within the complex. Repressed mRNPs must be activated for translation on ribosomes to introduce novel proteins into germ cells. The binding of eIF4E to interacting proteins (4EIPs) that sequester it represents a node that controls many aspects of mRNP fate including localization, stability, poly(A) elongation, deadenylation, and translational activation/repression. Furthermore, plants and animals have evolved to express multiple functionally distinct eIF4E and 4EIP variants within germ cells, giving rise to different modes of translational regulation.
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Affiliation(s)
- Hayden P Huggins
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
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14
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Parker DM, Winkenbach LP, Boyson S, Saxton MN, Daidone C, Al-Mazaydeh ZA, Nishimura MT, Mueller F, Osborne Nishimura E. mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage. Development 2020; 147:dev186817. [PMID: 32541012 PMCID: PMC7358130 DOI: 10.1242/dev.186817] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/30/2020] [Indexed: 01/01/2023]
Abstract
Caenorhabditis elegans early embryos generate cell-specific transcriptomes despite lacking active transcription, thereby presenting an opportunity to study mechanisms of post-transcriptional regulatory control. We observed that some cell-specific mRNAs accumulate non-homogenously within cells, localizing to membranes, P granules (associated with progenitor germ cells in the P lineage) and P-bodies (associated with RNA processing). The subcellular distribution of transcripts differed in their dependence on 3'UTRs and RNA binding proteins, suggesting diverse regulatory mechanisms. Notably, we found strong but imperfect correlations between low translational status and P granule localization within the progenitor germ lineage. By uncoupling translation from mRNA localization, we untangled a long-standing question: Are mRNAs directed to P granules to be translationally repressed, or do they accumulate there as a consequence of this repression? We found that translational repression preceded P granule localization and could occur independently of it. Further, disruption of translation was sufficient to send homogenously distributed mRNAs to P granules. These results implicate transcriptional repression as a means to deliver essential maternal transcripts to the progenitor germ lineage for later translation.
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Affiliation(s)
- Dylan M Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Lindsay P Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sam Boyson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Matthew N Saxton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Camryn Daidone
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zainab A Al-Mazaydeh
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biology and Biotechnology, Hashemite University, Zarqa, 13115, Jordan
| | - Marc T Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Florian Mueller
- Département Biologie Cellulaire et Infections, Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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15
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Manage KI, Rogers AK, Wallis DC, Uebel CJ, Anderson DC, Nguyen DAH, Arca K, Brown KC, Cordeiro Rodrigues RJ, de Albuquerque BF, Ketting RF, Montgomery TA, Phillips CM. A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans. eLife 2020; 9:56731. [PMID: 32338603 PMCID: PMC7255803 DOI: 10.7554/elife.56731] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, regulation of piRNA target genes is mediated by the mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, the steps between mRNA recognition by the piRNA pathway and siRNA amplification by the mutator complex are unknown. Here, we identify the Tudor domain protein, SIMR-1, as acting downstream of piRNA production and upstream of mutator complex-dependent siRNA biogenesis. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting mRNA regulation by the mutator complex. In the biological world, a process known as RNA interference helps cells to switch genes on and off and to defend themselves against harmful genetic material. This mechanism works by deactivating RNA sequences, the molecular templates cells can use to create proteins. Overall, RNA interference relies on the cell creating small RNA molecules that can target and inhibit the harmful RNA sequences that need to be silenced. More precisely, in round worms such as Caenorhabditis elegans, RNA interference happens in two steps. First, primary small RNAs identify the target sequences, which are then combatted by newly synthetised, secondary small RNAs. A number of proteins are also involved in both steps of the process. RNA interference is particularly important to preserve fertility, guarding sex cells against ‘rogue’ segments of genetic information that could be passed on to the next generation. In future sex cells, the proteins involved in RNA interference cluster together, forming a structure called a germ granule. Yet, little is known about the roles and identity of these proteins. To fill this knowledge gap, Manage et al. focused on the second stage of the RNA interference pathway in the germ granules of C. elegans, examining the molecules that physically interact with a key protein. This work revealed a new protein called SIMR-1. Looking into the role of SIMR-1 showed that the protein is required to amplify secondary small RNAs, but not to identify target sequences. However, it only promotes the creation of secondary small RNAs if a specific subtype of primary small RNAs have recognized the target RNAs for silencing. Further experiments also showed that within the germ granule, SIMR-1 is present in a separate substructure different from any compartment previously identified. This suggests that each substep of the RNA interference process takes place at a different location in the granule. In both C. elegans and humans, disruptions in the RNA interference pathway can lead to conditions such as cancer or infertility. Dissecting the roles of the proteins involved in this process in roundworms may help to better grasp how this process unfolds in mammals, and how it could be corrected in the case of disease.
