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Baduel P, Sammarco I, Barrett R, Coronado‐Zamora M, Crespel A, Díez‐Rodríguez B, Fox J, Galanti D, González J, Jueterbock A, Wootton E, Harney E. The evolutionary consequences of interactions between the epigenome, the genome and the environment. Evol Appl 2024; 17:e13730. [PMID: 39050763 PMCID: PMC11266121 DOI: 10.1111/eva.13730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/30/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024] Open
Abstract
The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'Ecole Normale SupérieurePSL University, CNRSParisFrance
| | - Iris Sammarco
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
| | - Rowan Barrett
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | | | | | | | - Janay Fox
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Dario Galanti
- Institute of Evolution and Ecology (EvE)University of TuebingenTübingenGermany
| | | | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Eric Wootton
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Ewan Harney
- Institute of Evolutionary BiologyCSIC, UPFBarcelonaSpain
- School of BiosciencesUniversity of SheffieldSheffieldUK
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2
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Phillips D, Noble D. Bubbling beyond the barrier: exosomal RNA as a vehicle for soma-germline communication. J Physiol 2024; 602:2547-2563. [PMID: 37936475 DOI: 10.1113/jp284420] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
'Weismann's barrier' has restricted theories of heredity to the transmission of genomic variation for the better part of a century. However, the discovery and elucidation of epigenetic mechanisms of gene regulation such as DNA methylation and histone modifications has renewed interest in studies on the inheritance of acquired traits and given them mechanistic plausibility. Although it is now clear that these mechanisms allow many environmentally acquired traits to be transmitted to the offspring, how phenotypic information is communicated from the body to its gametes has remained a mystery. Here, we discuss recent evidence that such communication is mediated by somatic RNAs that travel inside extracellular vesicles to the gametes where they reprogram the offspring epigenome and phenotype. How gametes learn about bodily changes has implications not only for the clinic, but also for evolutionary theory by bringing together intra- and intergenerational mechanisms of phenotypic plasticity and adaptation.
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Affiliation(s)
- Daniel Phillips
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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3
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Frézal L, Saglio M, Zhang G, Noble L, Richaud A, Félix MA. Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans. EMBO Rep 2023; 24:e58116. [PMID: 37983674 DOI: 10.15252/embr.202358116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, leading to sterility after several generations at 25°C. Using a genome-wide association approach, we detect a significant peak on chromosome III around 5 Mb, confirmed by introgressions. Thus, a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation, and indeed associated bacteria and microsporidia suppress the phenotype of wild isolates as well as mutants in small RNA inheritance (nrde-2) and histone modifications (set-2). Escherichia coli strains of the K-12 lineage suppress the phenotype compared to B strains. By shifting a wild strain from E. coli K-12 to E. coli B, we find that memory of the suppressing condition is maintained over several generations. Thus, the mortal germline phenotype of wild C. elegans is in part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non-genetic memory in the face of environmental variation.
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Affiliation(s)
- Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie Saglio
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Gaotian Zhang
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Luke Noble
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
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4
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Deshe N, Eliezer Y, Hoch L, Itskovits E, Bokman E, Ben-Ezra S, Zaslaver A. Inheritance of associative memories and acquired cellular changes in C. elegans. Nat Commun 2023; 14:4232. [PMID: 37454110 PMCID: PMC10349803 DOI: 10.1038/s41467-023-39804-8] [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: 11/12/2020] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Experiences have been shown to modulate behavior and physiology of future generations in some contexts, but there is limited evidence for inheritance of associative memory in different species. Here, we trained C. elegans nematodes to associate an attractive odorant with stressful starvation conditions and revealed that this associative memory was transmitted to the F1 progeny who showed odor-evoked avoidance behavior. Moreover, the F1 and the F2 descendants of trained animals exhibited odor-evoked cellular stress responses, manifested by the translocation of DAF-16/FOXO to cells' nuclei. Sperm, but not oocytes, transmitted these odor-evoked cellular stress responses which involved H3K9 and H3K36 methylations, the small RNA pathway machinery, and intact neuropeptide secretion. Activation of a single chemosensory neuron sufficed to induce a serotonin-mediated systemic stress response in both the parental trained generation and in its progeny. Moreover, inheritance of the cellular stress responses increased survival chances of the progeny as exposure to the training odorant allowed the animals to prepare in advance for an impending adversity. These findings suggest that in C. elegans associative memories and cellular changes may be transferred across generations.
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Affiliation(s)
- Noa Deshe
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Yifat Eliezer
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Lihi Hoch
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Eyal Itskovits
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Eduard Bokman
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Shachaf Ben-Ezra
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Alon Zaslaver
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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5
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Ewe CK, Rechavi O. The third barrier to transgenerational inheritance in animals: somatic epigenetic resetting. EMBO Rep 2023; 24:e56615. [PMID: 36862326 PMCID: PMC10074133 DOI: 10.15252/embr.202256615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
After early controversy, it is now increasingly clear that acquired responses to environmental factors may perpetuate across multiple generations-a phenomenon termed transgenerational epigenetic inheritance (TEI). Experiments with Caenorhabditis elegans, which exhibits robust heritable epigenetic effects, demonstrated small RNAs as key factors of TEI. Here, we discuss three major barriers to TEI in animals, two of which, the "Weismann barrier" and germline epigenetic reprogramming, have been known for decades. These are thought to effectively prevent TEI in mammals but not to the same extent in C. elegans. We argue that a third barrier-that we termed "somatic epigenetic resetting"-may further inhibit TEI and, unlike the other two, restricts TEI in C. elegans as well. While epigenetic information can overcome the Weismann barrier and transmit from the soma to the germline, it usually cannot "travel back" directly from the germline to the soma in subsequent generations. Nevertheless, heritable germline memory may still influence the animal's physiology by indirectly modifying gene expression in somatic tissues.
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Affiliation(s)
- Chee Kiang Ewe
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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6
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Potential of siRNA-Bearing Subtilosomes in the Treatment of Diethylnitrosamine-Induced Hepatocellular Carcinoma. Molecules 2023; 28:molecules28052191. [PMID: 36903437 PMCID: PMC10004640 DOI: 10.3390/molecules28052191] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
Therapeutics, based on small interfering RNA (siRNA), have demonstrated tremendous potential for treating cancer. However, issues such as non-specific targeting, premature degradation, and the intrinsic toxicity of the siRNA, have to be solved before they are ready for use in translational medicines. To address these challenges, nanotechnology-based tools might help to shield siRNA and ensure its specific delivery to the target site. Besides playing a crucial role in prostaglandin synthesis, the cyclo-oxygenase-2 (COX-2) enzyme has been reported to mediate carcinogenesis in various types of cancer, including hepatocellular carcinoma (HCC). We encapsulated COX-2-specific siRNA in Bacillus subtilis membrane lipid-based liposomes (subtilosomes) and evaluated their potential in the treatment of diethylnitrosamine (DEN)-induced hepatocellular carcinoma. Our findings suggested that the subtilosome-based formulation was stable, releasing COX-2 siRNA in a sustained manner, and has the potential to abruptly release encapsulated material at acidic pH. The fusogenic property of subtilosomes was revealed by FRET, fluorescence dequenching, content-mixing assay, etc. The subtilosome-based siRNA formulation was successful in inhibiting TNF-α expression in the experimental animals. The apoptosis study indicated that the subtilosomized siRNA inhibits DEN-induced carcinogenesis more effectively than free siRNA. The as-developed formulation also suppressed COX-2 expression, which in turn up-regulated the expression of wild-type p53 and Bax on one hand and down-regulated Bcl-2 expression on the other. The survival data established the increased efficacy of subtilosome-encapsulated COX-2 siRNA against hepatocellular carcinoma.
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7
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Legüe M, Caneo M, Aguila B, Pollak B, Calixto A. Interspecies effectors of a transgenerational memory of bacterial infection in Caenorhabditis elegans. iScience 2022; 25:104627. [PMID: 35800768 PMCID: PMC9254006 DOI: 10.1016/j.isci.2022.104627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/16/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
The inheritance of memory is an adaptive trait. Microbes challenge the immunity of organisms and trigger behavioral adaptations that can be inherited, but how bacteria produce inheritance of a trait is unknown. We use Caenorhabditis elegans and its bacteria to study the transgenerational RNA dynamics of interspecies crosstalk leading to a heritable behavior. A heritable response of C. elegans to microbes is the pathogen-induced diapause (PIDF), a state of suspended animation to evade infection. We identify RsmY, a small RNA involved in quorum sensing in Pseudomonas aeruginosa as a trigger of PIDF. The histone methyltransferase (HMT) SET-18/SMYD3 and the argonaute HRDE-1, which promotes multi-generational silencing in the germline, are also needed for PIDF initiation. The HMT SET-25/EHMT2 is necessary for memory maintenance in the transgenerational lineage. Our work is a starting point to understanding microbiome-induced inheritance of acquired traits, and the transgenerational influence of microbes in health and disease.
