1
|
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.
Collapse
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
| |
Collapse
|
2
|
Cao S, Chen ZJ. Transgenerational epigenetic inheritance during plant evolution and breeding. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00112-2. [PMID: 38806375 DOI: 10.1016/j.tplants.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024]
Abstract
Plants can program and reprogram their genomes to create genetic variation and epigenetic modifications, leading to phenotypic plasticity. Although consequences of genetic changes are comprehensible, the basis for transgenerational inheritance of epigenetic variation is elusive. This review addresses contributions of external (environmental) and internal (genomic) factors to the establishment and maintenance of epigenetic memory during plant evolution, crop domestication, and modern breeding. Dynamic and pervasive changes in DNA methylation and chromatin modifications provide a diverse repertoire of epigenetic variation potentially for transgenerational inheritance. Elucidating and harnessing epigenetic inheritance will help us develop innovative breeding strategies and biotechnological tools to improve crop yield and resilience in the face of environmental challenges. Beyond plants, epigenetic principles are shared across sexually reproducing organisms including humans with relevance to medicine and public health.
Collapse
Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
3
|
Alexanian AR. Epigenetic inheritance of acquired traits via stem cells dedifferentiation/differentiation or transdifferentiation cycles. Cells Dev 2024:203928. [PMID: 38768658 DOI: 10.1016/j.cdev.2024.203928] [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: 03/06/2024] [Revised: 04/20/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Inheritance of acquired characteristics is the once widely accepted idea that multiple modifications acquired by an organism during its life, can be inherited by the offspring. This belief is at least as old as Hippocrates and became popular in early 19th century, leading Lamarck to suggest his theory of evolution. Charles Darwin, along with other thinkers of the time attempted to explain the mechanism of acquired traits' inheritance by proposing the theory of pangenesis. While later this and similar theories were rejected because of the lack of hard evidence, the studies aimed at revealing the mechanism by which somatic information can be passed to germ cells have continued up to the present. In this paper, we present a new theory and provide supporting literature to explain this phenomenon. We hypothesize existence of pluripotent adult stem cells that can serve as collectors and carriers of new epigenetic traits by entering different developmentally active organ/tissue compartments through blood circulation and acquiring new epigenetic marks though cycles of differentiation/dedifferentiation or transdifferentiation. During gametogenesis, these epigenetically modified cells are attracted by gonads, transdifferentiate into germ cells, and pass the acquired epigenetic modifications collected from the entire body's somatic cells to the offspring.
Collapse
Affiliation(s)
- Arshak R Alexanian
- Cell Reprogramming & Therapeutics LLC, Wauwatosa (Milwaukee County), WI 53226, USA.
| |
Collapse
|
4
|
Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Murga-Garrido SM, Ting-Chun Pan J, Bhanap P, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally. Cell Rep 2024; 43:114029. [PMID: 38573852 PMCID: PMC11102039 DOI: 10.1016/j.celrep.2024.114029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
The host-microbiota relationship has evolved to shape mammalian physiology, including immunity, metabolism, and development. Germ-free models are widely used to study microbial effects on host processes such as immunity. Here, we find that both germ-free and T cell-deficient mice exhibit a robust sebum secretion defect persisting across multiple generations despite microbial colonization and T cell repletion. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that non-genetic information in the gametes is required for microbial-dependent phenotypic transmission. Accordingly, gene expression in early embryos derived from gametes from germ-free or T cell-deficient mice is strikingly and similarly altered. Our findings demonstrate that microbial- and immune-dependent regulation of non-genetic information in the gametes can transmit inherited phenotypes transgenerationally in mice. This mechanism could rapidly generate phenotypic diversity to enhance host adaptation to environmental perturbations.
Collapse
Affiliation(s)
- Jordan C Harris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bruktawit Goshu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuichi Yokoyama
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lenka Dohnalová
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ellen K White
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adele Harman
- Transgenic Core, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sofía M Murga-Garrido
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie Ting-Chun Pan
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Preeti Bhanap
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Grice
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
5
|
Abstract
Numerous examples of different phenotypic outcomes in response to varying environmental conditions have been described across phyla, from plants to mammals. Here, we examine the impact of the environment on different developmental traits, focusing in particular on one key environmental variable, nutrient availability. We present advances in our understanding of developmental plasticity in response to food variation using the nematode Caenorhabditis elegans, which provides a near-isogenic context while permitting lab-controlled environments and analysis of wild isolates. We discuss how this model has allowed investigators not only to describe developmental plasticity events at the organismal level but also to zoom in on the tissues involved in translating changes in the environment into a plastic response, as well as the underlying molecular pathways, and sometimes associated changes in behaviour. Lastly, we also discuss how early life starvation experiences can be logged to later impact adult physiological traits, and how such memory could be wired.
Collapse
Affiliation(s)
- Sophie Jarriault
- Université de Strasbourg, CNRS, Inserm, IGBMC, Development and Stem Cells Department, UMR 7104 - UMR-S 1258, F-67400 Illkirch, France
| | - Christelle Gally
- Université de Strasbourg, CNRS, Inserm, IGBMC, Development and Stem Cells Department, UMR 7104 - UMR-S 1258, F-67400 Illkirch, France
| |
Collapse
|
6
|
Rybnikov SR, Hübner S, Korol AB. A Numerical Model Supports the Evolutionary Advantage of Recombination Plasticity in Shifting Environments. Am Nat 2024; 203:E78-E91. [PMID: 38358806 DOI: 10.1086/728405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractNumerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions. Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario-when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination in individuals developing in a different environment than their parents and, optionally, also in offspring of such individuals. We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may also appear beneficial when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared with the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms, such as chromatin epigenetics remodeling.
Collapse
|
7
|
Dias BG. Legacies of salient environmental experiences-insights from chemosensation. Chem Senses 2024; 49:bjae002. [PMID: 38219073 PMCID: PMC10825851 DOI: 10.1093/chemse/bjae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 01/15/2024] Open
Abstract
Evidence for parental environments profoundly influencing the physiology, biology, and neurobiology of future generations has been accumulating in the literature. Recent efforts to understand this phenomenon and its underlying mechanisms have sought to use species like rodents and insects to model multi-generational legacies of parental experiences like stress and nutritional exposures. From these studies, we have come to appreciate that parental exposure to salient environmental experiences impacts the cadence of brain development, hormonal responses to stress, and the expression of genes that govern cellular responses to stress in offspring. Recent studies using chemosensory exposure have emerged as a powerful tool to shed new light on how future generations come to be influenced by environments to which parents are exposed. With a specific focus on studies that have leveraged such use of salient chemosensory experiences, this review synthesizes our current understanding of the concept, causes, and consequences of the inheritance of chemosensory legacies by future generations and how this field of inquiry informs the larger picture of how parental experiences can influence offspring biology.