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Affiliation(s)
- Kevin I Manage
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dylan C Wallis
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Celja J Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dorian C Anderson
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dieu An H Nguyen
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Katerina Arca
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Kristen C Brown
- Department of Biology, Colorado State University, Fort Collins, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, United States
| | - Ricardo J Cordeiro Rodrigues
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany.,International PhD Programme on Gene Regulation, Epigenetics, and Genome Stability, Mainz, Germany
| | | | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Carolyn Marie Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
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16
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Marnik EA, Fuqua JH, Sharp CS, Rochester JD, Xu EL, Holbrook SE, Updike DL. Germline Maintenance Through the Multifaceted Activities of GLH/Vasa in Caenorhabditis elegans P Granules. Genetics 2019; 213:923-939. [PMID: 31506335 PMCID: PMC6827368 DOI: 10.1534/genetics.119.302670] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
Vasa homologs are ATP-dependent DEAD-box helicases, multipotency factors, and critical components that specify and protect the germline. They regulate translation, amplify piwi-interacting RNAs (piRNAs), and act as RNA solvents; however, the limited availability of mutagenesis-derived alleles and their wide range of phenotypes have complicated their analysis. Now, with clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), these limitations can be mitigated to determine why protein domains have been lost or retained throughout evolution. Here, we define the functional motifs of GLH-1/Vasa in Caenorhabditis elegans using 28 endogenous, mutant alleles. We show that GLH-1's helicase activity is required to retain its association with P granules. GLH-1 remains in P granules when changes are made outside of the helicase and flanking domains, but fertility is still compromised. Removal of the glycine-rich repeats from GLH proteins progressively diminishes P-granule wetting-like interactions at the nuclear periphery. Mass spectrometry of GLH-1-associated proteins implies conservation of a transient piRNA-amplifying complex, and reveals a novel affinity between GLH-1 and three structurally conserved PCI (26S Proteasome Lid, COP9, and eIF3) complexes or "zomes," along with a reciprocal aversion for assembled ribosomes and the 26S proteasome. These results suggest that P granules compartmentalize the cytoplasm to exclude large protein assemblies, effectively shielding associated transcripts from translation and associated proteins from turnover. Within germ granules, Vasa homologs may act as solvents, ensuring mRNA accessibility by small RNA surveillance and amplification pathways, and facilitating mRNA export through germ granules to initiate translation.