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Affiliation(s)
- Marcela Legüe
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
| | - Mauricio Caneo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
| | - Blanca Aguila
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
- Programa de Doctorado en Microbiología, Universidad de Chile, Santiago de Chile, Chile
| | | | - Andrea Calixto
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
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8
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Naranjo-Galindo FJ, Ai R, Fang EF, Nilsen HL, SenGupta T. C. elegans as an Animal Model to Study the Intersection of DNA Repair, Aging and Neurodegeneration. FRONTIERS IN AGING 2022; 3:916118. [PMID: 35821838 PMCID: PMC9261396 DOI: 10.3389/fragi.2022.916118] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022]
Abstract
Since its introduction as a genetic model organism, Caenorhabditis elegans has yielded insights into the causes of aging. In addition, it has provided a molecular understanding of mechanisms of neurodegeneration, one of the devastating effects of aging. However, C. elegans has been less popular as an animal model to investigate DNA repair and genomic instability, which is a major hallmark of aging and also a cause of many rare neurological disorders. This article provides an overview of DNA repair pathways in C. elegans and the impact of DNA repair on aging hallmarks, such as mitochondrial dysfunction, telomere maintenance, and autophagy. In addition, we discuss how the combination of biological characteristics, new technical tools, and the potential of following precise phenotypic assays through a natural life-course make C. elegans an ideal model organism to study how DNA repair impact neurodegeneration in models of common age-related neurodegenerative diseases.
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Affiliation(s)
- Francisco José Naranjo-Galindo
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
| | - Ruixue Ai
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
| | - Evandro Fei Fang
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tanima SenGupta
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
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9
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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
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10
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Molecular insights into transgenerational inheritance of stress memory. J Genet Genomics 2021; 49:89-95. [PMID: 34923165 DOI: 10.1016/j.jgg.2021.11.015] [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: 10/08/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022]
Abstract
There is accumulating evidence to show that environmental stressors can regulate a variety of phenotypes in descendants through germline-mediated epigenetic inheritance. Studies of model organisms exposed to environmental cues (e.g., diet, heat stress, toxins) indicate that altered DNA methylations, histone modifications, or non-coding RNAs in the germ cells are responsible for the transgenerational effects. In addition, it has also become evident that maternal provision could provide a mechanism for the transgenerational inheritance of stress adaptations that result from ancestral environmental cues. However, how the signal of environmentally-induced stress response transmits from the soma to the germline, which may influence offspring fitness, remains largely elusive. Small RNAs could serve as signaling molecules that transmit between tissues and even across generations. Furthermore, a recent study revealed that neuronal mitochondrial perturbations induce a transgenerational induction of the mitochondrial unfolded protein response mediated by a Wnt-dependent increase in mitochondrial DNA levels. Here, we review recent work on the molecular mechanism by which parental experience can affect future generations and the importance of soma-to-germline signaling for transgenerational inheritance.
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11
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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.
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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
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12
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Qi W, Xu F, Heimbucher T, Baumeister R. Protection of germline immortality by the soma via a secreted endoribonuclease. Bioessays 2021; 43:e2100195. [PMID: 34655094 DOI: 10.1002/bies.202100195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 11/08/2022]
Abstract
In sexually reproducing organisms maintenance of germ stem cell immortality is fundamental for transmitting genetic material to future generations. While previous research has mainly considered intrinsic regulatory mechanisms in the germline, our recent study has found a direct contribution of somatic cells in preserving germline immortality via the somatically expressed endoribonuclease ENDU-2 in Caenorhabditis elegans. We have identified ENDU-2 as a secreted protein that can be taken up by the germline. Here, we discuss how ENDU-2 might uncouple its RNA-binding and RNA-cleavage activities to control gene expression via either an endoribonuclease dependent or an independent way. We also speculate on a possible functional conservation of its mammalian homologs in mediating cell-cell communication as well as its potential significance in understanding human pathogenesis such as cancer development.
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Affiliation(s)
- Wenjing Qi
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany
| | - Fan Xu
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Germany
| | - Thomas Heimbucher
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany
| | - Ralf Baumeister
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Germany.,Center for Biochemistry and Molecular Cell Research (Faculty of Medicine), Albert-Ludwigs-University Freiburg, Germany.,Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Germany
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13
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Abstract
More than a century ago, August Weissman defined a distinction between the germline (responsible for propagating heritable information from generation to generation) and the perishable soma. A central motivation for this distinction was to argue against the inheritance of acquired characters, as the germline was partly defined by its protection from external conditions. However, recent decades have seen an explosion of studies documenting the intergenerational and transgenerational effects of environmental conditions, forcing a re-evaluation of how external signals are sensed by, or communicated to, the germline epigenome. Here, motivated by the centrality of small RNAs in paradigms of epigenetic inheritance, we review across species the myriad examples of intercellular RNA trafficking from nurse cells or somatic tissues to developing gametes.
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14
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Wasson JA, Harris G, Keppler-Ross S, Brock TJ, Dar AR, Butcher RA, Fischer SEJ, Kagias K, Clardy J, Zhang Y, Mango SE. Neuronal control of maternal provisioning in response to social cues. SCIENCE ADVANCES 2021; 7:7/34/eabf8782. [PMID: 34417172 PMCID: PMC8378817 DOI: 10.1126/sciadv.abf8782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/30/2021] [Indexed: 05/03/2023]
Abstract
Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues between generations are not well understood. Here, we show that, in Caenorhabditis elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRFamide (Phe-Met-Arg-Phe)-like peptides. Parental FMRFamide-like peptide signaling dampens oxidative stress resistance and promotes the deposition of mRNAs for translational components in progeny, which, in turn, reduces gene silencing. This study identifies a previously unknown pathway for intergenerational communication that links neuronal responses to maternal provisioning. We suggest that loss of social cues in the parental environment represents an adverse environment that stimulates stress responses across generations.
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Affiliation(s)
| | - Gareth Harris
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Biology, California State University Channel Islands, Camarillo, CA, USA
| | | | | | - Abdul R Dar
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Sylvia E J Fischer
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Konstantinos Kagias
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA, USA
| | - Yun Zhang
- Department of Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.
| | - Susan E Mango
- Biozentrum, University of Basel, Basel, Switzerland.
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15
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Perez MF, Shamalnasab M, Mata-Cabana A, Della Valle S, Olmedo M, Francesconi M, Lehner B. Neuronal perception of the social environment generates an inherited memory that controls the development and generation time of C. elegans. Curr Biol 2021; 31:4256-4268.e7. [PMID: 34358445 DOI: 10.1016/j.cub.2021.07.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 12/31/2022]
Abstract
An old and controversial question in biology is whether information perceived by the nervous system of an animal can "cross the Weismann barrier" to alter the phenotypes and fitness of their progeny. Here, we show that such intergenerational transmission of sensory information occurs in the model organism, C. elegans, with a major effect on fitness. Specifically, that perception of social pheromones by chemosensory neurons controls the post-embryonic timing of the development of one tissue, the germline, relative to others in the progeny of an animal. Neuronal perception of the social environment thus intergenerationally controls the generation time of this animal.
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Affiliation(s)
- Marcos Francisco Perez
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Mehrnaz Shamalnasab
- Université de Lyon, ENS de Lyon, Université de Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, Site Jacques Monod, 69007 Lyon, France
| | - Alejandro Mata-Cabana
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Simona Della Valle
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - María Olmedo
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mirko Francesconi
- Université de Lyon, ENS de Lyon, Université de Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, Site Jacques Monod, 69007 Lyon, France.
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain.
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16
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Devanapally S, Raman P, Chey M, Allgood S, Ettefa F, Diop M, Lin Y, Cho YE, Jose AM. Mating can initiate stable RNA silencing that overcomes epigenetic recovery. Nat Commun 2021; 12:4239. [PMID: 34244495 PMCID: PMC8270896 DOI: 10.1038/s41467-021-24053-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/29/2021] [Indexed: 01/09/2023] Open
Abstract
Stable epigenetic changes appear uncommon, suggesting that changes typically dissipate or are repaired. Changes that stably alter gene expression across generations presumably require particular conditions that are currently unknown. Here we report that a minimal combination of cis-regulatory sequences can support permanent RNA silencing of a single-copy transgene and its derivatives in C. elegans simply upon mating. Mating disrupts competing RNA-based mechanisms to initiate silencing that can last for >300 generations. This stable silencing requires components of the small RNA pathway and can silence homologous sequences in trans. While animals do not recover from mating-induced silencing, they often recover from and become resistant to trans silencing. Recovery is also observed in most cases when double-stranded RNA is used to silence the same coding sequence in different regulatory contexts that drive germline expression. Therefore, we propose that regulatory features can evolve to oppose permanent and potentially maladaptive responses to transient change.
