1
|
Chernomas G, Griswold CK. Deleterious mutation/epimutation-selection balance with and without inbreeding: a population (epi)genetics model. Genetics 2024; 227:iyae080. [PMID: 38733620 PMCID: PMC11228854 DOI: 10.1093/genetics/iyae080] [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: 03/26/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Epigenetics in the form of DNA methylation and other processes is an established property of genotypes and a focus of empirical research. Yet, there remain fundamental gaps in the evolutionary theory of epigenetics. To support a comprehensive understanding of epigenetics, this paper investigates theoretically the combined effects of deleterious mutation and epimutation with and without inbreeding. Both spontaneous epimutation and paramutation are considered to cover a broader range of epigenetic phenomena. We find that inbreeding generally reduces the amount of segregating deleterious genetic and epigenetic variation at equilibrium, although interestingly inbreeding can also increase the amount of deleterious genetic or epigenetic variation. Furthermore, we also demonstrate that epimutation indirectly can cause increased or decreased deleterious genetic variation at equilibrium relative to classic expectations, which is particularly evident when paramutation is occurring. With the addition of deleterious epimutation, there may be significantly increased purging of deleterious variation in more inbred populations and a significantly increased amount of segregating deleterious variation in more outbred populations, with notable exceptions.
Collapse
Affiliation(s)
- Gregory Chernomas
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Cortland K Griswold
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
2
|
Xiao Y, Li J, Wang R, Fan Y, Han X, Fu Y, Alepuz P, Wang W, Liang A. eIF5A promotes +1 programmed ribosomal frameshifting in Euplotes octocarinatus. Int J Biol Macromol 2024; 254:127743. [PMID: 38287569 DOI: 10.1016/j.ijbiomac.2023.127743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 01/31/2024]
Abstract
Programmed ribosomal frameshifting (PRF) exists in all branches of life that regulate gene expression at the translational level. The single-celled eukaryote Euplotes exhibit high frequency of PRF. However, the molecular mechanism of modulating Euplotes PRF remains largely unknown. Here, we identified two novel eIF5A genes, eIF5A1 and eIF5A2, in Euplotes octocarinatus and found that the Eo-eIF5A2 gene requires a -1 PRF to produce complete protein product. Although both Eo-eIF5As showed significant structural similarity with yeast eIF5A, neither of them could functionally replace yeast eIF5A. Eo-eIF5A knockdown inhibited +1 PRF of the η-tubulin gene. Using an in vitro reconstituted translation system, we found that hypusinated Eo-eIF5A (Eo-eIF5AH) can promote +1 PRF at the canonical AAA_UAA frameshifting site of Euplotes. The results showed eIF5A is a novel trans-regulator of PRF in Euplotes and has an evolutionary conserved role in regulating +1 PRF in eukaryotes.
Collapse
Affiliation(s)
- Yu Xiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Jia Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Ruanlin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
| | - Yajiao Fan
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Xiaxia Han
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed) and Departamento de Bioquímica y Biología Molecular, Universitat de València, Spain
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
| | - Aihua Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
| |
Collapse
|
3
|
Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. EPIGENOMES 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
Collapse
Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
| |
Collapse
|
4
|
Du X, McManus DP, French JD, Sivakumaran H, Johnston RL, Kondrashova O, Fogarty CE, Jones MK, You H. Lentiviral Transduction-based CRISPR/Cas9 Editing of Schistosoma mansoni Acetylcholinesterase. Curr Genomics 2023; 24:155-170. [PMID: 38178986 PMCID: PMC10761339 DOI: 10.2174/1389202924666230823094608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/02/2023] [Accepted: 07/17/2023] [Indexed: 01/06/2024] Open
Abstract
Background Recent studies on CRISPR/Cas9-mediated gene editing in Schistosoma mansoni have shed new light on the study and control of this parasitic helminth. However, the gene editing efficiency in this parasite is modest. Methods To improve the efficiency of CRISPR/Cas9 genome editing in schistosomes, we used lentivirus, which has been effectively used for gene editing in mammalian cells, to deliver plasmid DNA encoding Cas9 nuclease, a sgRNA targeting acetylcholinesterase (SmAChE) and a mCherry fluorescence marker into schistosomes. Results MCherry fluorescence was observed in transduced eggs, schistosomula, and adult worms, indicating that the CRISPR components had been delivered into these parasite stages by lentivirus. In addition, clearly changed phenotypes were observed in SmAChE-edited parasites, including decreased SmAChE activity, reduced hatching ability of edited eggs, and altered behavior of miracidia hatched from edited eggs. Next-generation sequencing analysis demonstrated that the lentiviral transduction-based CRISPR/Cas9 gene modifications in SmAChE-edited schistosomes were homology-directed repair predominant but with much lower efficiency than that obtained using electroporation (data previously published by our laboratory) for the delivery of CRISPR components. Conclusion Taken together, electroporation is more efficient than lentiviral transduction in the delivery of CRISPR/Cas9 into schistosomes for programmed genome editing. The exploration of tactics for enhancing CRISPR/Cas9 gene editing provides the basis for the future improvement of programmed genome editing in S. mansoni.
Collapse
Affiliation(s)
- Xiaofeng Du
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Donald P. McManus
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Juliet D. French
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Haran Sivakumaran
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rebecca L. Johnston
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Olga Kondrashova
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Conor E. Fogarty
- Centre for Bioinnovation, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia
| | - Malcolm K. Jones
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Hong You
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| |
Collapse
|
5
|
Price IF, Wagner JA, Pastore B, Hertz HL, Tang W. C. elegans germ granules sculpt both germline and somatic RNAome. Nat Commun 2023; 14:5965. [PMID: 37749091 PMCID: PMC10520050 DOI: 10.1038/s41467-023-41556-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.
Collapse
Affiliation(s)
- Ian F Price
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Jillian A Wagner
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hannah L Hertz
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
6
|
Villalobos TV, Ghosh B, DeLeo KR, Alam S, Ricaurte-Perez C, Wang A, Mercola BM, Butsch TJ, Ramos CD, Das S, Eymard ED, Bohnert KA, Johnson AE. Tubular lysosome induction couples animal starvation to healthy aging. NATURE AGING 2023; 3:1091-1106. [PMID: 37580394 PMCID: PMC10501908 DOI: 10.1038/s43587-023-00470-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/17/2023] [Indexed: 08/16/2023]
Abstract
Dietary restriction promotes longevity in several species via autophagy activation. However, changes to lysosomes underlying this effect remain unclear. Here using the nematode Caenorhabditis elegans, we show that the induction of autophagic tubular lysosomes (TLs), which occurs upon dietary restriction or mechanistic target of rapamycin inhibition, is a critical event linking reduced food intake to lifespan extension. We find that starvation induces TLs not only in affected individuals but also in well-fed descendants, and the presence of gut TLs in well-fed progeny is predictive of enhanced lifespan. Furthermore, we demonstrate that expression of Drosophila small VCP-interacting protein, a TL activator in flies, artificially induces TLs in well-fed worms and improves C. elegans health in old age. These findings identify TLs as a new class of lysosomes that couples starvation to healthy aging.
Collapse
Affiliation(s)
- Tatiana V Villalobos
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Bhaswati Ghosh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Kathryn R DeLeo
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Sanaa Alam
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | | | - Andrew Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brennan M Mercola
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Tyler J Butsch
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Cara D Ramos
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Suman Das
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Eric D Eymard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - K Adam Bohnert
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
| | - Alyssa E Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
| |
Collapse
|
7
|
Sun CL, Van Gilst M, Crowder CM. Hypoxia-induced mitochondrial stress granules. Cell Death Dis 2023; 14:448. [PMID: 37468471 PMCID: PMC10356818 DOI: 10.1038/s41419-023-05988-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Perturbations of mitochondrial proteostasis have been associated with aging, neurodegenerative diseases, and recently with hypoxic injury. While examining hypoxia-induced mitochondrial protein aggregation in C. elegans, we found that sublethal hypoxia, sodium azide, or heat shock-induced abundant ethidium bromide staining mitochondrial granules that preceded evidence of protein aggregation. Genetic manipulations that reduce cellular and organismal hypoxic death block the formation of these mitochondrial stress granules (mitoSG). Knockdown of mitochondrial nucleoid proteins also blocked the formation of mitoSG by a mechanism distinct from the mitochondrial unfolded protein response. Lack of the major mitochondrial matrix protease LONP-1 resulted in the constitutive formation of mitoSG without external stress. Ethidium bromide-staining RNA-containing mitochondrial granules were also observed in rat cardiomyocytes treated with sodium azide, a hypoxia mimetic. Mitochondrial stress granules are an early mitochondrial pathology controlled by LONP and the nucleoid, preceding hypoxia-induced protein aggregation.