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Affiliation(s)
| | - J Heath Fuqua
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- The College of the Atlantic, Bar Harbor, Maine 04609
| | - Catherine S Sharp
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
| | - Jesse D Rochester
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
| | - Emily L Xu
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- The College of William and Mary, Williamsburg, Virginia 23185
| | - Sarah E Holbrook
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
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17
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Rothman J, Jarriault S. Developmental Plasticity and Cellular Reprogramming in Caenorhabditis elegans. Genetics 2019; 213:723-757. [PMID: 31685551 PMCID: PMC6827377 DOI: 10.1534/genetics.119.302333] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022] Open
Abstract
While Caenorhabditis elegans was originally regarded as a model for investigating determinate developmental programs, landmark studies have subsequently shown that the largely invariant pattern of development in the animal does not reflect irreversibility in rigidly fixed cell fates. Rather, cells at all stages of development, in both the soma and germline, have been shown to be capable of changing their fates through mutation or forced expression of fate-determining factors, as well as during the normal course of development. In this chapter, we review the basis for natural and induced cellular plasticity in C. elegans We describe the events that progressively restrict cellular differentiation during embryogenesis, starting with the multipotency-to-commitment transition (MCT) and subsequently through postembryonic development of the animal, and consider the range of molecular processes, including transcriptional and translational control systems, that contribute to cellular plasticity. These findings in the worm are discussed in the context of both classical and recent studies of cellular plasticity in vertebrate systems.
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Affiliation(s)
- Joel Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93111, and
| | - Sophie Jarriault
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Department of Development and Stem Cells, CNRS UMR7104, Inserm U1258, Université de Strasbourg, 67404 Illkirch CU Strasbourg, France
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18
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Costello ME, Petrella LN. C. elegans synMuv B proteins regulate spatial and temporal chromatin compaction during development. Development 2019; 146:dev174383. [PMID: 31515206 PMCID: PMC6803374 DOI: 10.1242/dev.174383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 09/04/2019] [Indexed: 12/15/2022]
Abstract
Tissue-specific establishment of repressive chromatin through creation of compact chromatin domains during development is necessary to ensure proper gene expression and cell fate. Caenorhabditis elegans synMuv B proteins are important for the soma/germline fate decision and mutants demonstrate ectopic germline gene expression in somatic tissue, especially at high temperature. We show that C. elegans synMuv B proteins regulate developmental chromatin compaction and that the timing of chromatin compaction is temperature sensitive in both wild type and synMuv B mutants. Chromatin compaction in mutants is delayed into developmental time periods when zygotic gene expression is upregulated and demonstrates an anterior-to-posterior pattern. Loss of this patterned compaction coincides with the developmental time period of ectopic germline gene expression, which leads to a developmental arrest in synMuv B mutants. Finally, accelerated cell division rates at elevated temperature may contribute to a lack of coordination between expression of tissue specific transcription programs and chromatin compaction at high temperature. Thus, chromatin organization during development is regulated both spatially and temporally by synMuv B proteins to establish repressive chromatin in a tissue-specific manner to ensure proper gene expression.
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Affiliation(s)
- Meghan E Costello
- 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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19
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3′-UTRs and the Control of Protein Expression in Space and Time. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:133-148. [DOI: 10.1007/978-3-030-31434-7_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Wu Y, Han B, Gauvin TJ, Smith J, Singh A, Griffin EE. Single-molecule dynamics of the P granule scaffold MEG-3 in the Caenorhabditis elegans zygote. Mol Biol Cell 2018; 30:333-345. [PMID: 30540524 PMCID: PMC6589573 DOI: 10.1091/mbc.e18-06-0402] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
During the asymmetric division of the Caenorhabditis elegans zygote, germ (P) granules are disassembled in the anterior cytoplasm and stabilized/assembled in the posterior cytoplasm, leading to their inheritance by the germline daughter cell. P granule segregation depends on MEG (maternal-effect germline defective)-3 and MEG-4, which are enriched in P granules and in the posterior cytoplasm surrounding P granules. Here we use single-molecule imaging and tracking to characterize the reaction/diffusion mechanisms that result in MEG-3::Halo segregation. We find that the anteriorly enriched RNA-binding proteins MEX (muscle excess)-5 and MEX-6 suppress the retention of MEG-3 in the anterior cytoplasm, leading to MEG-3 enrichment in the posterior. We provide evidence that MEX-5/6 may work in conjunction with PLK-1 kinase to suppress MEG-3 retention in the anterior. Surprisingly, we find that the retention of MEG-3::Halo in the posterior cytoplasm surrounding P granules does not appear to contribute significantly to the maintenance of P granule asymmetry. Rather, our findings suggest that the formation of the MEG-3 concentration gradient and the segregation of P granules are two parallel manifestations of MEG-3′s response to upstream polarity cues.