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Affiliation(s)
| | | | - Mary Chey
- University of Maryland, College Park, MD, USA
| | | | | | | | - Yixin Lin
- University of Maryland, College Park, MD, USA
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17
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Manterola M, Palominos MF, Calixto A. The Heritability of Behaviors Associated With the Host Gut Microbiota. Front Immunol 2021; 12:658551. [PMID: 34054822 PMCID: PMC8155505 DOI: 10.3389/fimmu.2021.658551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
What defines whether the interaction between environment and organism creates a genetic memory able to be transferred to subsequent generations? Bacteria and the products of their metabolism are the most ubiquitous biotic environments to which every living organism is exposed. Both microbiota and host establish a framework where environmental and genetic factors are integrated to produce adaptive life traits, some of which can be inherited. Thus, the interplay between host and microbe is a powerful model to study how phenotypic plasticity is inherited. Communication between host and microbe can occur through diverse molecules such as small RNAs (sRNAs) and the RNA interference machinery, which have emerged as mediators and carriers of heritable environmentally induced responses. Notwithstanding, it is still unclear how the organism integrates sRNA signaling between different tissues to orchestrate a systemic bacterially induced response that can be inherited. Here we discuss current evidence of heritability produced by the intestinal microbiota from several species. Neurons and gut are the sensing systems involved in transmitting changes through transcriptional and post-transcriptional modifications to the gonads. Germ cells express inflammatory receptors, and their development and function are regulated by host and bacterial metabolites and sRNAs thus suggesting that the dynamic interplay between host and microbe underlies the host's capacity to transmit heritable behaviors. We discuss how the host detects changes in the microbiota that can modulate germ cells genomic functions. We also explore the nature of the interactions that leave permanent or long-term memory in the host and propose mechanisms by which the microbiota can regulate the development and epigenetic reprogramming of germ cells, thus influencing the inheritance of the host. We highlight the vast contribution of the bacterivore nematode C. elegans and its commensal and pathogenic bacteria to the understanding on how behavioral adaptations can be inter and transgenerational inherited.
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Affiliation(s)
- Marcia Manterola
- Programa de Genética Humana, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - M. Fernanda Palominos
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
- Programa de Doctorado en Ciencias, mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
| | - Andrea Calixto
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
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18
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Chen LT, Lin CT, Lin LY, Hsu JM, Wu YC, Pan CL. Neuronal mitochondrial dynamics coordinate systemic mitochondrial morphology and stress response to confer pathogen resistance in C. elegans. Dev Cell 2021; 56:1770-1785.e12. [PMID: 33984269 DOI: 10.1016/j.devcel.2021.04.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/09/2020] [Accepted: 04/21/2021] [Indexed: 01/02/2023]
Abstract
Mitochondrial functions across different tissues are regulated in a coordinated fashion to optimize the fitness of an organism. Mitochondrial unfolded protein response (UPRmt) can be nonautonomously elicited by mitochondrial perturbation in neurons, but neuronal signals that propagate such response and its physiological significance remain incompletely understood. Here, we show that in C. elegans, loss of neuronal fzo-1/mitofusin induces nonautonomous UPRmt through multiple neurotransmitters and neurohormones, including acetylcholine, serotonin, glutamate, tyramine, and insulin-like peptides. Neuronal fzo-1 depletion also triggers nonautonomous mitochondrial fragmentation, which requires autophagy and mitophagy genes. Systemic activation of UPRmt and mitochondrial fragmentation in C. elegans via perturbing neuronal mitochondrial dynamics improves resistance to pathogenic Pseudomonas infection, which is supported by transcriptomic signatures of immunity and stress-response genes. We propose that C. elegans surveils neuronal mitochondrial dynamics to coordinate systemic UPRmt and mitochondrial connectivity for pathogen defense and optimized survival under bacterial infection.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Chih-Ta Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Liang-Yi Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Jiun-Min Hsu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Yu-Chun Wu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Chun-Liang Pan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, No.7 Chung-Shan South Road, Taipei 10002, Taiwan.
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19
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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?'
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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
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20
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Abstract
Memories encoded in the parent's brain should not be able to transfer to the progeny. This assumption, which is compatible with the tenets of modern neuroscience and genetics, is challenged by new insights regarding inheritance of transgenerational epigenetic responses. Here we reflect on new discoveries regarding "molecular memories" in light of older and scandalous work on "Memory transfer" spearheaded by James V. McConnell and Georges Ungar. While the history of this field is filled with controversies, mechanisms for transmission of information across generations are being elucidated in different organisms. Most strikingly, it is now clear that in Caenorhabditis elegans nematodes, somatic responses can control gene activity in descendants via heritable small RNA molecules, and that this type of inheritance is tightly regulated by dedicated machinery. In this perspective we will focus mostly on studies conducted using C. elegans, and examine recent work on the connection between small RNAs in the nervous system and germline. We will discuss the evidence for the inheritance of brain-orchestrated behavior, and its possible significance.
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Affiliation(s)
- Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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21
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Nono M, Kishimoto S, Sato-Carlton A, Carlton PM, Nishida E, Uno M. Intestine-to-Germline Transmission of Epigenetic Information Intergenerationally Ensures Systemic Stress Resistance in C. elegans. Cell Rep 2021; 30:3207-3217.e4. [PMID: 32160530 DOI: 10.1016/j.celrep.2020.02.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 01/29/2023] Open
Abstract
Changes in epigenetic states affect organismal homeostasis, including stress resistance. However, the mechanisms coordinating epigenetic states and systemic stress resistance remain largely unknown. Here, we identify the intestine-to-germline communication of epigenetic states, which intergenerationally enhances stress resistance in C. elegans. The alterations in epigenetic states by deficiency of the histone H3K4me3 modifier ASH-2 in the intestine or germline increase organismal stress resistance, which is abrogated by knockdown of the H3K4 demethylase RBR-2. Remarkably, the increase in stress resistance induced by ASH-2 deficiency in the intestine is abrogated by RBR-2 knockdown in the germline, suggesting the intestine-to-germline transmission of epigenetic information. This communication from intestine to germline in the parental generation increases stress resistance in the next generation. Moreover, the intertissue communication is mediated partly by transcriptional regulation of F08F1.3. These results reveal that intertissue communication of epigenetic information provides mechanisms for intergenerational regulation of systemic stress resistance.
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Affiliation(s)
- Masanori Nono
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Saya Kishimoto
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Aya Sato-Carlton
- Laboratory of Chromosome Function and Inheritance, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Peter Mark Carlton
- Laboratory of Chromosome Function and Inheritance, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Laboratory of Chromosome Function and Inheritance, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Eisuke Nishida
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
| | - Masaharu Uno
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
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22
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Cabej NR. A mechanism of inheritance of acquired traits in animals. Dev Biol 2021; 475:106-117. [PMID: 33741349 DOI: 10.1016/j.ydbio.2021.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/11/2023]
Abstract
Observational and experimental evidence for the inheritance of acquired traits in animals is slowly, but steadily accumulating. The onset and transmission of acquired traits implies the acquisition and transmission from parents to progeny of new information, which is different from the genetic information contained in DNA. The new non-genetic information most commonly is passed on from parents to the offspring via gamete(s), but how it is precisely transmitted to the successive generations is still unknown. Based on adequate empirical evidence presented herein, a hypothesis is proposed of the inheritance of acquired traits in animals and the flow of the relevant parental information to the offspring.
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Affiliation(s)
- Nelson R Cabej
- University of Tirana Faculty of Medicine, Universiteti i Mjekesise Tirane, Department of Biology, 147 Manhattan Terrace, Dumont, 07628, USA.
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23
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Developmental plasticity and the response to nutrient stress in Caenorhabditis elegans. Dev Biol 2021; 475:265-276. [PMID: 33549550 DOI: 10.1016/j.ydbio.2021.01.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/24/2020] [Accepted: 01/29/2021] [Indexed: 11/23/2022]
Abstract
Developmental plasticity refers the ability of an organism to adapt to various environmental stressors, one of which is nutritional stress. Caenorhabditis elegans require various nutrients to successfully progress through all the larval stages to become a reproductive adult. If nutritional criteria are not satisfied, development can slow or completely arrest. In poor growth conditions, the animal can enter various diapause stages, depending on its developmental progress. In C. elegans, there are three well-characterized diapauses: the L1 arrest, the dauer diapause, and adult reproductive diapause, each associated with drastic changes in metabolism and germline development. At the centre of these changes is AMP-activated protein kinase (AMPK). AMPK is a metabolic regulator that maintains energy homeostasis, particularly during times of nutrient stress. Without AMPK, metabolism is disrupted during dauer, leading to the rapid consumption of lipid stores as well as misregulation of metabolic enzymes, leading to reduced survival. During the L1 arrest and dauer diapause, AMPK is responsible for ensuring germline quiescence by modifying the germline chromatin landscape to maintain germ cell integrity until conditions improve. Similar to classic hormonal signalling, small RNAs also play a critical role in regulating development and behaviour in a cell non-autonomous fashion. Thus, during the challenges associated with developmental plasticity, AMPK summons an army of signalling pathways to work collectively to preserve reproductive fitness during these periods of unprecedented uncertainty.