Collapse
Affiliation(s)
- Chun-Ling Sun
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - Marc Van Gilst
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - C Michael Crowder
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Department of Genome Science, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
| |
Collapse
|
8
|
Cabej NR. On the origin and nature of nongenetic information in eumetazoans. Ann N Y Acad Sci 2023. [PMID: 37154677 DOI: 10.1111/nyas.15001] [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: 05/10/2023]
Abstract
Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.
Collapse
Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
| |
Collapse
|
9
|
Santilli F, Boskovic A. Mechanisms of transgenerational epigenetic inheritance: lessons from animal model organisms. Curr Opin Genet Dev 2023; 79:102024. [PMID: 36893483 DOI: 10.1016/j.gde.2023.102024] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/24/2022] [Accepted: 01/26/2023] [Indexed: 03/09/2023]
Abstract
Epigenetic inheritance is a phenomenon whereby stochastic or signal-induced changes to parental germline epigenome modulate phenotypic output in one or more subsequent generations, independently of mutations in the genomic DNA. While the number of reported epigenetic inheritance phenomena across phyla is exponentially growing, much remains to be elucidated about their mechanistic underpinnings, and their significance for organismal homeostasis and adaptation. Here, we review the most recent epigenetic inheritance examples in animal models, outlining molecular details behind environmental sensing by the germline, and the functional relationships connecting epigenetic mechanisms and phenotypic traits after fertilization. We touch upon the experimental challenges associated with studying the scope of environmental input on phenotypic outcomes between generations. Finally, we discuss the implications of mechanistic findings from model organisms for the emergent examples of parental effects in human populations.
Collapse
Affiliation(s)
- Flavio Santilli
- European Molecular Biology Laboratory Epigenetics & Neurobiology Unit, Monterotondo, RM, Italy. https://twitter.com/@santilli_flavio
| | - Ana Boskovic
- European Molecular Biology Laboratory Epigenetics & Neurobiology Unit, Monterotondo, RM, Italy.
| |
Collapse
|
10
|
Karin O, Miska EA, Simons BD. Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition. Cell Syst 2023; 14:24-40.e11. [PMID: 36657390 PMCID: PMC7614883 DOI: 10.1016/j.cels.2022.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/05/2022] [Accepted: 12/12/2022] [Indexed: 01/19/2023]
Abstract
Biological systems can maintain memories over long timescales, with examples including memories in the brain and immune system. It is unknown how functional properties of memory systems, such as memory persistence, can be established by biological circuits. To address this question, we focus on transgenerational epigenetic inheritance in Caenorhabditis elegans. In response to a trigger, worms silence a target gene for multiple generations, resisting strong dilution due to growth and reproduction. Silencing may also be maintained indefinitely upon selection according to silencing levels. We show that these properties imply the fine-tuning of biochemical rates in which the silencing system is positioned near the transition to bistability. We demonstrate that this behavior is consistent with a generic mechanism based on competition for synthesis resources, which leads to self-organization around a critical state with broad silencing timescales. The theory makes distinct predictions and offers insights into the design principles of long-term memory systems.
Collapse
Affiliation(s)
- Omer Karin
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, CB3 0WA, UK; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Mathematics, Imperial College London, London, SW7 2AZ, UK.
| | - Eric A Miska
- Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Benjamin D Simons
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, CB3 0WA, UK; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
| |
Collapse
|
11
|
Du X, McManus DP, French JD, Collinson N, Sivakumaran H, MacGregor SR, Fogarty CE, Jones MK, You H. CRISPR interference for sequence-specific regulation of fibroblast growth factor receptor A in Schistosoma mansoni. Front Immunol 2023; 13:1105719. [PMID: 36713455 PMCID: PMC9880433 DOI: 10.3389/fimmu.2022.1105719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Employing the flatworm parasite Schistosoma mansoni as a model, we report the first application of CRISPR interference (CRISPRi) in parasitic helminths for loss-of-function studies targeting the SmfgfrA gene which encodes the stem cell marker, fibroblast growth factor receptor A (FGFRA). SmFGFRA is essential for maintaining schistosome stem cells and critical in the schistosome-host interplay. The SmfgfrA gene was targeted in S. mansoni adult worms, eggs and schistosomula using a catalytically dead Cas9 (dCas9) fused to a transcriptional repressor KRAB. We showed that SmfgfrA repression resulted in considerable phenotypic differences in the modulated parasites compared with controls, including reduced levels of SmfgfrA transcription and decreased protein expression of SmFGFRA, a decline in EdU (thymidine analog 5-ethynyl-2'-deoxyuridine, which specifically stains schistosome stem cells) signal, and an increase in cell apoptosis. Notably, reduced SmfgfrA transcription was evident in miracidia hatched from SmfgfrA-repressed eggs, and resulted in a significant change in miracidial behavior, indicative of a durable repression effect caused by CRISPRi. Intravenous injection of mice with SmfgfrA-repressed eggs resulted in granulomas that were markedly reduced in size and a decline in the level of serum IgE, emphasizing the importance of SmFGFRA in regulating the host immune response induced during schistosome infection. Our findings show the feasibility of applying CRISPRi for effective, targeted transcriptional repression in schistosomes, and provide the basis for employing CRISPRi to selectively perturb gene expression in parasitic helminths on a genome-wide scale.
Collapse
Affiliation(s)
- Xiaofeng Du
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Donald P. McManus
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Juliet D. French
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Natasha Collinson
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Haran Sivakumaran
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Skye R. MacGregor
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Conor E. Fogarty
- Genecology Research Centre, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| | - Malcolm K. Jones
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Hong You
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia,*Correspondence: Hong You,
| |
Collapse
|
12
|
Ciliate Microtubule Diversities: Insights from the EFBTU3 Tubulin in the Antarctic Ciliate Euplotes focardii. Microorganisms 2022; 10:microorganisms10122415. [PMID: 36557668 PMCID: PMC9784925 DOI: 10.3390/microorganisms10122415] [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] [Received: 11/02/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Protozoans of the Phylum Ciliophora (ciliates) assemble many diverse microtubular structures in a single cell throughout the life cycle, a feature that made them useful models to study microtubule complexity and the role of tubulin isotypes. In the Antarctic ciliate Euplotes focardii we identified five β-tubulin isotypes by genome sequencing, named EFBTU1, EFBTU2, EFBTU3, EFBTU4 and EFBTU5. By using polyclonal antibodies directed against EFBTU2/EFBTU1 and EFBTU3, we show that the former isotypes appear to be involved in the formation of all microtubular structures and are particularly abundant in cilia, whereas the latter specifically localizes at the bases of cilia. By RNA interference (RNAi) technology, we silenced the EFBTU3 gene and provided evidence that this isotype has a relevant role in cilia regeneration upon deciliation and in cell division. These results support the long-standing concept that tubulin isotypes possess functional specificity in building diverse microtubular structures.
Collapse
|
13
|
Juliane Veigl S. Do heritable immune responses extend physiological individuality? HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:67. [PMID: 36427106 PMCID: PMC9700645 DOI: 10.1007/s40656-022-00549-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Immunology and its philosophy are a primary source for thinking about biological individuality. Through its discriminatory function, the immune system is believed to delineate organism and environment within one generation, thus defining the physiological individual. Based on the paradigmatic instantiations of immune systems, immune interactions and, thus, the physiological individual are believed to last only for one generation. However, in recent years, transgenerationally persisting immune responses have been reported in several phyla, but the consequences for physiological individuality have not yet been explored. In this article, I will introduce an invertebrate immune system that is RNA-based and operates through a heritable silencing/licensing paradigm. I will discuss how such a perspective on immune systems can illuminate our conceptions of individuality. I will particularly introduce an account of immunological individuality that is not restricted to one generation.