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Affiliation(s)
- Youjun Wu
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Bingjie Han
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Timothy J Gauvin
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Jarrett Smith
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Abhyudai Singh
- Departments of Electrical and Computer Engineering, Biomedical Engineering and Mathematical Sciences, University of Delaware, Newark, DE 19716
| | - Erik E Griffin
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
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21
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PIE-1 Translation in the Germline Lineage Contributes to PIE-1 Asymmetry in the Early Caenorhabditis elegans Embryo. G3-GENES GENOMES GENETICS 2018; 8:3791-3801. [PMID: 30279189 PMCID: PMC6288838 DOI: 10.1534/g3.118.200744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the C. elegans embryo, the germline lineage is established through successive asymmetric cell divisions that each generate a somatic and a germline daughter cell. PIE-1 is an essential maternal factor that is enriched in embryonic germline cells and is required for germline specification. We estimated the absolute concentration of PIE-1::GFP in germline cells and find that PIE-1::GFP concentration increases by roughly 4.5 fold, from 92 nM to 424 nM, between the 1 and 4-cell stages. Previous studies have shown that the preferential inheritance of PIE-1 by germline daughter cells and the degradation of PIE-1 in somatic cells are important for PIE-1 enrichment in germline cells. In this study, we provide evidence that the preferential translation of maternal PIE-1::GFP transcripts in the germline also contributes to PIE-1::GFP enrichment. Through an RNAi screen, we identified Y14 and MAG-1 (Drosophila tsunagi and mago nashi) as regulators of embryonic PIE-1::GFP levels. We show that Y14 and MAG-1 do not regulate PIE-1 degradation, segregation or synthesis in the early embryo, but do regulate the concentration of maternally-deposited PIE-1::GFP. Taken together, or findings point to an important role for translational control in the regulation of PIE-1 levels in the germline lineage.
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22
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Rochester JD, Tanner PC, Sharp CS, Andralojc KM, Updike DL. PQN-75 is expressed in the pharyngeal gland cells of Caenorhabditiselegans and is dispensable for germline development. Biol Open 2017; 6:1355-1363. [PMID: 28916707 PMCID: PMC5612245 DOI: 10.1242/bio.027987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Caenorhabditis elegans, five pharyngeal gland cells reside in the terminal bulb of the pharynx and extend anterior processes to five contact points in the pharyngeal lumen. Pharyngeal gland cells secrete mucin-like proteins thought to facilitate digestion, hatching, molting and assembly of the surface coat of the cuticle, but supporting evidence has been sparse. Here we show pharyngeal gland cell expression of PQN-75, a unique protein containing an N-terminal signal peptide, nucleoporin (Nup)-like phenylalanine/glycine (FG) repeats, and an extensive polyproline repeat domain with similarities to human basic salivary proline-rich pre-protein PRB2. Imaging of C-terminal tagged PQN-75 shows localization throughout pharyngeal gland cell processes but not the pharyngeal lumen; instead, aggregates of PQN-75 are occasionally found throughout the pharynx, suggesting secretion from pharyngeal gland cells into the surrounding pharyngeal muscle. PQN-75 does not affect fertility and brood size in C. elegans but confers some degree of stress resistance and thermotolerance through unknown mechanisms. Summary: PQN-75 is expressed in pharyngeal gland cells and shares similarity with human basic salivary proline-rich protein PBR2, suggesting evolutionary conservation between gland cells in the upper digestive tract.
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Affiliation(s)
- Jesse D Rochester
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | - Paige C Tanner
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | - Catherine S Sharp
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | | | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
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