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24
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Fernandes De Abreu DA, Salinas-Giegé T, Drouard L, Remy JJ. Alanine tRNAs Translate Environment Into Behavior in Caenorhabditis elegans. Front Cell Dev Biol 2020; 8:571359. [PMID: 33195203 PMCID: PMC7662486 DOI: 10.3389/fcell.2020.571359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Caenorhabditis elegans nematodes produce and maintain imprints of attractive chemosensory cues to which they are exposed early in life. Early odor-exposure increases adult chemo-attraction to the same cues. Imprinting is transiently or stably inherited, depending on the number of exposed generations. We show here that the Alanine tRNA (UGC) plays a central role in regulating C. elegans chemo-attraction. Naive worms fed on tRNAAla (UGC) purified from odor-experienced worms, acquire odor-specific imprints. Chemo-attractive responses require the tRNA-modifying Elongator complex sub-units 1 (elpc-1) and 3 (elpc-3) genes. elpc-3 deletions impair chemo-attraction, which is fully restored by wild-type tRNAAla (UGC) feeding. A stably inherited decrease of odor-specific responses ensues from early odor-exposition of elpc-1 deletion mutants. tRNAAla (UGC) may adopt various chemical forms to mediate the cross-talk between innately-programmed and environment-directed chemo-attractive behavior.
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Affiliation(s)
- Diana Andrea Fernandes De Abreu
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
| | - Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Jacques Remy
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
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25
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Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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26
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Baugh LR, Day T. Nongenetic inheritance and multigenerational plasticity in the nematode C. elegans. eLife 2020; 9:e58498. [PMID: 32840479 PMCID: PMC7447421 DOI: 10.7554/elife.58498] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
A rapidly growing body of literature in several organisms suggests that environmentally-induced adaptive changes in phenotype can be transmitted across multiple generations. Although within-generation plasticity has been well documented, multigenerational plasticity represents a significant departure from conventional evolutionary thought. Studies of C. elegans have been particularly influential because this species exhibits extensive phenotypic plasticity, it is often essentially isogenic, and it has well-documented molecular and cellular mechanisms through which nongenetic inheritance occurs. However, while experimentalists are eager to claim that nongenetic modes of inheritance characterized in this and other model systems enhance fitness, many biologists remain skeptical given the extraordinary nature of this claim. We establish three criteria to evaluate how compelling the evidence for adaptive multigenerational plasticity is, and we use these criteria to critically examine putative cases of it in C. elegans. We conclude by suggesting potentially fruitful avenues for future research.
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Affiliation(s)
- L Ryan Baugh
- Department of Biology, Center for Genomics and Computational Biology, Duke UniversityDurhamUnited States
| | - Troy Day
- Departments of Mathematics and Statistics, Department of Biology, Queens UniversityKingstonCanada
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27
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Baxter FA, Drake AJ. Non-genetic inheritance via the male germline in mammals. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180118. [PMID: 30966887 PMCID: PMC6460076 DOI: 10.1098/rstb.2018.0118] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Numerous studies in humans and in animal models have demonstrated that exposure to adverse environmental conditions in early life results in long-term structural and functional changes in an organism, increasing the risk of cardiometabolic, neurobehavioural and reproductive disorders in later life. Such effects are not limited to the first generation offspring but may be transmitted to a second or a number of subsequent generations, through non-genomic mechanisms. While the transmission of ‘programmed’ effects through the maternal line could occur as a consequence of multiple influences, for example, altered maternal physiology, the inheritance of effects through the male line is more difficult to explain and there is much interest in a potential role for transgenerational epigenetic inheritance. In this review, we will discuss the mechanisms by which induced effects may be transmitted through the paternal lineage, with a particular focus on the role of epigenetic inheritance. This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine’.
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Affiliation(s)
- Faye A Baxter
- 1 Royal Hospital for Sick Children , 9 Sciennes Road, Edinburgh EH9 1LF , UK
| | - Amanda J Drake
- 1 Royal Hospital for Sick Children , 9 Sciennes Road, Edinburgh EH9 1LF , UK.,2 University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh , 47 Little France Crescent, Edinburgh EH16 4TJ , UK
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28
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Anastasiadi D, Piferrer F. Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass. Mol Biol Evol 2020; 36:2252-2264. [PMID: 31289822 PMCID: PMC6759067 DOI: 10.1093/molbev/msz153] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Domestication of wild animals induces a set of phenotypic characteristics collectively known as the domestication syndrome. However, how this syndrome emerges is still not clear. Recently, the neural crest cell deficit hypothesis proposed that it is generated by a mildly disrupted neural crest cell developmental program, but clear support is lacking due to the difficulties of distinguishing pure domestication effects from preexisting genetic differences between farmed and wild mammals and birds. Here, we use a farmed fish as model to investigate the role of persistent changes in DNA methylation (epimutations) in the process of domestication. We show that early domesticates of sea bass, with no genetic differences with wild counterparts, contain epimutations in tissues with different embryonic origins. About one fifth of epimutations that persist into adulthood are established by the time of gastrulation and affect genes involved in developmental processes that are expressed in embryonic structures, including the neural crest. Some of these genes are differentially expressed in sea bass with lower jaw malformations, a key feature of domestication syndrome. Interestingly, these epimutations significantly overlap with cytosine-to-thymine polymorphisms after 25 years of selective breeding. Furthermore, epimutated genes coincide with genes under positive selection in other domesticates. We argue that the initial stages of domestication include dynamic alterations in DNA methylation of developmental genes that affect the neural crest. Our results indicate a role for epimutations during the beginning of domestication that could be fixed as genetic variants and suggest a conserved molecular process to explain Darwin’s domestication syndrome across vertebrates.
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Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Barcelona, Spain.,The New Zealand Institute for Plant & Food Research, Nelson, New Zealand
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Barcelona, Spain
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29
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Ravikumar S, Devanapally S, Jose AM. Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference. Nucleic Acids Res 2019; 47:10059-10071. [PMID: 31501873 PMCID: PMC6821342 DOI: 10.1093/nar/gkz748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematode Caenorhabditis elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissue-specific - EGO-1 in the germline and RRF-1 in somatic cells. Here we demonstrate that EGO-1 can compensate for the lack of RRF-1 when dsRNA from neurons is used to silence genes in intestinal cells. However, the lineal origins of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. Variability is masked in wild-type animals, which show extensive silencing by neuronal dsRNA. As a result, cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against inferring uniformity of mechanism based on uniformity of outcome. We speculate that functional mosaicism could contribute to escape from targeted therapies and could allow developmental systems to drift over evolutionary time.
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Affiliation(s)
- Snusha Ravikumar
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sindhuja Devanapally
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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30
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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.
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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
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31
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Wu S, Guo W, Li X, Liu Y, Li Y, Lei X, Yao J, Yang X. Paternal chronic folate supplementation induced the transgenerational inheritance of acquired developmental and metabolic changes in chickens. Proc Biol Sci 2019; 286:20191653. [PMID: 31506054 DOI: 10.1098/rspb.2019.1653] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Increasing evidence indicates that paternal diet can result in metabolic changes in offspring, but the definite mechanism remains unclear in birds. Here, we fed breeder cocks five different diets containing 0, 0.25, 1.25, 2.50 and 5.00 mg kg-1 folate throughout life. Paternal folate supplementation (FS) was beneficial to the growth and organ development of broiler offspring. Most importantly, the lipid and glucose metabolism of breeder cocks and broiler offspring were affected by paternal FS, according to biochemical and metabolomic analyses. We further employed global analyses of hepatic and spermatozoal messenger RNA (mRNA), long non-coding RNA (lncRNA) and micro RNA (miRNA). Some key genes involved in the glycolysis or gluconeogenesis pathway and the PPAR signalling pathway, including PEPCK, ANGPTL4 and THRSP, were regulated by differentially expressed hepatic and spermatozoal miRNAs and lncRNAs in breeder cocks and broiler offspring. Moreover, the expression of ANGPTL4 could also be regulated by differentially expressed miRNAs and lncRNAs in spermatozoa via competitive endogenous RNA (ceRNA) mechanisms. Overall, this model suggests that paternal folate could transgenerationally regulate lipid and glucose metabolism in broiler offspring and the epigenetic transmission may involve altered spermatozoal miRNAs and lncRNAs.