Collapse
|
14
|
Gajic Z, Kaur D, Ni J, Zhu Z, Zhebrun A, Gajic M, Kim M, Hong J, Priyadarshini M, Frøkjær-Jensen C, Gu S. Target-dependent suppression of siRNA production modulates the levels of endogenous siRNAs in the Caenorhabditis elegans germline. Development 2022; 149:dev200692. [PMID: 35876680 PMCID: PMC9481970 DOI: 10.1242/dev.200692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/14/2022] [Indexed: 08/24/2023]
Abstract
Despite the prominent role of endo-siRNAs in transposon silencing, their expression is not limited to these 'nonself' DNA elements. Transcripts of protein-coding genes ('self' DNA) in some cases also produce endo-siRNAs in yeast, plants and animals. How cells distinguish these two populations of siRNAs to prevent unwanted silencing of active genes in animals is not well understood. To address this question, we inserted various self-gene or gfp fragments into an LTR retrotransposon that produces abundant siRNAs and examined the propensity of these gene fragments to produce ectopic siRNAs in the Caenorhabditis elegans germline. We found that fragments of germline genes are generally protected from production of ectopic siRNAs. This phenomenon, which we termed 'target-directed suppression of siRNA production' (or siRNA suppression), is dependent on the germline expression of target mRNA and requires germline P-granule components. We found that siRNA suppression can also occur in naturally produced endo-siRNAs. We suggest that siRNA suppression plays an important role in regulating siRNA expression and preventing self-genes from aberrant epigenetic silencing. This article has an associated 'The people behind the papers' interview.
Collapse
Affiliation(s)
- Zoran Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Diljeet Kaur
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Julie Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zhaorong Zhu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Anna Zhebrun
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Maria Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Matthew Kim
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Julia Hong
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Monika Priyadarshini
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Kingdom of Saudi Arabia
| | - Christian Frøkjær-Jensen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Kingdom of Saudi Arabia
| | - Sam Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| |
Collapse
|
15
|
Quarato P, Singh M, Bourdon L, Cecere G. Inheritance and maintenance of small RNA-mediated epigenetic effects. Bioessays 2022; 44:e2100284. [PMID: 35338497 DOI: 10.1002/bies.202100284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 11/08/2022]
Abstract
Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA-dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs.
Collapse
Affiliation(s)
- Piergiuseppe Quarato
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Meetali Singh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Loan Bourdon
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Germano Cecere
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| |
Collapse
|
16
|
Reprogramming the piRNA pathway for multiplexed and transgenerational gene silencing in C. elegans. Nat Methods 2022; 19:187-194. [PMID: 35115715 PMCID: PMC9798472 DOI: 10.1038/s41592-021-01369-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023]
Abstract
Single-guide RNAs can target exogenous CRISPR-Cas proteins to unique DNA locations, enabling genetic tools that are efficient, specific and scalable. Here we show that short synthetic guide Piwi-interacting RNAs (piRNAs) (21-nucleotide sg-piRNAs) expressed from extrachromosomal transgenes can, analogously, reprogram the endogenous piRNA pathway for gene-specific silencing in the hermaphrodite germline, sperm and embryos of Caenorhabditis elegans. piRNA-mediated interference ('piRNAi') is more efficient than RNAi and can be multiplexed, and auxin-mediated degradation of the piRNA-specific Argonaute PRG-1 allows conditional gene silencing. Target-specific silencing results in decreased messenger RNA levels, amplification of secondary small interfering RNAs and repressive chromatin modifications. Short (300 base pairs) piRNAi transgenes amplified from arrayed oligonucleotide pools also induce silencing, potentially making piRNAi highly scalable. We show that piRNAi can induce transgenerational epigenetic silencing of two endogenous genes (him-5 and him-8). Silencing is inherited for four to six generations after target-specific sg-piRNAs are lost, whereas depleting PRG-1 leads to essentially permanent epigenetic silencing.
Collapse
|
17
|
Cayuela H, Jacob S, Schtickzelle N, Verdonck R, Philippe H, Laporte M, Huet M, Bernatchez L, Legrand D. Transgenerational plasticity of dispersal‐related traits in a ciliate: genotype‐dependency and fitness consequences. OIKOS 2022. [DOI: 10.1111/oik.08846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hugo Cayuela
- Dépt de Biologie, Inst. de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Pavillon Charles‐Eugène‐Marchand Québec QC Canada
- Dept of Ecology and Evolution, Univ. of Lausanne Lausanne Switzerland
| | - Staffan Jacob
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Nicolas Schtickzelle
- Univ. Catholique de Louvain, Earth and Life Inst., Biodiversity Research Centre Louvain‐la‐Neuve Belgium
| | - Rik Verdonck
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Hervé Philippe
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
- Dépt de Biochimie, Centre Robert‐Cedergren, Univ. de Montréal Montréal QC Canada
| | - Martin Laporte
- Ministère des Forêts, de la Faune et des Parc (MFFP) du Québec Québec QC Canada
| | - Michèle Huet
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Louis Bernatchez
- Dépt de Biologie, Inst. de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Pavillon Charles‐Eugène‐Marchand Québec QC Canada
| | - Delphine Legrand
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| |
Collapse
|
18
|
Abstract
Increasing evidence indicates that non-DNA sequence-based epigenetic information can be inherited across several generations in organisms ranging from yeast to plants to humans. This raises the possibility of heritable 'epimutations' contributing to heritable phenotypic variation and thus to evolution. Recent work has shed light on both the signals that underpin these epimutations, including DNA methylation, histone modifications and non-coding RNAs, and the mechanisms by which they are transmitted across generations at the molecular level. These mechanisms can vary greatly among species and have a more limited effect in mammals than in plants and other animal species. Nevertheless, common principles are emerging, with transmission occurring either via direct replicative mechanisms or indirect reconstruction of the signal in subsequent generations. As these processes become clearer we continue to improve our understanding of the distinctive features and relative contribution of DNA sequence and epigenetic variation to heritable differences in phenotype.
Collapse
|
19
|
Hotzy C, Fowler E, Kiehl B, Francis R, Mason J, Moxon S, Rostant W, Chapman T, Immler S. Evolutionary history of sexual selection affects microRNA profiles in Drosophila sperm. Evolution 2021; 76:310-319. [PMID: 34874067 DOI: 10.1111/evo.14411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 11/28/2022]
Abstract
The presence of small RNAs in sperm is a relatively recent discovery and little is currently known about their importance and functions. Environmental changes including social conditions and dietary manipulations are known to affect the composition and expression of some small RNAs in sperm and may elicit a physiological stress response resulting in an associated change in gamete miRNA profiles. Here, we tested how microRNA profiles in sperm are affected by variation in both sexual selection and dietary regimes in Drosophila melanogaster selection lines. The selection lines were exposed to standard versus low yeast diet treatments and three different population sex ratios (male-biased, female-biased or equal sex) in a full-factorial design. After 38 generations of selection, all males were maintained on their selected diet and in a common garden male-only environment prior to sperm sampling. We performed transcriptome analyses on miRNAs in purified sperm samples. We found 11 differentially expressed miRNAs with the majority showing differences between male- and female-biased lines. Dietary treatment only had a significant effect on miRNA expression levels in interaction with sex ratio. Our findings suggest that long-term adaptation may affect miRNA profiles in sperm and that these may show varied interactions with short-term environmental changes. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Cosima Hotzy
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Emily Fowler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Berrit Kiehl
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Roy Francis
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Janet Mason
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Wayne Rostant
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| |
Collapse
|
20
|
Abstract
DNA is central to the propagation and evolution of most living organisms due to the essential process of its self-replication. Yet it also encodes factors that permit epigenetic (not included in DNA sequence) flow of information from parents to their offspring and beyond. The known mechanisms of epigenetic inheritance include chemical modifications of DNA and chromatin, as well as regulatory RNAs. All these factors can modulate gene expression programs in the ensuing generations. The nematode Caenorhabditis elegans is recognized as a pioneer organism in transgenerational epigenetic inheritance research. Recent advances in C. elegans epigenetics include the discoveries of control mechanisms that limit the duration of RNA-based epigenetic inheritance, periodic DNA motifs that counteract epigenetic silencing establishment, new mechanistic insights into epigenetic inheritance carried by sperm, and the tantalizing examples of inheritance of sensory experiences. This review aims to highlight new findings in epigenetics research in C. elegans with the main focus on transgenerational epigenetic phenomena dependent on small RNAs.