Collapse
Affiliation(s)
- Brian G Dias
- Developmental Neuroscience and Neurogenetics Program, The Saban Research Institute, Los Angeles, CA, United States
- Division of Endocrinology, Diabetes and Metabolism, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, Keck School of Medicine of USC, Los Angeles, CA, United States
| |
Collapse
|
8
|
Zhang Y, Li J, Shi W, Lu L, Zhou Q, Zhang H, Liu R, Pu Y, Yin L. Di(2-ethylhexyl) phthalate induces reproductive toxicity and transgenerational reproductive aging in Caenorhabditis elegans. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122259. [PMID: 37541378 DOI: 10.1016/j.envpol.2023.122259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/06/2023]
Abstract
With the large-scale production and use of plastic products, the global plastic pollution problem is becoming more and more serious. The plasticizer di (2-ethylhexyl) phthalate (DEHP), which is widely used in the production of plastics, has caused great concern for the health of the population. Exposure of organisms to DEHP can cause a variety of health damage, of which reproductive system damage is an important part. At present, there are still few studies on DEHP in reproductive aging, and it is of great significance to explore the role of DEHP in promoting reproductive aging and its underlying mechanism. In this study, the model organism Caenorhabditis elegans (C. elegans) was used to preliminarily explore the mechanism of DEHP-induced female reproductive senescence. The results showed that DEHP reduced the number of offspring and gonad area of C. elegans, resulting in shortened reproductive and life span, abnormal phenotypes in somatic gonad structure including the Emo phenotype, the BOW phenotype, a twisted gonad arm, and atrophied oocytes. Biochemical studies showed that DEHP promoted oxidative stress and autophagy in C. elegans. Further, we found the decreased number of offspring, malformed somatic gonad structure, oxidative damage and autophagy induced by DEHP in parental worms can be inheritance to the not directly exposed offspring.
Collapse
Affiliation(s)
- Ying Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Jingjing Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Wei Shi
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Lu Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Qian Zhou
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Hu Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| |
Collapse
|
9
|
Guskjolen A, Cembrowski MS. Engram neurons: Encoding, consolidation, retrieval, and forgetting of memory. Mol Psychiatry 2023; 28:3207-3219. [PMID: 37369721 PMCID: PMC10618102 DOI: 10.1038/s41380-023-02137-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Tremendous strides have been made in our understanding of the neurobiological substrates of memory - the so-called memory "engram". Here, we integrate recent progress in the engram field to illustrate how engram neurons transform across the "lifespan" of a memory - from initial memory encoding, to consolidation and retrieval, and ultimately to forgetting. To do so, we first describe how cell-intrinsic properties shape the initial emergence of the engram at memory encoding. Second, we highlight how these encoding neurons preferentially participate in synaptic- and systems-level consolidation of memory. Third, we describe how these changes during encoding and consolidation guide neural reactivation during retrieval, and facilitate memory recall. Fourth, we describe neurobiological mechanisms of forgetting, and how these mechanisms can counteract engram properties established during memory encoding, consolidation, and retrieval. Motivated by recent experimental results across these four sections, we conclude by proposing some conceptual extensions to the traditional view of the engram, including broadening the view of cell-type participation within engrams and across memory stages. In collection, our review synthesizes general principles of the engram across memory stages, and describes future avenues to further understand the dynamic engram.
Collapse
Affiliation(s)
- Axel Guskjolen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
10
|
Abay-Nørgaard S, Tapia MC, Zeijdner M, Kim JH, Won KJ, Porse B, Salcini AE. Inter and transgenerational impact of H3K4 methylation in neuronal homeostasis. Life Sci Alliance 2023; 6:e202301970. [PMID: 37225426 PMCID: PMC10209521 DOI: 10.26508/lsa.202301970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
Epigenetic marks and associated traits can be transmitted for one or more generations, phenomena known respectively as inter- or transgenerational epigenetic inheritance. It remains unknown if genetically and conditionally induced aberrant epigenetic states can influence the development of the nervous system across generations. Here, we show, using Caenorhabditis elegans as a model system, that alteration of H3K4me3 levels in the parental generation, caused by genetic manipulation or changes in parental conditions, has, respectively, trans- and intergenerational effects on H3K4 methylome, transcriptome, and nervous system development. Thus, our study reveals the relevance of H3K4me3 transmission and maintenance in preventing long-lasting deleterious effects in nervous system homeostasis.
Collapse
Affiliation(s)
- Steffen Abay-Nørgaard
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marta Cecylia Tapia
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Mandoh Zeijdner
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeonghwan Henry Kim
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Porse
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
11
|
Silva-García CG. Devo-Aging: Intersections Between Development and Aging. GeroScience 2023; 45:2145-2159. [PMID: 37160658 PMCID: PMC10651630 DOI: 10.1007/s11357-023-00809-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/25/2023] [Indexed: 05/11/2023] Open
Abstract
There are two fundamental questions in developmental biology. How does a single fertilized cell give rise to a whole body? and how does this body later produce progeny? Synchronization of these embryonic and postembryonic developments ensures continuity of life from one generation to the next. An enormous amount of work has been done to unravel the molecular mechanisms behind these processes, but more recently, modern developmental biology has been expanded to study development in wider contexts, including regeneration, environment, disease, and even aging. However, we have just started to understand how the mechanisms that govern development also regulate aging. This review discusses examples of signaling pathways involved in development to elucidate how their regulation influences healthspan and lifespan. Therefore, a better knowledge of developmental signaling pathways stresses the possibility of using them as innovative biomarkers and targets for aging and age-related diseases.
Collapse
Affiliation(s)
- Carlos Giovanni Silva-García
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
- Center on the Biology of Aging, Brown University, Providence, RI, USA.