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Affiliation(s)
- Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
| | - Wei Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
| | - Xinyi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
| | - Yulong Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
| | - Xinyu Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100 Shaanxi, People's Republic of China
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Steele EJ, Gorczynski RM, Lindley RA, Liu Y, Temple R, Tokoro G, Wickramasinghe DT, Wickramasinghe NC. Lamarck and Panspermia - On the Efficient Spread of Living Systems Throughout the Cosmos. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:10-32. [PMID: 31445944 DOI: 10.1016/j.pbiomolbio.2019.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 08/14/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
We review the main lines of evidence (molecular, cellular and whole organism) published since the 1970s demonstrating Lamarckian Inheritance in animals, plants and microorganisms viz. the transgenerational inheritance of environmentally-induced acquired characteristics. The studies in animals demonstrate the genetic permeability of the soma-germline Weismann Barrier. The widespread nature of environmentally-directed inheritance phenomena reviewed here contradicts a key pillar of neo-Darwinism which affirms the rigidity of the Weismann Barrier. These developments suggest that neo-Darwinian evolutionary theory is in need of significant revision. We argue that Lamarckian inheritance strategies involving environmentally-induced rapid directional genetic adaptations make biological sense in the context of cosmic Panspermia allowing the efficient spread of living systems and genetic innovation throughout the Universe. The Hoyle-Wickramasinghe Panspermia paradigm also developed since the 1970s, unlike strictly geocentric neo-Darwinism provides a cogent biological rationale for the actual widespread existence of Lamarckian modes of inheritance - it provides its raison d'être. Under a terrestrially confined neo-Darwinian viewpoint such an association may have been thought spurious in the past. Our aim is to outline the conceptual links between rapid Lamarckian-based evolutionary hypermutation processes dependent on reverse transcription-coupled mechanisms among others and the effective cosmic spread of living systems. For example, a viable, or cryo-preserved, living system travelling through space in a protective matrix will need of necessity to rapidly adapt and proliferate on landing in a new cosmic niche. Lamarckian mechanisms thus come to the fore and supersede the slow (blind and random) genetic processes expected under a traditional neo-Darwinian evolutionary paradigm.
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Affiliation(s)
- Edward J Steele
- C.Y.O'Connor ERADE Village Foundation, Piara Waters, Perth, 6112, WA, Australia; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Melville Analytics Pty Ltd, Melbourne, Vic, Australia.
| | | | - Robyn A Lindley
- Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of MelbourneVic, Australia; GMDx Group Ltd, Melbourne, Vic, Australia
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Robert Temple
- The History of Chinese Science and Culture Foundation, Conway Hall, London, UK
| | - Gensuke Tokoro
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Dayal T Wickramasinghe
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; College of Physical and Mathematical Sciences, Australian National University, Canberra, Australia
| | - N Chandra Wickramasinghe
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan; Buckingham Centre for Astrobiology, University of Buckingham, UK
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Posner R, Toker IA, Antonova O, Star E, Anava S, Azmon E, Hendricks M, Bracha S, Gingold H, Rechavi O. Neuronal Small RNAs Control Behavior Transgenerationally. Cell 2019; 177:1814-1826.e15. [PMID: 31178120 PMCID: PMC6579485 DOI: 10.1016/j.cell.2019.04.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/18/2019] [Accepted: 04/13/2019] [Indexed: 12/21/2022]
Abstract
It is unknown whether the activity of the nervous system can be inherited. In Caenorhabditis elegans nematodes, parental responses can transmit heritable small RNAs that regulate gene expression transgenerationally. In this study, we show that a neuronal process can impact the next generations. Neurons-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous small interfering RNAs (siRNAs) and germline gene expression for multiple generations. Further, the production of small RNAs in neurons controls the chemotaxis behavior of the progeny for at least three generations via the germline Argonaute HRDE-1. Among the targets of these small RNAs, we identified the conserved gene saeg-2, which is transgenerationally downregulated in the germline. Silencing of saeg-2 following neuronal small RNA biogenesis is required for chemotaxis under stress. Thus, we propose a small-RNA-based mechanism for communication of neuronal processes transgenerationally. C. elegans neuronal small RNAs are characterized by RNA sequencing RDE-4-dependent neuronal endogenous small RNAs communicate with the germline Germline HRDE-1 mediates transgenerational regulation by neuronal small RNAs Neuronal small RNAs regulate germline genes to control behavior transgenerationally
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Affiliation(s)
- Rachel Posner
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itai Antoine Toker
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Olga Antonova
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ekaterina Star
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sarit Anava
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eran Azmon
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michael Hendricks
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Shahar Bracha
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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Kadekar P, Roy R. AMPK regulates germline stem cell quiescence and integrity through an endogenous small RNA pathway. PLoS Biol 2019; 17:e3000309. [PMID: 31166944 PMCID: PMC6576793 DOI: 10.1371/journal.pbio.3000309] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 06/17/2019] [Accepted: 05/16/2019] [Indexed: 01/07/2023] Open
Abstract
During suboptimal growth conditions, Caenorhabditis elegans larvae undergo a global developmental arrest called "dauer." During this stage, the germline stem cells (GSCs) become quiescent in an AMP-activated Protein Kinase (AMPK)-dependent manner, and in the absence of AMPK, the GSCs overproliferate and lose their reproductive capacity, leading to sterility when mutant animals resume normal growth. These defects correlate with the altered abundance and distribution of a number of chromatin modifications, all of which can be corrected by disabling components of the endogenous small RNA pathway, suggesting that AMPK regulates germ cell integrity by targeting an RNA interference (RNAi)-like pathway during dauer. The expression of AMPK in somatic cells restores all the germline defects, potentially through the transmission of small RNAs. Our findings place AMPK at a pivotal position linking energy stress detected in the soma to a consequent endogenous small RNA-mediated adaptation in germline gene expression, thereby challenging the "permeability" of the Weismann barrier.
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Affiliation(s)
- Pratik Kadekar
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Richard Roy
- Department of Biology, McGill University, Montreal, Quebec, Canada
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35
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Danchin É, Pocheville A, Huneman P. Early in life effects and heredity: reconciling neo-Darwinism with neo-Lamarckism under the banner of the inclusive evolutionary synthesis. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180113. [PMID: 30966884 PMCID: PMC6460090 DOI: 10.1098/rstb.2018.0113] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2018] [Indexed: 12/22/2022] Open
Abstract
Recent discoveries show that early in life effects often have long-lasting influences, sometimes even spanning several generations. Such intergenerational effects of early life events appear not easily reconcilable with strict genetic inheritance. However, an integrative evolutionary medicine of early life effects needs a sound view of inheritance in development and evolution. Here, we show how to articulate the gene-centred and non-gene-centred visions of inheritance. We first recall the coexistence of two gene concepts in scientific discussions, a statistical one (focused on patterns of parent-offspring resemblance, and implicitly including non-DNA-sequence-based resemblance), and a molecular one (based on the DNA sequence). We then show how all the different mechanisms of inheritance recently discovered can be integrated into an inclusive theory of evolution where different mechanisms would enable adaptation to changing environments at different timescales. One surprising consequence of this integrative vision of inheritance is that early in life effects start much earlier than fertilization. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
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Affiliation(s)
- Étienne Danchin
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Arnaud Pocheville
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
- Department of Philosophy and Charles Perkins Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Philippe Huneman
- Institut d'Histoire et de Philosophie des Sciences et des Techniques, CNRS/Université Paris I Panthéon-Sorbonne, Paris, France
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36
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Found in Translation: The Utility of C. elegans Alpha-Synuclein Models of Parkinson's Disease. Brain Sci 2019; 9:brainsci9040073. [PMID: 30925741 PMCID: PMC6523935 DOI: 10.3390/brainsci9040073] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 01/18/2023] Open
Abstract
Parkinson's Disease (PD) is the second-most common neurodegenerative disease in the world, yet the fundamental and underlying causes of the disease are largely unknown, and treatments remain sparse and impotent. Several biological systems have been employed to model the disease but the nematode roundworm Caenorhabditis elegans (C. elegans) shows unique promise among these to disinter the elusive factors that may prevent, halt, and/or reverse PD phenotypes. Some of the most salient of these C. elegans models of PD are those that position the misfolding-prone protein alpha-synuclein (α-syn), a hallmark pathological component of PD, as the primary target for scientific interrogation. By transgenic expression of human α-syn in different tissues, including dopamine neurons and muscle cells, the primary cellular phenotypes of PD in humans have been recapitulated in these C. elegans models and have already uncovered multifarious genetic factors and chemical compounds that attenuate dopaminergic neurodegeneration. This review describes the paramount discoveries obtained through the application of different α-syn models of PD in C. elegans and highlights their established utility and respective promise to successfully uncover new conserved genetic modifiers, functional mechanisms, therapeutic targets and molecular leads for PD with the potential to translate to humans.