Collapse
Affiliation(s)
- Alla Grishok
- Department of Biochemistry, BU Genome Science Institute, Boston University School of Medicine, 72 E. Concord St. K422, Boston, MA 02118, USA
| |
Collapse
|
21
|
Li J, Zhu Z, Bi J, Feng Q, Beerntsen BT, Song Q. Neuropeptide Bursicon Influences Reproductive Physiology in Tribolium Castaneum. Front Physiol 2021; 12:717437. [PMID: 34744761 PMCID: PMC8567023 DOI: 10.3389/fphys.2021.717437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Bursicon is a neuropeptide belonging to the cystine knot family and is composed of burs and partner of burs (pburs) subunits. It can form heterodimers or homodimers to execute different biological functions. Bursicon heterodimers regulate cuticle sclerotization and wing maturation, whereas bursicon homodimers mediate innate immunity and midgut stem cell proliferation. A recent study has shown that bursicon potentially induces the expression of vitellogenin (Vg) in the black tiger shrimp Penaeus monodon; however, the underlying mechanism remains unknown. In this study, we investigated the role of bursicon in the reproductive physiology of the red flour beetle, Tribolium castaneum. The knockdown of burs, pburs, or its receptor T. castaneum rickets (Tcrk) in 2-day pupae significantly downregulated the expression levels of Vg1, Vg2, and Vg receptor (VgR) genes in females 3- and 5-day post-adult emergence, leading to abnormal oocytes with limited Vg content. The silencing of burs repressed the number of eggs laid and completely inhibited egg hatch, whereas the silencing of pburs dramatically decreased the number of eggs laid, hatch rate, and offspring larval size, and this RNA interference (RNAi) effects persisted to the next generation. Furthermore, the knockdown of burs or pburs downregulated the expression of the insulin/insulin-like signaling/target of rapamycin (TOR) signaling genes encoding insulin receptor (InR), protein kinase B (Akt), TOR, and ribosomal protein S6 kinase (S6K). Most importantly, the injection of recombinant pburs (r-pburs) protein was able to upregulate the expression of Vg, VgR, InR, Akt, TOR, S6K, JH synthesis (JHAMT), Methoprene-tolerant (Met), and Taiman (Tai) in normal females and rescue the expression of Vg and VgR in pburs RNAi females but failed to rescue Vg and VgR in Tcrk knockdown females. We infer that bursicon homodimers influence Vg expression via the receptor Tcrk, possibly by mediating the expression of the juvenile hormone (JH) and IIS/TOR pathway genes, thereby regulating reproduction in T. castaneum.
Collapse
Affiliation(s)
- Jingjing Li
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Zidan Zhu
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States.,Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jingxiu Bi
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States.,Institution of Quality Standard and Testing Technology for Agro-Product, Shandong Academy of Agricultural Science, Jinan, China
| | - Qili Feng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Brenda T Beerntsen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, United States
| | - Qisheng Song
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| |
Collapse
|
22
|
Shukla A, Perales R, Kennedy S. piRNAs coordinate poly(UG) tailing to prevent aberrant and perpetual gene silencing. Curr Biol 2021; 31:4473-4485.e3. [PMID: 34428467 DOI: 10.1016/j.cub.2021.07.076] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/03/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Noncoding RNAs have emerged as mediators of transgenerational epigenetic inheritance (TEI) in a number of organisms. A robust example of such RNA-directed TEI is the inheritance of gene-silencing states following RNA interference (RNAi) in the metazoan C. elegans. During RNAi inheritance, gene silencing is transmitted by a self-perpetuating cascade of siRNA-directed poly(UG) tailing of mRNA fragments (pUGylation), followed by siRNA synthesis from poly(UG)-tailed mRNA templates (termed pUG RNA/siRNA cycling). Despite the self-perpetuating nature of pUG RNA/siRNA cycling, RNAi inheritance is finite, suggesting that systems likely exist to prevent indefinite RNAi-triggered gene silencing. Here we show that, in the absence of Piwi-interacting RNAs (piRNAs), an animal-specific class of small noncoding RNA, RNAi-based gene silencing can become essentially permanent, lasting at near 100% penetrance for more than 5 years and hundreds of generations. This perpetual gene silencing is mediated by continuous pUG RNA/siRNA cycling. Further, we find that piRNAs coordinate endogenous RNAi pathways to prevent germline-expressed genes, which are not normally subjected to TEI, from entering a state of continual and irreversible epigenetic silencing also mediated by continuous maintenance of pUG RNA/siRNA cycling. Together, our results show that one function of C. elegans piRNAs is to insulate germline-expressed genes from aberrant and runaway inactivation by the pUG RNA/siRNA epigenetic inheritance system.
Collapse
Affiliation(s)
- Aditi Shukla
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Roberto Perales
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA; Shape Therapeutics, Seattle, WA 98109, USA
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
23
|
Cecere G. Small RNAs in epigenetic inheritance: from mechanisms to trait transmission. FEBS Lett 2021; 595:2953-2977. [PMID: 34671979 PMCID: PMC9298081 DOI: 10.1002/1873-3468.14210] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 01/02/2023]
Abstract
Inherited information is transmitted to progeny primarily by the genome through the gametes. However, in recent years, epigenetic inheritance has been demonstrated in several organisms, including animals. Although it is clear that certain post‐translational histone modifications, DNA methylation, and noncoding RNAs regulate epigenetic inheritance, the molecular mechanisms responsible for epigenetic inheritance are incompletely understood. This review focuses on the role of small RNAs in transmitting epigenetic information across generations in animals. Examples of documented cases of transgenerational epigenetic inheritance are discussed, from the silencing of transgenes to the inheritance of complex traits, such as fertility, stress responses, infections, and behavior. Experimental evidence supporting the idea that small RNAs are epigenetic molecules capable of transmitting traits across generations is highlighted, focusing on the mechanisms by which small RNAs achieve such a function. Just as the role of small RNAs in epigenetic processes is redefining the concept of inheritance, so too our understanding of the molecular pathways and mechanisms that govern epigenetic inheritance in animals is radically changing.
Collapse
Affiliation(s)
- Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
| |
Collapse
|
24
|
|
25
|
Croft DP, Weiss MN, Nielsen MLK, Grimes C, Cant MA, Ellis S, Franks DW, Johnstone RA. Kinship dynamics: patterns and consequences of changes in local relatedness. Proc Biol Sci 2021; 288:20211129. [PMID: 34403632 PMCID: PMC8370800 DOI: 10.1098/rspb.2021.1129] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/26/2021] [Indexed: 01/16/2023] Open
Abstract
Mounting evidence suggests that patterns of local relatedness can change over time in predictable ways, a process termed kinship dynamics. Kinship dynamics may occur at the level of the population or social group, where the mean relatedness across all members of the population or group changes over time, or at the level of the individual, where an individual's relatedness to its local group changes with age. Kinship dynamics are likely to have fundamental consequences for the evolution of social behaviour and life history because they alter the inclusive fitness payoffs to actions taken at different points in time. For instance, growing evidence suggests that individual kinship dynamics have shaped the evolution of menopause and age-specific patterns of helping and harming. To date, however, the consequences of kinship dynamics for social evolution have not been widely explored. Here we review the patterns of kinship dynamics that can occur in natural populations and highlight how taking a kinship dynamics approach has yielded new insights into behaviour and life-history evolution. We discuss areas where analysing kinship dynamics could provide new insight into social evolution, and we outline some of the challenges in predicting and quantifying kinship dynamics in natural populations.
Collapse
Affiliation(s)
- Darren P. Croft
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Michael N. Weiss
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
- Center for Whale Research, Friday Harbour, WA, USA
| | - Mia L. K. Nielsen
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Charli Grimes
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Michael A. Cant
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall, UK
| | - Samuel Ellis
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Daniel W. Franks
- Department of Biology, University of York, York, UK
- Department of Computer Science, University of York, York, UK
| | - Rufus A. Johnstone
- Behaviour and Evolution Group, Department of Zoology, University of Cambridge, Cambridge, UK
| |
Collapse
|
26
|
Fare CM, Villani A, Drake LE, Shorter J. Higher-order organization of biomolecular condensates. Open Biol 2021; 11:210137. [PMID: 34129784 PMCID: PMC8205532 DOI: 10.1098/rsob.210137] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A guiding principle of biology is that biochemical reactions must be organized in space and time. One way this spatio-temporal organization is achieved is through liquid–liquid phase separation (LLPS), which generates biomolecular condensates. These condensates are dynamic and reactive, and often contain a complex mixture of proteins and nucleic acids. In this review, we discuss how underlying physical and chemical processes generate internal condensate architectures. We then outline the diverse condensate architectures that are observed in biological systems. Finally, we discuss how specific condensate organization is critical for specific biological functions.