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Gaeta AL, Willicott K, Willicott CW, McKay LE, Keogh CM, Altman TJ, Kimble LC, Yarbrough AL, Caldwell KA, Caldwell GA. Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson's disease. iScience 2023; 26:106859. [PMID: 37260751 PMCID: PMC10227375 DOI: 10.1016/j.isci.2023.106859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/03/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Failure of inherently protective cellular processes and misfolded protein-associated stress contribute to the progressive loss of dopamine (DA) neurons characteristic of Parkinson's disease (PD). A disease-modifying role for the microbiome has recently emerged in PD, representing an impetus to employ the soil-dwelling nematode, Caenorhabditis elegans, as a preclinical model to correlate changes in gene expression with neurodegeneration in transgenic animals grown on distinct bacterial food sources. Even under tightly controlled conditions, hundreds of differentially expressed genes and a robust neuroprotective response were discerned between clonal C. elegans strains overexpressing human alpha-synuclein in the DA neurons fed either one of only two subspecies of Escherichia coli. Moreover, this neuroprotection persisted in a transgenerational manner. Genetic analysis revealed a requirement for the double-stranded RNA (dsRNA)-mediated gene silencing machinery in conferring neuroprotection. In delineating the contribution of individual genes, evidence emerged for endopeptidase activity and heme-associated pathway(s) as mechanistic components for modulating dopaminergic neuroprotection.
Collapse
Affiliation(s)
- Anthony L. Gaeta
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Karolina Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Corey W. Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Luke E. McKay
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Candice M. Keogh
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Tyler J. Altman
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Logan C. Kimble
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Abigail L. Yarbrough
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
14
|
Cabej NR. On the origin and nature of nongenetic information in eumetazoans. Ann N Y Acad Sci 2023. [PMID: 37154677 DOI: 10.1111/nyas.15001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.
Collapse
Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
| |
Collapse
|
15
|
Vogt MC, Hobert O. Starvation-induced changes in somatic insulin/IGF-1R signaling drive metabolic programming across generations. SCIENCE ADVANCES 2023; 9:eade1817. [PMID: 37027477 PMCID: PMC10081852 DOI: 10.1126/sciadv.ade1817] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/08/2023] [Indexed: 05/30/2023]
Abstract
Exposure to adverse nutritional and metabolic environments during critical periods of development can exert long-lasting effects on health outcomes of an individual and its descendants. Although such metabolic programming has been observed in multiple species and in response to distinct nutritional stressors, conclusive insights into signaling pathways and mechanisms responsible for initiating, mediating, and manifesting changes to metabolism and behavior across generations remain scarce. By using a starvation paradigm in Caenorhabditis elegans, we show that starvation-induced changes in dauer formation-16/forkhead box transcription factor class O (DAF-16/FoxO) activity, the main downstream target of insulin/insulin-like growth factor 1 (IGF-1) receptor signaling, are responsible for metabolic programming phenotypes. Tissue-specific depletion of DAF-16/FoxO during distinct developmental time points demonstrates that DAF-16/FoxO acts in somatic tissues, but not directly in the germline, to both initiate and manifest metabolic programming. In conclusion, our study deciphers multifaceted and critical roles of highly conserved insulin/IGF-1 receptor signaling in determining health outcomes and behavior across generations.
Collapse
|
16
|
Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and immune system non-genetically affect offspring phenotypes transgenerationally. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535940. [PMID: 37066207 PMCID: PMC10104111 DOI: 10.1101/2023.04.06.535940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The host-microbiota relationship has evolved to shape mammalian processes, including immunity, metabolism, and development 1-3 . Host phenotypes change in direct response to microbial exposures by the individual. Here we show that the microbiota induces phenotypic change not only in the individual but also in their succeeding generations of progeny. We found that germ-free mice exhibit a robust sebum secretion defect and transcriptional changes in various organs, persisting across multiple generations despite microbial colonization and breeding with conventional mice. Host-microbe interactions could be involved in this process, since T cell-deficient mice, which display defective sebum secretion 4 , also transgenerationally transmit their phenotype to progeny. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that epigenetic information in the gametes is required for phenotypic transmission. Accordingly, small non-coding RNAs that can regulate embryonic gene expression 5 were strikingly and similarly altered in gametes of germ-free and T cell-deficient mice. Thus, we have uncovered a novel mechanism whereby the microbiota and immune system induce phenotypic changes in successive generations of offspring. This epigenetic form of inheritance could be advantageous for host adaptation to environmental perturbation, where phenotypic diversity can be introduced more rapidly than by genetic mutation.
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Wilson R, Le Bourgeois M, Perez M, Sarkies P. Fluctuations in chromatin state at regulatory loci occur spontaneously under relaxed selection and are associated with epigenetically inherited variation in C. elegans gene expression. PLoS Genet 2023; 19:e1010647. [PMID: 36862744 PMCID: PMC10013927 DOI: 10.1371/journal.pgen.1010647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 02/01/2023] [Indexed: 03/03/2023] Open
Abstract
Some epigenetic information can be transmitted between generations without changes in the underlying DNA sequence. Changes in epigenetic regulators, termed epimutations, can occur spontaneously and be propagated in populations in a manner reminiscent of DNA mutations. Small RNA-based epimutations occur in C. elegans and persist for around 3-5 generations on average. Here, we explored whether chromatin states also undergo spontaneous change and whether this could be a potential alternative mechanism for transgenerational inheritance of gene expression changes. We compared the chromatin and gene expression profiles at matched time points from three independent lineages of C. elegans propagated at minimal population size. Spontaneous changes in chromatin occurred in around 1% of regulatory regions each generation. Some were heritable epimutations and were significantly enriched for heritable changes in expression of nearby protein-coding genes. Most chromatin-based epimutations were short-lived but a subset had longer duration. Genes subject to long-lived epimutations were enriched for multiple components of xenobiotic response pathways. This points to a possible role for epimutations in adaptation to environmental stressors.
Collapse
Affiliation(s)
- Rachel Wilson
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom.,Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Marcos Perez
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
19
|
Wang X, Ramat A, Simonelig M, Liu MF. Emerging roles and functional mechanisms of PIWI-interacting RNAs. Nat Rev Mol Cell Biol 2023; 24:123-141. [PMID: 36104626 DOI: 10.1038/s41580-022-00528-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 02/02/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with proteins of the PIWI clade of the Argonaute family. First identified in animal germ line cells, piRNAs have essential roles in germ line development. The first function of PIWI-piRNA complexes to be described was the silencing of transposable elements, which is crucial for maintaining the integrity of the germ line genome. Later studies provided new insights into the functions of PIWI-piRNA complexes by demonstrating that they regulate protein-coding genes. Recent studies of piRNA biology, including in new model organisms such as golden hamsters, have deepened our understanding of both piRNA biogenesis and piRNA function. In this Review, we discuss the most recent advances in our understanding of piRNA biogenesis, the molecular mechanisms of piRNA function and the emerging roles of piRNAs in germ line development mainly in flies and mice, and in infertility, cancer and neurological diseases in humans.