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37
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Estill MS, Hauser R, Krawetz SA. RNA element discovery from germ cell to blastocyst. Nucleic Acids Res 2019; 47:2263-2275. [PMID: 30576549 PMCID: PMC6411832 DOI: 10.1093/nar/gky1223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/31/2018] [Accepted: 11/24/2018] [Indexed: 12/19/2022] Open
Abstract
Recent studies have shown that tissue-specific transcriptomes contain multiple types of RNAs that are transcribed from intronic and intergenic sequences. The current study presents a tool for the discovery of transcribed, unannotated sequence elements from RNA-seq libraries. This RNA Element (RE) discovery algorithm (REDa) was applied to a spectrum of tissues and cells representing germline, embryonic, and somatic tissues and examined as a function of differentiation through the first set of cell divisions of human development. This highlighted extensive transcription throughout the genome, yielding previously unidentified human spermatogenic RNAs. Both exonic and novel X-chromosome REs were subject to robust meiotic sex chromosome inactivation, although an extensive de-repression occurred in the post-meiotic stages of spermatogenesis. Surprisingly, 2.4% of the 10,395 X chromosome exonic REs were present in mature sperm. Transcribed genomic repetitive sequences, including simple centromeric repeats, HERVE and HSAT1, were also shown to be associated with RE expression during spermatogenesis. These results suggest that pervasive intergenic repetitive sequence expression during human spermatogenesis may play a role in regulating chromatin dynamics. Repetitive REs switching repeat classes during differentiation upon fertilization and embryonic genome activation was evident.
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MESH Headings
- Algorithms
- Blastocyst/cytology
- Blastocyst/metabolism
- Cell Differentiation
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomes, Human, X/genetics
- Embryonic Development/genetics
- Exons/genetics
- Female
- Fertilization
- Gene Expression Regulation, Developmental
- Genomics
- Humans
- Liver/cytology
- Liver/metabolism
- Male
- Meiosis/genetics
- Oocytes/cytology
- Oocytes/metabolism
- Poly A/analysis
- Poly A/genetics
- Poly A/isolation & purification
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- Regulatory Sequences, Ribonucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, RNA
- Spermatogenesis/genetics
- Spermatozoa/cytology
- Spermatozoa/metabolism
- Transcription, Genetic
- X Chromosome Inactivation
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Affiliation(s)
- Molly S Estill
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Russ Hauser
- Vincent Memorial Obstetrics and Gynecology Service, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
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38
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Bezler A, Braukmann F, West SM, Duplan A, Conconi R, Schütz F, Gönczy P, Piano F, Gunsalus K, Miska EA, Keller L. Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment. PLoS Genet 2019; 15:e1007905. [PMID: 30735500 PMCID: PMC6383947 DOI: 10.1371/journal.pgen.1007905] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/21/2019] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) related pathways are essential for germline development and fertility in metazoa and can contribute to inter- and trans-generational inheritance. In the nematode Caenorhabditis elegans, environmental double-stranded RNA provided by feeding can lead to heritable changes in phenotype and gene expression. Notably, transmission efficiency differs between the male and female germline, yet the underlying mechanisms remain elusive. Here we use high-throughput sequencing of dissected gonads to quantify sex-specific endogenous piRNAs, miRNAs and siRNAs in the C. elegans germline and the somatic gonad. We identify genes with exceptionally high levels of secondary 22G RNAs that are associated with low mRNA expression, a signature compatible with silencing. We further demonstrate that contrary to the hermaphrodite germline, the male germline, but not male soma, is resistant to environmental RNAi triggers provided by feeding, in line with previous work. This sex-difference in silencing efficacy is associated with lower levels of gonadal RNAi amplification products. Moreover, this tissue- and sex-specific RNAi resistance is regulated by the germline, since mutant males with a feminized germline are RNAi sensitive. This study provides important sex- and tissue-specific expression data of miRNA, piRNA and siRNA as well as mechanistic insights into sex-differences of gene regulation in response to environmental cues.
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Affiliation(s)
- Alexandra Bezler
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Fabian Braukmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Sean M. West
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Arthur Duplan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Raffaella Conconi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Bioinformatics Core Facility; SIB Swiss Institute of Bioinformatics and Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Fabio Piano
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin Gunsalus
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Eric A. Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Norouzitallab P, Baruah K, Vanrompay D, Bossier P. Can epigenetics translate environmental cues into phenotypes? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:1281-1293. [PMID: 30180336 DOI: 10.1016/j.scitotenv.2018.08.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/03/2018] [Accepted: 08/04/2018] [Indexed: 05/17/2023]
Abstract
Living organisms are constantly exposed to wide ranges of environmental cues. They react to these cues by undergoing a battery of phenotypic responses, such as by altering their physiological and behavioral traits, in order to adapt and survive in the changed environments. The adaptive response of a species induced by environmental cues is typically thought to be associated with its genetic diversity such that higher genetic diversity provides increased adaptive potential. This originates from the general consensus that phenotypic traits have a genetic basis and are subject to Darwinian natural selection and Mendelian inheritance. There is no doubt about the validity of these principles, supported by the successful introgression of specific traits during (selective) breeding. However, a range of recent studies provided fascinating evidences suggesting that environmental effects experienced by an organism during its lifetime can have marked influences on its phenotype, and additionally the organism can pass on the acquired phenotypes to its subsequent generations through non-genetic mechanisms (also termed as epigenetic mechanism) - a notion that dates back to Lamarck and has been controversial ever since. In this review, we describe how the epigenetics has reshaped our long perception about the inheritance/development of phenotypes within organisms, contrasting with the classical gene-based view of inheritance. We particularly highlighted recent developments in our understanding of inheritance of parental environmental induced phenotypic traits in multicellular organisms under different environmental conditions, and discuss how modifications of the epigenome contribute to the determination of the adult phenotype of future generations.
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Affiliation(s)
- Parisa Norouzitallab
- Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium; Laboratory of Aquaculture &Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium.
| | - Kartik Baruah
- Laboratory of Aquaculture &Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium; Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Daisy Vanrompay
- Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture &Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium
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40
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Perez MF, Lehner B. Intergenerational and transgenerational epigenetic inheritance in animals. Nat Cell Biol 2019; 21:143-151. [PMID: 30602724 DOI: 10.1038/s41556-018-0242-9] [Citation(s) in RCA: 291] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022]
Abstract
Animals transmit not only DNA but also other molecules, such as RNA, proteins and metabolites, to their progeny via gametes. It is currently unclear to what extent these molecules convey information between generations and whether this information changes according to their physiological state and environment. Here, we review recent work on the molecular mechanisms by which 'epigenetic' information is transmitted between generations over different timescales, and the importance of this information for development and physiology.
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Affiliation(s)
- Marcos Francisco Perez
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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41
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Zhang X, Lai T, Zhang P, Zhang X, Yuan C, Jin Z, Li H, Yu Z, Qin C, Tör M, Ma P, Cheng Q, Hong Y. Mini review: Revisiting mobile RNA silencing in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 278:113-117. [PMID: 30471724 PMCID: PMC6556431 DOI: 10.1016/j.plantsci.2018.10.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/28/2018] [Accepted: 10/30/2018] [Indexed: 05/19/2023]
Abstract
Non-cell autonomous RNA silencing can spread from cell to cell and over long-distances in animals and plants. This process is genetically determined and requires mobile RNA signals. Genetic requirement and molecular nature of the mobile signals for non-cell-autonomous RNA silencing were intensively investigated in past few decades. No consensus dogma for mobile silencing can be reached in plants, yet published data are sometimes inconsistent and controversial. Thus, the genetic requirements and molecular signals involved in plant mobile silencing are still poorly understood. This article revisits our present understanding of intercellular and systemic non-cell autonomous RNA silencing, and summarises current debates on RNA signals for mobile silencing. In particular, we discuss new evidence on siRNA mobility, a DCL2-dependent genetic network for mobile silencing and its potential biological relevance as well as 22 nt siRNA being a mobile signal for non-cell-autonomous silencing in both Arabidopsis and Nicotiana benthamiana. This sets up a new trend in unravelling genetic components and small RNA signal molecules for mobile silencing in (across) plants and other organisms of different kingdoms. Finally we raise several outstanding questions that need to be addressed in future plant silencing research.
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Affiliation(s)
- Xian Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Tongfei Lai
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Chen Yuan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhenhui Jin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Hongmei Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, UK
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Qi Cheng
- Nitrogen Fixation Laboratory, Qi Institute, Jiaxing 314000, Zhejiang, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, UK; Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, UK.