Collapse
Affiliation(s)
- Charlotte M Fare
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - James Shorter
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
27
|
Frolows N, Ashe A. Small RNAs and chromatin in the multigenerational epigenetic landscape of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200112. [PMID: 33866817 DOI: 10.1098/rstb.2020.0112] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
For decades, it was thought that the only heritable information transmitted from one individual to another was that encoded in the DNA sequence. However, it has become increasingly clear that this is not the case and that the transmission of molecules from within the cytoplasm of the gamete also plays a significant role in heritability. The roundworm, Caenorhabditis elegans, has emerged as one of the leading model organisms in which to study the mechanisms of transgenerational epigenetic inheritance (TEI). Collaborative efforts over the past few years have revealed that RNA molecules play a critical role in transmitting transgenerational responses, but precisely how they do so is as yet uncertain. In addition, the role of histone modifications in epigenetic inheritance is increasingly apparent, and RNA and histones interact in a way that we do not yet fully understand. Furthermore, both exogenous and endogenous RNA molecules, as well as other environmental triggers, are able to induce heritable epigenetic changes that affect transcription across the genome. In most cases, these epigenetic changes last only for a handful of generations, but occasionally can be maintained much longer: perhaps indefinitely. In this review, we discuss the current understanding of the role of RNA and histones in TEI, as well as making clear the gaps in our knowledge. We also speculate on the evolutionary implications of epigenetic inheritance, particularly in the context of a short-lived, clonally propagating species. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
Collapse
Affiliation(s)
- Natalya Frolows
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia.,CSIRO Health and Biosecurity, Sydney, New South Wales, 2113, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| |
Collapse
|
28
|
Veigl SJ. Small RNA research and the scientific repertoire: a tale about biochemistry and genetics, crops and worms, development and disease. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:30. [PMID: 33624250 DOI: 10.1007/s40656-021-00382-x] [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: 05/17/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
The discovery of RNA interference in 1998 has made a lasting impact on biological research. Identifying the regulatory role of small RNAs changed the modes of molecular biological inquiry as well as biologists' understanding of genetic regulation. This article examines the early years of small RNA biology's success story. I query which factors had to come together so that small RNA research came into life in the blink of an eye. I primarily look at scientific repertoires as facilitators of rapid scientific change. I show that for a short period of time, between the years 1998 and 2002, different model organism communities, investigative strategies, technological innovations, and research interests could be successfully aligned to take small RNA research off the ground. I discuss how the keystone discoveries were situated in specific experimental traditions and what strategies were employed to establish these discoveries as more general phenomena. Providing thus a practice-based approach of rapid scientific change, I ask how to relate the change in propositional bits of scientific knowledge with changes in scientific practice.
Collapse
Affiliation(s)
- Sophie Juliane Veigl
- Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv, Israel.
| |
Collapse
|
29
|
How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans? Biochem Soc Trans 2021; 48:1019-1034. [PMID: 32539084 DOI: 10.1042/bst20190944] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022]
Abstract
Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.
Collapse
|
30
|
Wan G, Bajaj L, Fields B, Dodson AE, Pagano D, Fei Y, Kennedy S. ZSP-1 is a Z granule surface protein required for Z granule fluidity and germline immortality in Caenorhabditis elegans. EMBO J 2021; 40:e105612. [PMID: 33438773 DOI: 10.15252/embj.2020105612] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 12/02/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Germ granules are biomolecular condensates that form in germ cells of all/most animals, where they regulate mRNA expression to promote germ cell function and totipotency. In the adult Caenorhabditis elegans germ cell, these granules are composed of at least four distinct sub-compartments, one of which is the Z granule. To better understand the role of the Z granule in germ cell biology, we conducted a genetic screen for genes specifically required for Z granule assembly or morphology. Here, we show that zsp-1, which encodes a low-complexity/polyampholyte-domain protein, is required for Z granule homeostasis. ZSP-1 localizes to the outer surface of Z granules. In the absence of ZSP-1, Z granules swell to an abnormal size, fail to segregate with germline blastomeres during development, and lose their liquid-like character. Finally, ZSP-1 promotes piRNA- and siRNA-directed gene regulation and germline immortality. Our data suggest that Z granules coordinate small RNA-based gene regulation to promote germ cell function and that ZSP-1 helps/is need to maintain Z granule morphology and liquidity.
Collapse
Affiliation(s)
- Gang Wan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, GuangZhou, GuangDong, China.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Lakshya Bajaj
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brandon Fields
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anne E Dodson
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel Pagano
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yuhan Fei
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
31
|
Lev I, Rechavi O. Germ Granules Allow Transmission of Small RNA-Based Parental Responses in the "Germ Plasm". iScience 2020; 23:101831. [PMID: 33305186 PMCID: PMC7718480 DOI: 10.1016/j.isci.2020.101831] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the recent decade small RNA-based inheritance has been implicated in a variety of transmitted physiological responses to the environment. In Caenorhabditis elegans, heritable small RNAs rely on RNA-dependent RNA polymerases, RNA-processing machinery, chromatin modifiers, and argonauts for their biogenesis and gene-regulatory effects. Importantly, many of these factors reside in evolutionary conserved germ granules that are required for maintaining germ cell identity and gene expression. Recent literature demonstrated that transient disturbance to the stability of the germ granules leads to changes in the pools of heritable small RNAs and the physiology of the progeny. In this piece, we discuss the heritable consequences of transient destabilization of germ granules and elaborate on the various small RNA-related processes that act in the germ granules. We further propose that germ granules may serve as environment sensors that translate environmental changes to inheritable small RNA-based responses.
Collapse
Affiliation(s)
- Itamar Lev
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
32
|
Ewe CK, Alok G, Rothman JH. Stressful development: integrating endoderm development, stress, and longevity. Dev Biol 2020; 471:34-48. [PMID: 33307045 DOI: 10.1016/j.ydbio.2020.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
In addition to performing digestion and nutrient absorption, the intestine serves as one of the first barriers to the external environment, crucial for protecting the host from environmental toxins, pathogenic invaders, and other stress inducers. The gene regulatory network (GRN) governing embryonic development of the endoderm and subsequent differentiation and maintenance of the intestine has been well-documented in C. elegans. A key regulatory input that initiates activation of the embryonic GRN for endoderm and mesoderm in this animal is the maternally provided SKN-1 transcription factor, an ortholog of the vertebrate Nrf1 and 2, which, like C. elegans SKN-1, perform conserved regulatory roles in mediating a variety of stress responses across metazoan phylogeny. Other key regulatory factors in early gut development also participate in stress response as well as in innate immunity and aging and longevity. In this review, we discuss the intersection between genetic nodes that mediate endoderm/intestine differentiation and regulation of stress and homeostasis. We also consider how direct signaling from the intestine to the germline, in some cases involving SKN-1, facilitates heritable epigenetic changes, allowing transmission of adaptive stress responses across multiple generations. These connections between regulation of endoderm/intestine development and stress response mechanisms suggest that varying selective pressure exerted on the stress response pathways may influence the architecture of the endoderm GRN, thereby leading to genetic and epigenetic variation in early embryonic GRN regulatory events.
Collapse
Affiliation(s)
- Chee Kiang Ewe
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Geneva Alok
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Joel H Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| |
Collapse
|
33
|
Mao K, Breen P, Ruvkun G. Mitochondrial dysfunction induces RNA interference in C. elegans through a pathway homologous to the mammalian RIG-I antiviral response. PLoS Biol 2020; 18:e3000996. [PMID: 33264285 PMCID: PMC7735679 DOI: 10.1371/journal.pbio.3000996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/14/2020] [Accepted: 11/09/2020] [Indexed: 12/27/2022] Open
Abstract
RNA interference (RNAi) is an antiviral pathway common to many eukaryotes that detects and cleaves foreign nucleic acids. In mammals, mitochondrially localized proteins such as mitochondrial antiviral signaling (MAVS), retinoic acid-inducible gene I (RIG-I), and melanoma differentiation-associated protein 5 (MDA5) mediate antiviral responses. Here, we report that mitochondrial dysfunction in Caenorhabditis elegans activates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. The induction of RNAi also requires the conserved RNA decapping enzyme EOL-1/DXO. The transcriptional induction of eol-1 requires DRH-1 as well as the mitochondrial unfolded protein response (UPRmt). Upon mitochondrial dysfunction, EOL-1 is concentrated into foci that depend on the transcription of mitochondrial RNAs that may form double-stranded RNA (dsRNA), as has been observed in mammalian antiviral responses. Enhanced RNAi triggered by mitochondrial dysfunction is necessary for the increase in longevity that is induced by mitochondrial dysfunction. Surveillance of mitochondrial dysfunction in the nematode Caenorhabditis elegans triggers the activation of an RNA interference pathway to mediate antiviral defense, in a manner homologous to the mammalian RIG-I helicase viral response pathway.