Collapse
Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Anne Ramat
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. .,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
| |
Collapse
|
20
|
Rodriguez JD, Katz DJ. Lineage Tracing and Single-Cell RNA-seq in C. elegans to Analyze Transgenerational Epigenetic Phenotypes Inherited from Germ Cells. Methods Mol Biol 2023; 2677:61-79. [PMID: 37464235 DOI: 10.1007/978-1-0716-3259-8_3] [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] [Indexed: 07/20/2023]
Abstract
The last several years have seen an increasing number of examples of transgenerational epigenetic inheritance, in which phenotypes are inherited for three or more generations without changes to the underlying DNA sequence. One model system that has been particularly useful for studying transgenerational epigenetic inheritance is C. elegans. Their short generation time and hermaphroditic reproduction have allowed multiple transgenerational phenotypes to be identified, including aging, fertility, and behavior. However, it is still not clear how transgenerational epigenetic inheritance from the germline affects embryogenesis. Fortunately, the C. elegans embryo has a unique property that makes it ideal for addressing this question: they develop via an invariant lineage, with each cell undergoing stereotypical cell divisions to adopt the same cell fate in every individual embryo. Because of this invariant cell lineage, automated lineage tracing and single-cell RNA-seq can be employed to determine how transgenerational epigenetic inheritance from the germline affects developmental timing and cell fate. Unfortunately, difficulties with these techniques have severely limited their adoption in the community. Here, we provide a practical guide to automated lineage tracing coupled with single-cell RNA-seq to facilitate their use in studying transgenerational epigenetic inheritance in C. elegans embryos.
Collapse
Affiliation(s)
- Juan D Rodriguez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Katz
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
21
|
Wang SY, Kim K, O'Brown ZK, Levan A, Dodson AE, Kennedy SG, Chernoff C, Greer EL. Hypoxia induces transgenerational epigenetic inheritance of small RNAs. Cell Rep 2022; 41:111800. [PMID: 36516753 PMCID: PMC9847139 DOI: 10.1016/j.celrep.2022.111800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/23/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
Animals sense and adapt to decreased oxygen availability, but whether and how hypoxia exposure in ancestors can elicit phenotypic consequences in normoxia-reared descendants are unclear. We show that hypoxia educes an intergenerational reduction in lipids and a transgenerational reduction in fertility in the nematode Caenorhabditis elegans. The transmission of these epigenetic phenotypes is dependent on repressive histone-modifying enzymes and the argonaute HRDE-1. Feeding naive C. elegans small RNAs extracted from hypoxia-treated worms is sufficient to induce a fertility defect. Furthermore, the endogenous small interfering RNA F44E5.4/5 is upregulated intergenerationally in response to hypoxia, and soaking naive normoxia-reared C. elegans with F44E5.4/5 double-stranded RNA (dsRNA) is sufficient to induce an intergenerational fertility defect. Finally, we demonstrate that labeled F44E5.4/5 dsRNA is itself transmitted from parents to children. Our results suggest that small RNAs respond to the environment and are sufficient to transmit non-genetic information from parents to their naive children.
Collapse
Affiliation(s)
- Simon Yuan Wang
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Kathleen Kim
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zach Klapholz O'Brown
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Aileen Levan
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Anne Elizabeth Dodson
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Scott G Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Chaim Chernoff
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| |
Collapse
|
22
|
PRETTY: A Parallel Transgenerational Learning-Assisted Evolutionary Algorithm for Computationally Expensive Multi-Objective Optimization. Inf Sci (N Y) 2022. [DOI: 10.1016/j.ins.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
23
|
Duxbury EML, Carlsson H, Sales K, Sultanova Z, Immler S, Chapman T, Maklakov AA. Multigenerational downregulation of insulin/IGF-1 signaling in adulthood improves lineage survival, reproduction, and fitness in Caenorhabditis elegans supporting the developmental theory of ageing. Evolution 2022; 76:2829-2845. [PMID: 36199198 PMCID: PMC10092551 DOI: 10.1111/evo.14640] [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: 03/21/2022] [Revised: 07/18/2022] [Accepted: 09/08/2022] [Indexed: 01/22/2023]
Abstract
Adulthood-only downregulation of insulin/IGF-1 signaling (IIS), an evolutionarily conserved pathway regulating resource allocation between somatic maintenance and reproduction, increases life span without fecundity cost in the nematode, Caenorhabditis elegans. However, long-term multigenerational effects of reduced IIS remain unexplored and are proposed to carry costs for offspring quality. To test this hypothesis, we ran a mutation accumulation (MA) experiment and downregulated IIS in half of the 400 MA lines by silencing daf-2 gene expression using RNA interference (RNAi) across 40 generations. Contrary to the prediction, adulthood-only daf-2 RNAi reduced extinction of MA lines both under UV-induced and spontaneous MA. Fitness of the surviving UV-induced MA lines was higher under daf-2 RNAi. Reduced IIS increased intergenerational F1 offspring fitness under UV stress but had no quantifiable transgenerational effects. Functional hrde-1 was required for the benefits of multigenerational daf-2 RNAi. Overall, we found net benefit to fitness from multigenerational reduction of IIS and the benefits became more apparent under stress. Because reduced daf-2 expression during development carries fitness costs, we suggest that our findings are best explained by the developmental theory of ageing, which maintains that the decline in the force of selection with age results in poorly regulated gene expression in adulthood.