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42
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Chavez DR, Snow AK, Smith JR, Stanfield GM. Soma-germ line interactions and a role for muscle in the regulation of C. elegans sperm motility. Development 2018; 145:dev.167734. [PMID: 30470702 DOI: 10.1242/dev.167734] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/12/2018] [Indexed: 12/13/2022]
Abstract
The development of highly differentiated sperm cells that are specialized for navigating to and fusing with an oocyte is essential for sexual reproduction. As a major part of differentiation, sperm undergo extensive post-meiotic maturation en route to the oocyte. This is regulated largely by soma-derived cues. In Caenorhabditis elegans, this process is called sperm activation, and it transforms immotile spermatids into migratory fertilization-competent cells. Here, we show that the negative regulator of sperm activation, SWM-1, is produced in an unexpected cell type: body wall muscle. SWM-1 is secreted into the body cavity and enters the gonad; there, it is present with its likely target, TRY-5, a spermiogenesis activator. We show that, in addition to SWM-1, the somatic gonad and body fluid can exchange other factors, suggesting that soma-germ line transfer could affect other reproductive processes. In addition, we show that SWM-1 may have a separate role in the sperm migratory environment, to which it is contributed by both males and hermaphrodites. These findings reveal that late stages in gamete differentiation can be regulated at the whole-organism level by broadly secreted factors.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Daniela R Chavez
- Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA.,Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Ave. NW, Washington, DC 20008, USA
| | - Angela K Snow
- Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA
| | - Joseph R Smith
- Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA
| | - Gillian M Stanfield
- Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA
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Danchin E, Pocheville A, Rey O, Pujol B, Blanchet S. Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis. Biol Rev Camb Philos Soc 2018. [PMCID: PMC6378602 DOI: 10.1111/brv.12453] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
After decades of debate about the existence of non‐genetic inheritance, the focus is now slowly shifting towards dissecting its underlying mechanisms. Here, we propose a new mechanism that, by integrating non‐genetic and genetic inheritance, may help build the long‐sought inclusive vision of evolution. After briefly reviewing the wealth of evidence documenting the existence and ubiquity of non‐genetic inheritance in a table, we review the categories of mechanisms of parent–offspring resemblance that underlie inheritance. We then review several lines of argument for the existence of interactions between non‐genetic and genetic components of inheritance, leading to a discussion of the contrasting timescales of action of non‐genetic and genetic inheritance. This raises the question of how the fidelity of the inheritance system can match the rate of environmental variation. This question is central to understanding the role of different inheritance systems in evolution. We then review and interpret evidence indicating the existence of shifts from inheritance systems with low to higher transmission fidelity. Based on results from different research fields we propose a conceptual hypothesis linking genetic and non‐genetic inheritance systems. According to this hypothesis, over the course of generations, shifts among information systems allow gradual matching between the rate of environmental change and the inheritance fidelity of the corresponding response. A striking conclusion from our review is that documented shifts between types of inherited non‐genetic information converge towards epigenetics (i.e. inclusively heritable molecular variation in gene expression without change in DNA sequence). We then interpret the well‐documented mutagenicity of epigenetic marks as potentially generating a final shift from epigenetic to genetic encoding. This sequence of shifts suggests the existence of a relay in inheritance systems from relatively labile ones to gradually more persistent modes of inheritance, a relay that could constitute a new mechanistic basis for the long‐proposed, but still poorly documented, hypothesis of genetic assimilation. A profound difference between the genocentric and the inclusive vision of heredity revealed by the genetic assimilation relay proposed here lies in the fact that a given form of inheritance can affect the rate of change of other inheritance systems. To explore the consequences of such inter‐connection among inheritance systems, we briefly review published theoretical models to build a model of genetic assimilation focusing on the shift in the engraving of environmentally induced phenotypic variation into the DNA sequence. According to this hypothesis, when environmental change remains stable over a sufficient number of generations, the relay among inheritance systems has the potential to generate a form of genetic assimilation. In this hypothesis, epigenetics appears as a hub by which non‐genetically inherited environmentally induced variation in traits can become genetically encoded over generations, in a form of epigenetically facilitated mutational assimilation. Finally, we illustrate some of the major implications of our hypothetical framework, concerning mutation randomness, the central dogma of molecular biology, concepts of inheritance and the curing of inherited disorders, as well as for the emergence of the inclusive evolutionary synthesis.
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Affiliation(s)
- Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
| | - Arnaud Pocheville
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
- Department of Philosophy and Charles Perkins Centre; University of Sydney; Sydney NSW 2006 Australia
| | - Olivier Rey
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321; 09200 Moulis France
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier; F-66860 Perpignan France
| | - Benoit Pujol
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
| | - Simon Blanchet
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321; 09200 Moulis France
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Liu Y. Darwin's Pangenesis and the Lamarckian Inheritance of Acquired Characters. ADVANCES IN GENETICS 2018; 101:115-144. [PMID: 30037391 DOI: 10.1016/bs.adgen.2018.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Since the earliest days of evolutionary thought, the problem of the inheritance of acquired characters has been a central debate. Darwin accepted the inheritance of acquired characters as an established fact and gave many instances. His Pangenesis was more than anything else an attempt to provide a theory for its explanation. Over the past several decades, there has been increasing evidence for the inheritance of acquired habit and immunity, and for heritable changes induced by food and fertilizer, stress, chemicals, temperature, light and other environmental factors. Many studies also suggest that parental age has certain influences on the characters of offspring. The current explanations include environmentally induced DNA changes (mainly DNA rearrangements and DNA methylation), RNA-mediated inheritance, and horizontal gene transfer. These mechanistic explanations are consistent with Darwin's Pangenesis.
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Affiliation(s)
- Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China; Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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Evolution without standing genetic variation: change in transgenerational plastic response under persistent predation pressure. Heredity (Edinb) 2018; 121:266-281. [PMID: 29959428 DOI: 10.1038/s41437-018-0108-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/22/2018] [Accepted: 06/03/2018] [Indexed: 11/08/2022] Open
Abstract
Transgenerational phenotypic plasticity is a fast non-genetic response to environmental modifications that can buffer the effects of environmental stresses on populations. However, little is known about the evolution of plasticity in the absence of standing genetic variation although several non-genetic inheritance mechanisms have now been identified. Here we monitored the pea aphid transgenerational phenotypic response to ladybird predators (production of winged offspring) during 27 generations of experimental evolution in the absence of initial genetic variation (clonal multiplication starting from a single individual). We found that the frequency of winged aphids first increased rapidly in response to predators and then remained stable over 25 generations, implying a stable phenotypic reconstruction at each generation. We also found that the high frequency of winged aphids persisted for one generation after removing predators. Winged aphid frequency then entered a refractory phase during which it dropped below the level of control lines for at least two generations before returning to it. Interestingly, the persistence of the winged phenotype decreased and the refractory phase lasted longer with the increasing number of generations of exposure to predators. Finally, we found that aphids continuously exposed to predators for 22 generations evolved a significantly weaker plastic response than aphids never exposed to predators, which, in turn, increased their fitness in presence of predators. Our findings therefore showcased an example of experimental evolution of plasticity in the absence of initial genetic variation and highlight the importance of integrating several components of non-genetic inheritance to detect evolutionary responses to environmental changes.
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Cartier J, Smith T, Thomson JP, Rose CM, Khulan B, Heger A, Meehan RR, Drake AJ. Investigation into the role of the germline epigenome in the transmission of glucocorticoid-programmed effects across generations. Genome Biol 2018; 19:50. [PMID: 29636086 PMCID: PMC5891941 DOI: 10.1186/s13059-018-1422-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/16/2018] [Indexed: 12/13/2022] Open
Abstract
Background Early life exposure to adverse environments affects cardiovascular and metabolic systems in the offspring. These programmed effects are transmissible to a second generation through both male and female lines, suggesting germline transmission. We have previously shown that prenatal overexposure to the synthetic glucocorticoid dexamethasone (Dex) in rats reduces birth weight in the first generation (F1), a phenotype which is transmitted to a second generation (F2), particularly through the male line. We hypothesize that Dex exposure affects developing germ cells, resulting in transmissible alterations in DNA methylation, histone marks and/or small RNA in the male germline. Results We profile epigenetic marks in sperm from F1 Sprague Dawley rats expressing a germ cell-specific GFP transgene following Dex or vehicle treatment of the mothers, using methylated DNA immunoprecipitation sequencing, small RNA sequencing and chromatin immunoprecipitation sequencing for H3K4me3, H3K4me1, H3K27me3 and H3K9me3. Although effects on birth weight are transmitted to the F2 generation through the male line, no differences in DNA methylation, histone modifications or small RNA were detected between germ cells and sperm from Dex-exposed animals and controls. Conclusions Although the phenotype is transmitted to a second generation, we are unable to detect specific changes in DNA methylation, common histone modifications or small RNA profiles in sperm. Dex exposure is associated with more variable 5mC levels, particularly at non-promoter loci. Although this could be one mechanism contributing to the observed phenotype, other germline epigenetic modifications or non-epigenetic mechanisms may be responsible for the transmission of programmed effects across generations in this model. Electronic supplementary material The online version of this article (10.1186/s13059-018-1422-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessy Cartier
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Thomas Smith
- MRC Computational Genomics Analysis and Training Programme, University of Oxford, MRC WIMM Centre for Computational Biology, The Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS, UK
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Catherine M Rose
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Batbayar Khulan
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Andreas Heger
- MRC Computational Genomics Analysis and Training Programme, University of Oxford, MRC WIMM Centre for Computational Biology, The Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Amanda J Drake
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
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Jose AM. Replicating and Cycling Stores of Information Perpetuate Life. Bioessays 2018; 40:e1700161. [PMID: 29493806 PMCID: PMC7303024 DOI: 10.1002/bies.201700161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Indexed: 12/12/2022]
Abstract
Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information - one replicating with each cell division and the other cycling with a period of one generation - coevolve while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. See also the video abstract here: https://youtu.be/IdWEL-T6TPU.