Collapse
Affiliation(s)
- Kai Mao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
34
|
Evidence For Long-Lasting Transgenerational Antiviral Immunity in Insects. Cell Rep 2020; 33:108506. [PMID: 33326778 PMCID: PMC7758158 DOI: 10.1016/j.celrep.2020.108506] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/04/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Transgenerational immune priming (TGIP) allows memory-like immune responses to be transmitted from parents to offspring in many invertebrates. Despite increasing evidence for TGIP in insects, the mechanisms involved in the transfer of information remain largely unknown. Here, we show that Drosophila melanogaster and Aedes aegypti transmit antiviral immunological memory to their progeny that lasts throughout generations. We observe that TGIP, which is virus and sequence specific but RNAi independent, is initiated by a single exposure to disparate RNA viruses and also by inoculation of a fragment of viral double-stranded RNA. The progeny, which inherit a viral DNA that is only a fragment of the viral RNA used to infect the parents, display enriched expression of genes related to chromatin and DNA binding. These findings represent a demonstration of TGIP for RNA viruses in invertebrates, broadly increasing our understanding of the immune response, host genome plasticity, and antiviral memory of the germline.
Collapse
|
35
|
Wan G, Yan J, Fei Y, Pagano DJ, Kennedy S. A Conserved NRDE-2/MTR-4 Complex Mediates Nuclear RNAi in Caenorhabditis elegans. Genetics 2020; 216:1071-1085. [PMID: 33055090 PMCID: PMC7768265 DOI: 10.1534/genetics.120.303631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022] Open
Abstract
Small regulatory RNAs, such as small interfering RNAs (siRNAs) and PIWI-interacting RNAs, regulate splicing, transcription, and genome integrity in many eukaryotes. In Caenorhabditis elegans, siRNAs bind nuclear Argonautes (AGOs), which interact with homologous premessenger RNAs to recruit downstream silencing effectors, such as NRDE-2, to direct cotranscriptional gene silencing [or nuclear RNA interference (RNAi)]. To further our understanding of the mechanism of nuclear RNAi, we conducted immunoprecipitation-mass spectrometry on C. elegans NRDE-2 The major NRDE-2 interacting protein identified was the RNA helicase MTR-4 Co-immunoprecipitation analyses confirmed a physical association between NRDE-2 and MTR-4 MTR-4 colocalizes with NRDE-2 within the nuclei of most/all C. elegans somatic and germline cells. MTR-4 is required for nuclear RNAi, and interestingly, MTR-4 is recruited to premessenger RNAs undergoing nuclear RNAi via a process requiring nuclear siRNAs, the nuclear AGO HRDE-1, and NRDE-2, indicating that MTR-4 is a component of the C. elegans nuclear RNAi machinery. Finally, we confirm previous reports showing that human (Hs)NRDE2 and HsMTR4 also physically interact. Our data show that the NRDE-2/MTR-4 interactions are evolutionarily conserved, and that, in C. elegans, the NRDE-2/MTR-4 complex contributes to siRNA-directed cotranscriptional gene silencing.
Collapse
Affiliation(s)
- Gang Wan
- Ministry Of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China 510275
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
| | - Jenny Yan
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
| | - Yuhan Fei
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China 210095
| | - Daniel J Pagano
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
| |
Collapse
|
36
|
Du X, McManus DP, French JD, Jones MK, You H. CRISPR/Cas9: A new tool for the study and control of helminth parasites. Bioessays 2020; 43:e2000185. [PMID: 33145822 DOI: 10.1002/bies.202000185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022]
Abstract
Recent reports of CRISPR/Cas9 genome editing in parasitic helminths open up new avenues for research on these dangerous pathogens. However, the complex morphology and life cycles inherent to these parasites present obstacles for the efficient application of CRISPR/Cas9-targeted mutagenesis. This is especially true with the trematode flukes where only modest levels of gene mutation efficiency have been achieved. Current major challenges in the application of CRISPR/Cas9 for study of parasitic worms thus lie in enhancing gene mutation efficiency and overcoming issues involved in host passage so that mutated parasites survive. Strategies developed for CRISPR/Cas9 studies on Caenorhabditis elegans, protozoa and mammalian cells, including novel delivery methods, the choice of selectable markers, and refining mutation precision represent novel tactics whereby these impediments can be overcome. Furthermore, employing CRISPR/Cas9-mediated gene drive to interfere with vector transmission represents a novel approach for the control of parasitic worms that is worthy of further exploration.
Collapse
Affiliation(s)
- Xiaofeng Du
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Juliet D French
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Malcolm K Jones
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| |
Collapse
|
37
|
Shakeel M, Du J, Li SW, Zhou YJ, Sarwar N, Bukhari SAH. Characterization, Knockdown and Parental Effect of Hexokinase Gene of Cnaphalocrocis medinalis (Lepidoptera: Pyralidae) Revealed by RNA Interference. Genes (Basel) 2020; 11:genes11111258. [PMID: 33114530 PMCID: PMC7693289 DOI: 10.3390/genes11111258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
Hexokinase (HK) is a key enzyme in chitin biosynthesis in insects and plays an important role in development and energy regulation. It also performs a crucial role in the synthesis of Glucose-6-phosphate and its putative functions are studied via injection of dsRNA corresponding to the hexokinase gene from Cnaphalocrocis medinalis (CmHK). This study was designed to analyze the characteristics and expression patterns of HK-related genes in various tissues of C. medinalis at different developmental stages. The CmHK ORF is a 1359 bp in length, encoding a protein of 452 amino acids, with homology and cluster analysis showing that CmHK shares an 85.11% sequence similarity with hexokinase from Ostrinia furnacalis.CmHK was highly expressed in the ovary and in the fifth instar larvae. Injection of dsCmHK significantly suppressed mRNA expression (73.6%) 120 h post-dsRNA injection as compared to a control group. The results demonstrated an increased incidence of larval and pupal mortality of 80% and 78%, respectively, with significant variation in the sex ratio between males (68.33%) and females (35%), overt larval deformities, and a reduction in average weight gain observed 120 h post-dsRNA injection. In addition, dsCmHK-injected C. medinalis showed a significant reduction in ovulation per female and larval hatching rate, along with increased larval and pupal mortality and variation in male and female emergence over three generations (G1, G2, and G3). Taken together, the outcomes of the study provide a foundation to study gene function and a new dimension to control C. medinalis by transgenic RNAi technology.
Collapse
Affiliation(s)
- Muhammad Shakeel
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China; (M.S.); (J.D.); (Y.-J.Z.)
| | - Juan Du
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China; (M.S.); (J.D.); (Y.-J.Z.)
| | - Shang-Wei Li
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China; (M.S.); (J.D.); (Y.-J.Z.)
- Correspondence: ; Tel.: +86-137-6506-6957
| | - Yuan-Jin Zhou
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang, Guizhou 550025, China; (M.S.); (J.D.); (Y.-J.Z.)
| | - Naeem Sarwar
- Department of Agronomy, Bahauddin Zakariya University, Multan 60800, Pakistan; (N.S.); (S.A.H.B.)
| | | |
Collapse
|
38
|
Pereira AG, Gracida X, Kagias K, Zhang Y. C. elegans aversive olfactory learning generates diverse intergenerational effects. J Neurogenet 2020; 34:378-388. [PMID: 32940103 DOI: 10.1080/01677063.2020.1819265] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Parental experience can modulate the behavior of their progeny. While the molecular mechanisms underlying parental effects or inheritance of behavioral traits have been studied under several environmental conditions, it remains largely unexplored how the nature of parental experience affects the information transferred to the next generation. To address this question, we used C. elegans, a nematode that feeds on bacteria in its habitat. Some of these bacteria are pathogenic and the worm learns to avoid them after a brief exposure. We found, unexpectedly, that a short parental experience increased the preference for the pathogen in the progeny. Furthermore, increasing the duration of parental exposure switched the response of the progeny from attraction to avoidance. To characterize the underlying molecular mechanisms, we found that the RNA-dependent RNA Polymerase (RdRP) RRF-3, required for the biogenesis of 26 G endo-siRNAs, regulated both types of intergenerational effects. Together, we show that different parental experiences with the same environmental stimulus generate different effects on the behavior of the progeny through small RNA-mediated regulation of gene expression.