Collapse
Affiliation(s)
- Elizabeth M L Duxbury
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Hanne Carlsson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Kris Sales
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Zahida Sultanova
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Alexei A Maklakov
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Ohno H, Bao Z. Small RNAs couple embryonic developmental programs to gut microbes. SCIENCE ADVANCES 2022; 8:eabl7663. [PMID: 35319987 PMCID: PMC8942359 DOI: 10.1126/sciadv.abl7663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Embryogenesis has long been known for its robustness to environmental factors. Although developmental tuning of embryogenesis to the environment experienced by the parent may be beneficial, little is understood on whether and how developmental patterns proactively change. Here, we show that Caenorhabditis elegans undergoes alternative embryogenesis in response to maternal gut microbes. Harmful microbes result in altered endodermal cell divisions; morphological changes, including left-right asymmetric development; double association between intestinal and primordial germ cells; and partial rescue of fecundity. The miR-35 microRNA family, which is controlled by systemic endogenous RNA interference and targets the β-transducin repeat-containing protein/cell division cycle 25 (CDC25) pathway, transmits intergenerational information to regulate cell divisions and reproduction. Our findings challenge the widespread assumption that C. elegans has an invariant cell lineage that consists of a fixed cell number and provide insights into how organisms optimize embryogenesis to adapt to environmental changes through epigenetic control.
Collapse
|
26
|
Quarato P, Singh M, Bourdon L, Cecere G. Inheritance and maintenance of small RNA-mediated epigenetic effects. Bioessays 2022; 44:e2100284. [PMID: 35338497 DOI: 10.1002/bies.202100284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 11/08/2022]
Abstract
Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA-dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs.
Collapse
Affiliation(s)
- Piergiuseppe Quarato
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Meetali Singh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Loan Bourdon
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Germano Cecere
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| |
Collapse
|
27
|
Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nat Rev Mol Cell Biol 2022; 23:185-203. [PMID: 34707241 PMCID: PMC9208737 DOI: 10.1038/s41580-021-00425-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.
Collapse
Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
28
|
Zagoskin MV, Wang J, Neff AT, Veronezi GMB, Davis RE. Small RNA pathways in the nematode Ascaris in the absence of piRNAs. Nat Commun 2022; 13:837. [PMID: 35149688 PMCID: PMC8837657 DOI: 10.1038/s41467-022-28482-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Small RNA pathways play key and diverse regulatory roles in C. elegans, but our understanding of their conservation and contributions in other nematodes is limited. We analyzed small RNA pathways in the divergent parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that associate with secondary 5’-triphosphate 22-24G-RNAs. These small RNAs target repetitive sequences or mature mRNAs and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Even in the absence of a piRNA pathway, Ascaris CSR-1 may still function to “license” as well as fine-tune or repress gene expression. Ascaris ALG-4 and its associated 26G-RNAs target and likely repress specific mRNAs during testis meiosis. Ascaris WAGO small RNAs demonstrate target plasticity changing their targets between repeats and mRNAs during development. We provide a unique and comprehensive view of mRNA and small RNA expression throughout spermatogenesis. Overall, our study illustrates the conservation, divergence, dynamics, and flexibility of small RNA pathways in nematodes. The parasitic nematode Ascaris lacks piRNAs. Here the authors compare Argonaute proteins and small RNAs from C. elegans and Ascaris, expanding our understanding of the conservation, divergence, and flexibility of Argonautes and small RNA pathways in nematodes.
Collapse
Affiliation(s)
- Maxim V Zagoskin
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA. .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA. .,UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA.
| | - Ashley T Neff
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.
| |
Collapse
|
29
|
Toker IA, Lev I, Mor Y, Gurevich Y, Fisher D, Houri-Zeevi L, Antonova O, Doron H, Anava S, Gingold H, Hadany L, Shaham S, Rechavi O. Transgenerational inheritance of sexual attractiveness via small RNAs enhances evolvability in C. elegans. Dev Cell 2022; 57:298-309.e9. [PMID: 35134343 PMCID: PMC8826646 DOI: 10.1016/j.devcel.2022.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 09/12/2021] [Accepted: 01/05/2022] [Indexed: 11/16/2022]
Abstract
It is unknown whether transient transgenerational epigenetic responses to environmental challenges affect the process of evolution, which typically unfolds over many generations. Here, we show that in C. elegans, inherited small RNAs control genetic variation by regulating the crucial decision of whether to self-fertilize or outcross. We found that under stressful temperatures, younger hermaphrodites secrete a male-attracting pheromone. Attractiveness transmits transgenerationally to unstressed progeny via heritable small RNAs and the Argonaute Heritable RNAi Deficient-1 (HRDE-1). We identified an endogenous small interfering RNA pathway, enriched in endo-siRNAs that target sperm genes, that transgenerationally regulates sexual attraction, male prevalence, and outcrossing rates. Multigenerational mating competition experiments and mathematical simulations revealed that over generations, animals that inherit attractiveness mate more and their alleles spread in the population. We propose that the sperm serves as a "stress-sensor" that, via small RNA inheritance, promotes outcrossing in challenging environments when increasing genetic variation is advantageous.
Collapse
Affiliation(s)
- Itai Antoine Toker
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - Itamar Lev
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - Yael Mor
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - Yael Gurevich
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Doron Fisher
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Leah Houri-Zeevi
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Olga Antonova
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hila Doron
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Sarit Anava
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hila Gingold
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Lilach Hadany
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY, USA
| | - Oded Rechavi
- Department of Neurobiology, Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
30
|
Abstract
Increasing evidence indicates that non-DNA sequence-based epigenetic information can be inherited across several generations in organisms ranging from yeast to plants to humans. This raises the possibility of heritable 'epimutations' contributing to heritable phenotypic variation and thus to evolution. Recent work has shed light on both the signals that underpin these epimutations, including DNA methylation, histone modifications and non-coding RNAs, and the mechanisms by which they are transmitted across generations at the molecular level. These mechanisms can vary greatly among species and have a more limited effect in mammals than in plants and other animal species. Nevertheless, common principles are emerging, with transmission occurring either via direct replicative mechanisms or indirect reconstruction of the signal in subsequent generations. As these processes become clearer we continue to improve our understanding of the distinctive features and relative contribution of DNA sequence and epigenetic variation to heritable differences in phenotype.
Collapse
|
31
|
How Epigenetics Can Enhance Pig Welfare? Animals (Basel) 2021; 12:ani12010032. [PMID: 35011138 PMCID: PMC8749669 DOI: 10.3390/ani12010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetics works as an interface between the individual and its environment to provide phenotypic plasticity to increase individual adaptation capabilities. Recently, a wide variety of epi-genetic findings have indicated evidence for its application in the development of putative epi-biomarkers of stress in farm animals. The purpose of this study was to evaluate previously reported stress epi-biomarkers in swine and encourage researchers to investigate potential paths for the development of a robust molecular tool for animal welfare certification. In this literature review, we report on the scientific concerns in the swine production chain, the management carried out on the farms, and the potential implications of these practices for the animals' welfare and their epigenome. To assess reported epi-biomarkers, we identified, from previous studies, potentially stress-related genes surrounding epi-biomarkers. With those genes, we carried out a functional enrichment analysis of differentially methylated regions (DMRs) of the DNA of swine subjected to different stress-related conditions (e.g., heat stress, intrauterine insult, and sanitary challenges). We identified potential epi-biomarkers for target analysis, which could be added to the current guidelines and certification schemes to guarantee and certify animal welfare on farms. We believe that this technology may have the power to increase consumers' trust in animal welfare.