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Affiliation(s)
- Antony M. Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Chen W, Zhang X, Fan Y, Li B, Ryabov E, Shi N, Zhao M, Yu Z, Qin C, Zheng Q, Zhang P, Wang H, Jackson S, Cheng Q, Liu Y, Gallusci P, Hong Y. A Genetic Network for Systemic RNA Silencing in Plants. PLANT PHYSIOLOGY 2018; 176:2700-2719. [PMID: 29439213 PMCID: PMC5884585 DOI: 10.1104/pp.17.01828] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/25/2018] [Indexed: 05/20/2023]
Abstract
Non-cell autonomous RNA silencing can spread from cell to cell and over long distances in animals and plants. However, the genetic requirements and signals involved in plant mobile gene silencing are poorly understood. Here, we identified a DICER-LIKE2 (DCL2)-dependent mechanism for systemic spread of posttranscriptional RNA silencing, also known as posttranscriptional gene silencing (PTGS), in Nicotiana benthamiana Using a suite of transgenic DCL RNAi lines coupled with a GFP reporter, we demonstrated that N. benthamiana DCL1, DCL2, DCL3, and DCL4 are required to produce microRNAs and 22, 24, and 21nt small interfering RNAs (siRNAs), respectively. All investigated siRNAs produced in local incipient cells were present at low levels in distal tissues. Inhibition of DCL2 expression reduced the spread of gene silencing, while suppression of DCL3 or DCL4 expression enhanced systemic PTGS. In contrast to DCL4 RNAi lines, DCL2-DCL4 double-RNAi lines developed systemic PTGS similar to that observed in DCL2 RNAi. We further showed that the 21 or 24 nt local siRNAs produced by DCL4 or DCL3 were not involved in long-distance gene silencing. Grafting experiments demonstrated that DCL2 was required in the scion to respond to the signal, but not in the rootstock to produce/send the signal. These results suggest a coordinated DCL genetic pathway in which DCL2 plays an essential role in systemic PTGS in N. benthamiana, while both DCL4 and DCL3 attenuate systemic PTGS. We discuss the potential role of 21, 22, and 24 nt siRNAs in systemic PTGS.
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Affiliation(s)
- Weiwei Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Yaya Fan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Bin Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Eugene Ryabov
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Mei Zhao
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Qianqian Zheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Qi Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, United Kingdom
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Steele EJ, Al-Mufti S, Augustyn KA, Chandrajith R, Coghlan JP, Coulson SG, Ghosh S, Gillman M, Gorczynski RM, Klyce B, Louis G, Mahanama K, Oliver KR, Padron J, Qu J, Schuster JA, Smith WE, Snyder DP, Steele JA, Stewart BJ, Temple R, Tokoro G, Tout CA, Unzicker A, Wainwright M, Wallis J, Wallis DH, Wallis MK, Wetherall J, Wickramasinghe DT, Wickramasinghe JT, Wickramasinghe NC, Liu Y. Cause of Cambrian Explosion - Terrestrial or Cosmic? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 136:3-23. [PMID: 29544820 DOI: 10.1016/j.pbiomolbio.2018.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion - life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.
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Affiliation(s)
- Edward J Steele
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka.
| | - Shirwan Al-Mufti
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Kenneth A Augustyn
- Center for the Physics of Living Organisms, Department of Physics, Michigan Technological University, Michigan, United States
| | | | - John P Coghlan
- University of Melbourne, Office of the Dean, Faculty Medicine, Dentistry and Health Sciences, 3rd Level, Alan Gilbert Building, Australia
| | - S G Coulson
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Sudipto Ghosh
- Metallurgical & Materials Engineering IIT, Kanpur, India
| | - Mark Gillman
- South African Brain Research Institute, 6 Campbell Street, Waverly, Johannesburg, South Africa
| | - Reginald M Gorczynski
- University Toronto Health Network, Toronto General Hospital, University of Toronto, Canada
| | - Brig Klyce
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Godfrey Louis
- Department of Physics, Cochin University of Science and Technology Cochin, India
| | | | - Keith R Oliver
- School of Veterinary and Life Sciences Murdoch University, Perth, WA, Australia
| | - Julio Padron
- Studio Eutropi, Clinical Pathology and Nutrition, Via Pompei 46, Ardea, 00040, Rome, Italy
| | - Jiangwen Qu
- Department of Infectious Disease Control, Tianjin Center for Disease Control and Prevention, China
| | - John A Schuster
- School of History and Philosophy of Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - W E Smith
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Duane P Snyder
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Julian A Steele
- Centre for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Brent J Stewart
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
| | - Robert Temple
- The History of Chinese Culture Foundation, Conway Hall, London, UK
| | - Gensuke Tokoro
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Christopher A Tout
- Institute of Astronomy, The Observatories, Madingley Road, Cambridge, CB3 0HA, UK
| | | | - Milton Wainwright
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka
| | - Jamie Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Daryl H Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Max K Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - John Wetherall
- School of Biomedical Sciences, Perth, Curtin University, WA, Australia
| | - D T Wickramasinghe
- College of Physical and Mathematical Sciences, Australian National University, Canberra, Australia
| | | | - N Chandra Wickramasinghe
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Ow MC, Borziak K, Nichitean AM, Dorus S, Hall SE. Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans. PLoS Genet 2018; 14:e1007219. [PMID: 29447162 PMCID: PMC5831748 DOI: 10.1371/journal.pgen.1007219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 02/28/2018] [Accepted: 01/24/2018] [Indexed: 01/16/2023] Open
Abstract
Environmental stress during early development in animals can have profound effects on adult phenotypes via programmed changes in gene expression. Using the nematode C. elegans, we demonstrated previously that adults retain a cellular memory of their developmental experience that is manifested by differences in gene expression and life history traits; however, the sophistication of this system in response to different environmental stresses, and how it dictates phenotypic plasticity in adults that contribute to increased fitness in response to distinct environmental challenges, was unknown. Using transcriptional profiling, we show here that C. elegans adults indeed retain distinct cellular memories of different environmental conditions. We identified approximately 500 genes in adults that entered dauer due to starvation that exhibit significant opposite (“seesaw”) transcriptional phenotypes compared to adults that entered dauer due to crowding, and are distinct from animals that bypassed dauer. Moreover, we show that two-thirds of the genes in the genome experience a 2-fold or greater seesaw trend in gene expression, and based upon the direction of change, are enriched in large, tightly linked regions on different chromosomes. Importantly, these transcriptional programs correspond to significant changes in brood size depending on the experienced stress. In addition, we demonstrate that while the observed seesaw gene expression changes occur in both somatic and germline tissue, only starvation-induced changes require a functional GLP-4 protein necessary for germline development, and both programs require the Argonaute CSR-1. Thus, our results suggest that signaling between the soma and the germ line can generate phenotypic plasticity as a result of early environmental experience, and likely contribute to increased fitness in adverse conditions and the evolution of the C. elegans genome. Environmental stress during early development in animals can have profound effects on adult behavior and physiology due to programmed changes in gene expression. However, whether different stresses result in distinct changes in traits that allow stressed animals to better survive and reproduce in future adverse conditions is largely unknown. Using the animal model system, C. elegans, we show that adults that experienced starvation exhibit opposite (“seesaw”) genome-wide gene expression changes compared to adults that experienced crowding, and are distinct from animals that experienced favorable conditions. Genes that are similarly up- or downregulated due to either starvation or crowding are located in clusters on the same chromosomes. Importantly, these gene expression changes of differently-stressed animals result in corresponding changes in progeny number, a life history trait of evolutionary significance. These distinct gene expression programs require different signaling pathways that communicate across somatic and germline tissue types. Thus, different environmental stresses experienced early in development induce distinct signaling mechanisms to result in changes in gene expression and reproduction in adults, and likely contribute to increased survival in future adverse conditions.
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Affiliation(s)
- Maria C. Ow
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | - Kirill Borziak
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | | | - Steve Dorus
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | - Sarah E. Hall
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
- * E-mail:
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