Collapse
Affiliation(s)
- Ana Goncalves Pereira
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Xicotencatl Gracida
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Konstantinos Kagias
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yun Zhang
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| |
Collapse
|
39
|
Houri-Zeevi L, Korem Kohanim Y, Antonova O, Rechavi O. Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans. Cell 2020; 182:1186-1197.e12. [PMID: 32841602 PMCID: PMC7479518 DOI: 10.1016/j.cell.2020.07.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/21/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
Experiences trigger transgenerational small RNA-based responses in C. elegans nematodes. Dedicated machinery ensures that heritable effects are reset, but how the responses segregate in the population is unknown. We show that isogenic individuals differ dramatically in the persistence of transgenerational responses. By examining lineages of more than 20,000 worms, three principles emerge: (1) The silencing each mother initiates is distributed evenly among her descendants; heritable RNAi dissipates but is uniform in every generation. (2) Differences between lineages arise because the mothers that initiate heritable responses stochastically assume different "inheritance states" that determine the progeny's fate. (3) The likelihood that an RNAi response would continue to be inherited increases the more generations it lasts. The inheritance states are determined by HSF-1, which regulates silencing factors and, accordingly, small RNA levels. We found that, based on the parents' inheritance state, the descendants' developmental rate in response to stress can be predicted.
Collapse
Affiliation(s)
- Leah Houri-Zeevi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Yael Korem Kohanim
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Olga Antonova
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|
40
|
Schwartz-Orbach L, Zhang C, Sidoli S, Amin R, Kaur D, Zhebrun A, Ni J, Gu SG. Caenorhabditis elegans nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3. eLife 2020; 9:e54309. [PMID: 32804637 PMCID: PMC7431132 DOI: 10.7554/elife.54309] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 08/04/2020] [Indexed: 12/29/2022] Open
Abstract
Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies have indicated that the regulation and function of nuclear RNAi-mediated heterochromatin are highly complex. Our knowledge of histone modifications and the corresponding histonemodifying enzymes involved in the system remains limited. In this study, we show that the heterochromatin mark, H3K23me3, is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, dsRNA-induced H3K23me3 can persist for multiple generations after the dsRNA exposure has stopped. We demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as an additional chromatin modification in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.
Collapse
Affiliation(s)
- Lianna Schwartz-Orbach
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Chenzhen Zhang
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, BronxNew YorkUnited States
| | - Richa Amin
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Diljeet Kaur
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Anna Zhebrun
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Julie Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Sam G Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| |
Collapse
|
41
|
Camacho MP. What's all the fuss about? The inheritance of acquired traits is compatible with the Central Dogma. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:32. [PMID: 32691291 DOI: 10.1007/s40656-020-00329-8] [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: 02/04/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
The Central Dogma of molecular biology, which holds that DNA makes protein and not the other way around, is as influential as it is controversial. Some believe the Dogma has outlived its usefulness, either because it fails to fully capture the ins-and-outs of protein synthesis (Griffiths and Stotz in Genetics and philosophy Cambridge introductions to philosophy and biology, Cambridge University Press, Cambridge, 2013; Stotz in Hist Philos Life Sci 28(4):533-548, 2006), because it turns on a confused notion of information (Sarkar in Molecular models of life, MIT Press, Cambridge, 2004), or because it problematically assumes the unidirectional flow of information from DNA to protein (Gottlieb, in: Oyama, Griffiths, Gray (eds), Cycles of contingency: developmental systems and evolution, MIT Press, Cambridge, 2001). This paper evaluates an underexplored defense of the Dogma, which relies on the assumption that the Dogma and the Inheritance of Acquired Traits, a principle which dates as far back as Jean Baptiste-Lamarck, are incompatible principles (Smith in The theory of evolution, Cambridge University Press, Cambridge, 1993; Judson in The eighth day of creation, Jonathan Cape, London, 1979; Dawkins in The extended phenotype, Oxford University Press, Oxford, 1970; Cobb in PLoS Biol 15(9):e2003243, 2017. https://doi.org/10.1371/journal.pbio.2003243 ; Wilkins in BioEssays 24(10):960-973, 2002. https://doi.org/10.1002/bies.10167 ; Graur The fallacious commingling of two unrelated hypotheses: 'the central dogma' and 'dna makes rna makes protein'. Judge Starling., 2018. http://judgestarling.tumblr.com/post/177554581856/the-fallacious-commingling-of-two-unrelated ). By appealing to empirical evidence in molecular science, I argue that this apparent incompatibility is indeed merely apparent. I conclude by briefly demonstrating how these considerations bear on the topic of conceptual pluralism in the philosophy of science (Stencel and Proszewska in Found Sci 23(4):603-620, 2018. https://doi.org/10.1007/s10699-017-9543-x ; Lu and Bourrat in Br J Philos Sci 69(3):775-800, 2018. https://doi.org/10.1093/bjps/axx019 ).
Collapse
Affiliation(s)
- M Polo Camacho
- University of Kansas, 1445 Jayhawk Blvd., Wescoe Hall, Room 3108, Lawrence, KS, 66045-7590, USA.
| |
Collapse
|
42
|
Tavares NC, Gava SG, Torres GP, de Paiva CÊS, Moreira BP, Lunkes FMN, Montresor LC, Caldeira RL, Mourão MM. Schistosoma mansoni FES Tyrosine Kinase Involvement in the Mammalian Schistosomiasis Outcome and Miracidia Infection Capability in Biomphalaria glabrata. Front Microbiol 2020; 11:963. [PMID: 32595609 PMCID: PMC7300192 DOI: 10.3389/fmicb.2020.00963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
Schistosomiasis is a neglected tropical disease (NTD) caused by helminthes from the Schistosoma genus. This NTD can cause systemic symptoms induced by the deposition of parasite eggs in the host liver, promoting severe complications. Functional studies to increase knowledge about parasite biology are required for the identification of new drug targets, because the treatment is solely based on praziquantel administration, a drug in which the mechanism of action is still unknown. Protein kinases are important for cellular adaptation and maintenance of many organisms homeostasis and, thus, are considered good drug targets for many pathologies. Accordingly, those proteins are also important for Schistosoma mansoni, as the parasite relies on specific environmental signals to develop into its different stages. However, the specific roles of protein kinases in S. mansoni biology are not well understood. This work aims at investigating the tyrosine-protein kinase FES (Feline Sarcoma) functions in the maintenance of S. mansoni life cycle, especially in the establishment of mammalian and invertebrate hosts' infection. In this regard, the verification of Smfes expression among S. mansoni stages showed that Smfes is more expressed in infective free-living stages: miracidia and cercariae. Schistosomula exposed to SmFES-dsRNA in vitro presented a reduction in movement and size and increased mortality. Mice infected with Smfes-knocked-down schistosomula exhibited a striking reduction in the area of liver granuloma and an increased rate of immature eggs in the intestine. Female adult worms recovered from mice presented a reduced size and changes in the ovary and vitellarium; and males exhibited damage in the gynecophoral canal. Subsequently, miracidia hatched from eggs exposed to SmFES-dsRNA presented changes in its capability to infect and to sense the snail mucus. In addition, the SmFES RNAi effect was stable from miracidia to cercariae. The establishment of infection with those cercariae reproduced the same alterations observed for the knocked-down schistosomula infection. Our findings show that SmFES tyrosine kinase (1) is important in schistosomula development and survival; (2) has a role in adult worms pairing and, consequently, female maturation; (3) might be essential for egg antigen expression, thus responsible for inducing granuloma formation and immunomodulation; and (4) is essential for miracidia infection capability. In addition, this is the first time that a gene is kept knocked down during three different S. mansoni life stages and that a tyrosine kinase is implicated in the parasite reproduction and infection establishment in the mammalian host. Accordingly, SmFES should be explored as an alternative to support schistosomiasis treatment and morbidity control.
Collapse
Affiliation(s)
- Naiara Clemente Tavares
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Sandra Grossi Gava
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Gabriella Parreiras Torres
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Clara Ênia Soares de Paiva
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Bernardo Pereira Moreira
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Felipe Miguel Nery Lunkes
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Langia Colli Montresor
- Moluscário Lobato Paraense, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Roberta Lima Caldeira
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Marina Moraes Mourão
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| |
Collapse
|
43
|
poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature 2020; 582:283-288. [PMID: 32499657 PMCID: PMC8396162 DOI: 10.1038/s41586-020-2323-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/16/2020] [Indexed: 12/17/2022]
Abstract
Mobile genetic elements threaten genome integrity in all organisms. MUT-2/RDE-3 is a ribonucleotidyltransferase required for transposon silencing and RNA interference (RNAi) in C. elegans1–4. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3’ termini of these RNAs (poly(UG) or pUG tails)5. Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNAi, as well as to transposon RNAs. pUG tails with more than 16 perfectly alternating 3’ U and G nucleotides convert RNA fragments into agents of gene silencing. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases (RdRPs), which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA–templated siRNA synthesis and siRNA-directed mRNA pUGylation underlie dsRNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA/siRNA silencing loop allows parents to inoculate progeny against the expression of unwanted or parasitic genetic elements
Collapse
|
44
|
Tung A, Levin M. Extra-genomic instructive influences in morphogenesis: A review of external signals that regulate growth and form. Dev Biol 2020; 461:1-12. [PMID: 31981561 DOI: 10.1016/j.ydbio.2020.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
Embryonic development and regeneration accomplish a remarkable feat: individual cells work together to create or repair complex anatomical structures. What is the source of the instructive signals that specify these invariant and robust organ-level outcomes? The most frequently studied source of morphogenetic control is the host genome and its transcriptional circuits. However, it is now apparent that significant information affecting patterning also arrives from outside of the body. Both biotic and physical factors, including temperature and various molecular signals emanating from pathogens, commensals, and conspecific organisms, affect developmental outcomes. Here, we review examples in which anatomical patterning decisions are strongly impacted by lateral signals that originate from outside of the zygotic genome. The endogenous pathways targeted by these influences often show transgenerational effects, enabling them to shape the evolution of anatomies even faster than traditional Baldwin-type assimilation. We also discuss recent advances in the biophysics of morphogenetic controls and speculate on additional sources of important patterning information which could be exploited to better understand the evolution of bodies and to design novel approaches for regenerative medicine.