Collapse
|
32
|
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.
Collapse
|
33
|
Seroussi U, Li C, Sundby AE, Lee TL, Claycomb JM, Saltzman AL. Mechanisms of epigenetic regulation by C. elegans nuclear RNA interference pathways. Semin Cell Dev Biol 2021; 127:142-154. [PMID: 34876343 DOI: 10.1016/j.semcdb.2021.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/17/2021] [Accepted: 11/17/2021] [Indexed: 01/06/2023]
Abstract
RNA interference (RNAi) is a highly conserved gene regulatory phenomenon whereby Argonaute/small RNA (AGO/sRNA) complexes target transcripts by antisense complementarity to modulate gene expression. While initially appreciated as a cytoplasmic process, RNAi can also occur in the nucleus where AGO/sRNA complexes are recruited to nascent transcripts. Nuclear AGO/sRNA complexes recruit co-factors that regulate transcription by inhibiting RNA Polymerase II, modifying histones, compacting chromatin and, in some organisms, methylating DNA. C. elegans has a longstanding history in unveiling the mechanisms of RNAi and has become an outstanding model to delineate the mechanisms underlying nuclear RNAi. In this review we highlight recent discoveries in the field of nuclear RNAi in C. elegans and the roles of nuclear RNAi in the regulation of gene expression, chromatin organization, genome stability, and transgenerational epigenetic inheritance.
Collapse
Affiliation(s)
- Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chengyin Li
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Adam E Sundby
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tammy L Lee
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Arneet L Saltzman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
34
|
Das S, Min S, Prahlad V. Gene bookmarking by the heat shock transcription factor programs the insulin-like signaling pathway. Mol Cell 2021; 81:4843-4860.e8. [PMID: 34648748 PMCID: PMC8642288 DOI: 10.1016/j.molcel.2021.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/09/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022]
Abstract
Maternal stress can have long-lasting epigenetic effects on offspring. To examine how epigenetic changes are triggered by stress, we examined the effects of activating the universal stress-responsive heat shock transcription factor HSF-1 in the germline of Caenorhabditis elegans. We show that, when activated in germ cells, HSF-1 recruits MET-2, the putative histone 3 lysine 9 (H3K9) methyltransferase responsible for repressive H3K9me2 (H3K9 dimethyl) marks in chromatin, and negatively bookmarks the insulin receptor daf-2 and other HSF-1 target genes. Increased H3K9me2 at these genes persists in adult progeny and shifts their stress response strategy away from inducible chaperone expression as a mechanism to survive stress and instead rely on decreased insulin/insulin growth factor (IGF-1)-like signaling (IIS). Depending on the duration of maternal heat stress exposure, this epigenetic memory is inherited by the next generation. Thus, paradoxically, HSF-1 recruits the germline machinery normally responsible for erasing transcriptional memory but, instead, establishes a heritable epigenetic memory of prior stress exposure.
Collapse
Affiliation(s)
- Srijit Das
- Department of Biology, Aging Mind and Brain Initiative, 143 Biology Building, Iowa City, IA 52242-1324, USA
| | - Sehee Min
- Department of Biology, Aging Mind and Brain Initiative, 143 Biology Building, Iowa City, IA 52242-1324, USA
| | - Veena Prahlad
- Department of Biology, Aging Mind and Brain Initiative, 143 Biology Building, Iowa City, IA 52242-1324, USA; Department of Biology, 143 Biology Building, Iowa City, IA 52242-1324, USA; Iowa Neuroscience Institute, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA 52242, USA.
| |
Collapse
|
35
|
Özdemir I, Steiner FA. Transmission of chromatin states across generations in C. elegans. Semin Cell Dev Biol 2021; 127:133-141. [PMID: 34823984 DOI: 10.1016/j.semcdb.2021.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
Abstract
Epigenetic inheritance refers to the transmission of phenotypes across generations without affecting the genomic DNA sequence. Even though it has been documented in many species in fungi, animals and plants, the mechanisms underlying epigenetic inheritance are not fully uncovered. Epialleles, the heritable units of epigenetic information, can take the form of several biomolecules, including histones and their post-translational modifications (PTMs). Here, we review the recent advances in the understanding of the transmission of histone variants and histone PTM patterns across generations in C. elegans. We provide a general overview of the intergenerational and transgenerational inheritance of histone PTMs and their modifiers and discuss the interplay among different histone PTMs. We also evaluate soma-germ line communication and its impact on the inheritance of epigenetic traits.
Collapse
Affiliation(s)
- Isa Özdemir
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland.
| |
Collapse
|
36
|
Cecere G. Small RNAs in epigenetic inheritance: from mechanisms to trait transmission. FEBS Lett 2021; 595:2953-2977. [PMID: 34671979 PMCID: PMC9298081 DOI: 10.1002/1873-3468.14210] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 01/02/2023]
Abstract
Inherited information is transmitted to progeny primarily by the genome through the gametes. However, in recent years, epigenetic inheritance has been demonstrated in several organisms, including animals. Although it is clear that certain post‐translational histone modifications, DNA methylation, and noncoding RNAs regulate epigenetic inheritance, the molecular mechanisms responsible for epigenetic inheritance are incompletely understood. This review focuses on the role of small RNAs in transmitting epigenetic information across generations in animals. Examples of documented cases of transgenerational epigenetic inheritance are discussed, from the silencing of transgenes to the inheritance of complex traits, such as fertility, stress responses, infections, and behavior. Experimental evidence supporting the idea that small RNAs are epigenetic molecules capable of transmitting traits across generations is highlighted, focusing on the mechanisms by which small RNAs achieve such a function. Just as the role of small RNAs in epigenetic processes is redefining the concept of inheritance, so too our understanding of the molecular pathways and mechanisms that govern epigenetic inheritance in animals is radically changing.
Collapse
Affiliation(s)
- Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR3738, CNRS, Paris, France
| |
Collapse
|
37
|
Huang S, Yoshitake K, Asakawa S. A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans. Int J Mol Sci 2021; 22:ijms222011166. [PMID: 34681826 PMCID: PMC8538981 DOI: 10.3390/ijms222011166] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.
Collapse
Affiliation(s)
- Songqian Huang
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
| | | | - Shuichi Asakawa
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
| |
Collapse
|
38
|
Burton NO, Willis A, Fisher K, Braukmann F, Price J, Stevens L, Baugh LR, Reinke A, Miska EA. Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs. eLife 2021; 10:e73425. [PMID: 34622777 PMCID: PMC8570697 DOI: 10.7554/elife.73425] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Despite reports of parental exposure to stress promoting physiological adaptations in progeny in diverse organisms, there remains considerable debate over the significance and evolutionary conservation of such multigenerational effects. Here, we investigate four independent models of intergenerational adaptations to stress in Caenorhabditis elegans - bacterial infection, eukaryotic infection, osmotic stress, and nutrient stress - across multiple species. We found that all four intergenerational physiological adaptations are conserved in at least one other species, that they are stress -specific, and that they have deleterious tradeoffs in mismatched environments. By profiling the effects of parental bacterial infection and osmotic stress exposure on progeny gene expression across species, we established a core set of 587 genes that exhibited a greater than twofold intergenerational change in expression in response to stress in C. elegans and at least one other species, as well as a set of 37 highly conserved genes that exhibited a greater than twofold intergenerational change in expression in all four species tested. Furthermore, we provide evidence suggesting that presumed adaptive and deleterious intergenerational effects are molecularly related at the gene expression level. Lastly, we found that none of the effects we detected of these stresses on C. elegans F1 progeny gene expression persisted transgenerationally three generations after stress exposure. We conclude that intergenerational responses to stress play a substantial and evolutionarily conserved role in regulating animal physiology and that the vast majority of the effects of parental stress on progeny gene expression are reversible and not maintained transgenerationally.
Collapse
Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Van Andel InstituteGrand RapidsUnited States
| | - Alexandra Willis
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Kinsey Fisher
- Department of Biology, Duke UniversityDurhamUnited States
| | - Fabian Braukmann
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Jonathan Price
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - L Ryan Baugh
- Department of Biology, Duke UniversityDurhamUnited States
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - Aaron Reinke
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Eric A Miska
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| |
Collapse
|
39
|
Nieberding CM, Marcantonio M, Voda R, Enriquez T, Visser B. The Evolutionary Relevance of Social Learning and Transmission in Non-Social Arthropods with a Focus on Oviposition-Related Behaviors. Genes (Basel) 2021; 12:genes12101466. [PMID: 34680861 PMCID: PMC8536077 DOI: 10.3390/genes12101466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 12/04/2022] Open
Abstract
Research on social learning has centered around vertebrates, but evidence is accumulating that small-brained, non-social arthropods also learn from others. Social learning can lead to social inheritance when socially acquired behaviors are transmitted to subsequent generations. Using oviposition site selection, a critical behavior for most arthropods, as an example, we first highlight the complementarities between social and classical genetic inheritance. We then discuss the relevance of studying social learning and transmission in non-social arthropods and document known cases in the literature, including examples of social learning from con- and hetero-specifics. We further highlight under which conditions social learning can be adaptive or not. We conclude that non-social arthropods and the study of oviposition behavior offer unparalleled opportunities to unravel the importance of social learning and inheritance for animal evolution.
Collapse
Affiliation(s)
- Caroline M. Nieberding
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UCLouvain, 1348 Louvain-la-Neuve, Belgium; (M.M.); (R.V.)
- Correspondence:
| | - Matteo Marcantonio
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UCLouvain, 1348 Louvain-la-Neuve, Belgium; (M.M.); (R.V.)
| | - Raluca Voda
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UCLouvain, 1348 Louvain-la-Neuve, Belgium; (M.M.); (R.V.)
| | - Thomas Enriquez
- Evolution and Ecophysiology Group, Earth and Life Institute, UCLouvain, 1348 Louvain-la-Neuve, Belgium; (T.E.); (B.V.)
| | - Bertanne Visser
- Evolution and Ecophysiology Group, Earth and Life Institute, UCLouvain, 1348 Louvain-la-Neuve, Belgium; (T.E.); (B.V.)
| |
Collapse
|
40
|
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.
Collapse
|
41
|
Olivares-Castro G, Cáceres-Jensen L, Guerrero-Bosagna C, Villagra C. Insect Epigenetic Mechanisms Facing Anthropogenic-Derived Contamination, an Overview. INSECTS 2021; 12:780. [PMID: 34564220 PMCID: PMC8468710 DOI: 10.3390/insects12090780] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/14/2022]
Abstract
Currently, the human species has been recognized as the primary species responsible for Earth's biodiversity decline. Contamination by different chemical compounds, such as pesticides, is among the main causes of population decreases and species extinction. Insects are key for ecosystem maintenance; unfortunately, their populations are being drastically affected by human-derived disturbances. Pesticides, applied in agricultural and urban environments, are capable of polluting soil and water sources, reaching non-target organisms (native and introduced). Pesticides alter insect's development, physiology, and inheritance. Recently, a link between pesticide effects on insects and their epigenetic molecular mechanisms (EMMs) has been demonstrated. EMMs are capable of regulating gene expression without modifying genetic sequences, resulting in the expression of different stress responses as well as compensatory mechanisms. In this work, we review the main anthropogenic contaminants capable of affecting insect biology and of triggering EMMs. EMMs are involved in the development of several diseases in native insects affected by pesticides (e.g., anomalous teratogenic reactions). Additionally, EMMs also may allow for the survival of some species (mainly pests) under contamination-derived habitats; this may lead to biodiversity decline and further biotic homogenization. We illustrate these patterns by reviewing the effect of neonicotinoid insecticides, insect EMMs, and their ecological consequences.