Collapse
Affiliation(s)
- Angela Tung
- Department of Biology and Allen Discovery Center at Tufts University, Medford, MA, USA
| | - Michael Levin
- Department of Biology and Allen Discovery Center at Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| |
Collapse
|
45
|
Small RNAs in the Transgenerational Inheritance of Epigenetic Information. Trends Genet 2020; 36:203-214. [DOI: 10.1016/j.tig.2019.12.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/19/2019] [Accepted: 12/06/2019] [Indexed: 01/21/2023]
|
46
|
Colicchio JM, Herman J. Empirical patterns of environmental variation favor adaptive transgenerational plasticity. Ecol Evol 2020; 10:1648-1665. [PMID: 32076541 PMCID: PMC7029079 DOI: 10.1002/ece3.6022] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 12/16/2019] [Indexed: 12/27/2022] Open
Abstract
Effects of parental environment on offspring traits have been well known for decades. Interest in this transgenerational form of phenotypic plasticity has recently surged due to advances in our understanding of its mechanistic basis. Theoretical research has simultaneously advanced by predicting the environmental conditions that should favor the adaptive evolution of transgenerational plasticity. Yet whether such conditions actually exist in nature remains largely unexplored. Here, using long-term climate data, we modeled optimal levels of transgenerational plasticity for an organism with a one-year life cycle at a spatial resolution of 4 km2 across the continental United States. Both annual temperature and precipitation levels were often autocorrelated, but the strength and direction of these autocorrelations varied considerably even among nearby sites. When present, such environmental autocorrelations render offspring environments statistically predictable based on the parental environment, a key condition for the adaptive evolution of transgenerational plasticity. Results of our optimality models were consistent with this prediction: High levels of transgenerational plasticity were favored at sites with strong environmental autocorrelations, and little-to-no transgenerational plasticity was favored at sites with weak or nonexistent autocorrelations. These results are among the first to show that natural patterns of environmental variation favor the evolution of adaptive transgenerational plasticity. Furthermore, these findings suggest that transgenerational plasticity is likely variable in nature, depending on site-specific patterns of environmental variation.
Collapse
Affiliation(s)
- Jack M. Colicchio
- Department of Plant and Microbial BiologyUniversity of California BerkeleyBerkeleyCAUSA
| | - Jacob Herman
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| |
Collapse
|
47
|
Woodhouse RM, Buchmann G, Hoe M, Harney DJ, Low JKK, Larance M, Boag PR, Ashe A. Chromatin Modifiers SET-25 and SET-32 Are Required for Establishment but Not Long-Term Maintenance of Transgenerational Epigenetic Inheritance. Cell Rep 2019; 25:2259-2272.e5. [PMID: 30463020 DOI: 10.1016/j.celrep.2018.10.085] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 09/25/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Some epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNAi phenotypes in Caenorhabditis elegans provides an excellent model to study this phenomenon, and although studies have implicated both chromatin modifications and small RNA pathways in heritable silencing, their relative contributions remain unclear. Here, we demonstrate that the putative histone methyltransferases SET-25 and SET-32 are required for establishment of a transgenerational silencing signal but not for long-term maintenance of this signal between subsequent generations, suggesting that transgenerational epigenetic inheritance is a multi-step process with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNAs (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.
Collapse
Affiliation(s)
- Rachel M Woodhouse
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Gabriele Buchmann
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Matthew Hoe
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Dylan J Harney
- The University of Sydney, Charles Perkins Centre, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Jason K K Low
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Mark Larance
- The University of Sydney, Charles Perkins Centre, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Peter R Boag
- Monash University, Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Clayton, VIC 3800, Australia
| | - Alyson Ashe
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia; The University of Wollongong, School of Biological Sciences and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| |
Collapse
|
48
|
Xu F, Feng X, Chen X, Weng C, Yan Q, Xu T, Hong M, Guang S. A Cytoplasmic Argonaute Protein Promotes the Inheritance of RNAi. Cell Rep 2019; 23:2482-2494. [PMID: 29791857 DOI: 10.1016/j.celrep.2018.04.072] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/24/2018] [Accepted: 04/16/2018] [Indexed: 01/02/2023] Open
Abstract
RNAi-elicited gene silencing is heritable and can persist for multiple generations after its initial induction in C. elegans. However, the mechanism by which parental-acquired trait-specific information from RNAi is inherited by the progenies is not fully understood. Here, we identified a cytoplasmic Argonaute protein, WAGO-4, necessary for the inheritance of RNAi. WAGO-4 exhibits asymmetrical translocation to the germline during early embryogenesis, accumulates at the perinuclear foci in the germline, and is required for the inheritance of exogenous RNAi targeting both germline- and soma-expressed genes. WAGO-4 binds to 22G-RNAs and their mRNA targets. Interestingly, WAGO-4-associated endogenous 22G-RNAs target the same cohort of germline genes as CSR-1 and contain untemplated addition of uracil at the 3' ends. The poly(U) polymerase CDE-1 is required for the untemplated uridylation of 22G-RNAs and inheritance of RNAi. Therefore, we conclude that, in addition to the nuclear RNAi pathway, the cytoplasmic RNAi machinery also promotes RNAi inheritance.
Collapse
Affiliation(s)
- Fei Xu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiangyang Chen
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chenchun Weng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Qi Yan
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ting Xu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Minjie Hong
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
49
|
Richard G, Le Trionnaire G, Danchin E, Sentis A. Epigenetics and insect polyphenism: mechanisms and climate change impacts. CURRENT OPINION IN INSECT SCIENCE 2019; 35:138-145. [PMID: 31557627 DOI: 10.1016/j.cois.2019.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 06/10/2023]
Abstract
Phenotypic plasticity is a ubiquitous process found in all living organisms. Polyphenism is an extreme case of phenotypic plasticity which shares a common scheme in insects such as honeybees, locusts or aphids: an initial perception of environmental stimuli, a neuroendocrine transmission of these signals to the target tissues, the activation of epigenetic mechanisms allowing the setup of alternative transcriptional programs responsible for the establishment of discrete phenotypes. Climate change can modulate the environmental stimuli triggering polyphenisms, and/or some epigenetics marks, thus modifying on the short and long terms the discrete phenotype proportions within populations. This might result in critical ecosystem changes.
Collapse
Affiliation(s)
- Gautier Richard
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany; IGEPP, INRA, Agrocampus Ouest, Univ Rennes, 35600 Le Rheu, France
| | | | - Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse, CNRS, IRD. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Arnaud Sentis
- IRSTEA, Aix Marseille Univ., UMR RECOVER, 3275 route Cézanne, 13182 Aix-en-Provence, France
| |
Collapse
|
50
|
Gaps and barriers: Gap junctions as a channel of communication between the soma and the germline. Semin Cell Dev Biol 2019; 97:167-171. [PMID: 31558347 DOI: 10.1016/j.semcdb.2019.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022]
Abstract
Gap junctions, expressed in most tissues of the body, allow for the cytoplasmic coupling of adjacent cells and promote tissue cooperation. Gap junctions connect also the soma and the germline in many animals, and transmit somatic signals that are crucial for germline maturation and integrity. In this review, we examine the involvement of gap junctions in the relay of information between the soma and the germline, and ask whether such communication could have consequences for the progeny. While the influence of parental experiences on descendants is of great interest, the possibility that gap junctions participate in the transmission of information across generations is largely unexplored.
Collapse
|