Collapse
Affiliation(s)
- Gabriela Olivares-Castro
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
| | - Lizethly Cáceres-Jensen
- Laboratorio de Físicoquímica Analítica, Departamento de Química, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Santiago 7760197, Chile;
| | - Carlos Guerrero-Bosagna
- Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden;
- Environmental Toxicology Program, Department of Integrative Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Cristian Villagra
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
| |
Collapse
|
42
|
Burton NO, Greer EL. Multigenerational epigenetic inheritance: Transmitting information across generations. Semin Cell Dev Biol 2021; 127:121-132. [PMID: 34426067 DOI: 10.1016/j.semcdb.2021.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023]
Abstract
Inherited epigenetic information has been observed to regulate a variety of complex organismal phenotypes across diverse taxa of life. This continually expanding body of literature suggests that epigenetic inheritance plays a significant, and potentially fundamental, role in inheritance. Despite the important role these types of effects play in biology, the molecular mediators of this non-genetic transmission of information are just now beginning to be deciphered. Here we provide an intellectual framework for interpreting these findings and how they can interact with each other. We also define the different types of mechanisms that have been found to mediate epigenetic inheritance and to regulate whether epigenetic information persists for one or many generations. The field of epigenetic inheritance is entering an exciting phase, in which we are beginning to understand the mechanisms by which non-genetic information is transmitted to, and deciphered by, subsequent generations to maintain essential environmental information without permanently altering the genetic code. A more complete understanding of how and when epigenetic inheritance occurs will advance our understanding of numerous different aspects of biology ranging from how organisms cope with changing environments to human pathologies influenced by a parent's environment.
Collapse
Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.
| |
Collapse
|
43
|
The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels. Nat Cell Biol 2021; 23:870-880. [PMID: 34341532 DOI: 10.1038/s41556-021-00724-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/29/2021] [Indexed: 02/06/2023]
Abstract
The memory of stresses experienced by parents can be passed on to descendants as a forecast of the challenges to come. Here, we discovered that the neuronal mitochondrial perturbation-induced systemic mitochondrial unfolded protein response (UPRmt) in Caenorhabditis elegans can be transmitted to offspring over multiple generations. The transgenerational activation of UPRmt is mediated by maternal inheritance of elevated levels of mitochondrial DNA (mtDNA), which causes the proteostasis stress within mitochondria. Furthermore, results from intercrossing studies using wild C. elegans strains further support that maternal inheritance of higher levels of mtDNA can induce the UPRmt in descendants. The mitokine Wnt signalling pathway is required for the transmission of elevated mtDNA levels across generations, thereby conferring lifespan extension and stress resistance to offspring. Collectively, our results reveal that the nervous system can transmit stress signals across generations by increasing mtDNA in the germline, enabling descendants to better cope with anticipated challenges.
Collapse
|
44
|
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.
Collapse
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.
| |
Collapse
|
45
|
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.
Collapse
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.
| |
Collapse
|
46
|
Lior C, Hodge F, De-Souza EA, Bourboulia D, Calderwood SK, David D, Allan Drummond D, Edkins A, Morimoto RI, Prahlad V, Rechavi O, Sistonen L, Wilson M, Wiseman RL, Zanetti M, Taylor R, Scherz-Shouval R, van Oosten-Hawle P. The 2021 FASEB Virtual Catalyst Conference on Extracellular and Organismal Proteostasis in Health and Disease, February 3-4, 2021. FASEB J 2021; 35:e21631. [PMID: 34046940 DOI: 10.1096/fj.202100566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022]
Affiliation(s)
- Chen Lior
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Francesca Hodge
- School of Molecular and Cell Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Evandro A De-Souza
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Dimitra Bourboulia
- Department of Urology, Department of Biochemistry and Molecular Biology, Upstate Cancer Center, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Della David
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Adrienne Edkins
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Richard I Morimoto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Veena Prahlad
- Department of Biology, Aging Mind and Brain Initiative, University of Iowa, Iowa City, IA, USA
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Lea Sistonen
- Department of Cell Biology, Åbo Akademi University, Turku, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mark Wilson
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Maurizio Zanetti
- Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Rebecca Taylor
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| |
Collapse
|
47
|
Chavda V, Madhwani K, Chaurasia B. PiWi RNA in Neurodevelopment and Neurodegenerative disorders. Curr Mol Pharmacol 2021; 15:517-531. [PMID: 34212832 DOI: 10.2174/1874467214666210629164535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 11/22/2022]
Abstract
Shedding light on the mysterious dark matter of the genome gears up the knowledge of modern biology. Beyond the genome, epigenome layers an untraveled path of fundamental biological and functional roles of gene regulation. Extraordinary character- P element wimpy testis-induced (PiWi)-interacting RNA (piRNA) is a type of small non-coding RNA that serves as a defender that imposes genomic and cellular defense by silencing nucleic and structural invaders. PIWI proteins and piRNAs appear in both reproductive and somatic cells, though germ line richness is partially unraveled more as it was originally discovered. The foremost function is to suppress invasive DNA sequences, which move within genomic DNA referred to as transposon elements (TEs) and downstream target genes via Transcriptional gene silencing (TGS) and Post-translational gene silencing (PTGS). Germline piRNAs maintain genomic integrity, stability, sternness, and impact imprinting expression. Somatic tissue-specific piRNAs have been surprised by their novel roles. piRNA regulates neurodevelopmental processes in metazoans, including humans. Neural heterogeneity, neurogenesis, neural plasticity, and transgenerational inheritance of adaptive and long-term memory are governed by the PIWI pathway. Neuro-developmental, neurodegenerative or psychiatric illness are the outcome of dysregulated piRNA. Aberrant piRNA signature causes inappropriate switching on or off genes by activation of TEs, incorrect epigenetic tags on DNA, and or histones. Defective piRNA regulation leads to abnormal brain development and neurodegenerative etiology, promoting life-threatening disorders. Exemplification of exciting roles of piRNA is in infancy, so future investigation may expand on these observations using innovative techniques and launch them as impending biomarkers for diagnostics and therapeutics. In this current review, we have summarized the possible gene molecular role of piRNAs regulating neurobiology and contributing as uncharted biomarkers and therapeutic targets for life-threatening diseases.
Collapse
Affiliation(s)
- Vishal Chavda
- Department of Pharmacology, Nirma University, Ahmadabad, Gujarat, India
| | - Kajal Madhwani
- Department of Microbiology, Nirma University, Ahmadabad, Gujarat, India
| | | |
Collapse
|
48
|
Breton CV, Landon R, Kahn LG, Enlow MB, Peterson AK, Bastain T, Braun J, Comstock SS, Duarte CS, Hipwell A, Ji H, LaSalle JM, Miller RL, Musci R, Posner J, Schmidt R, Suglia SF, Tung I, Weisenberger D, Zhu Y, Fry R. Exploring the evidence for epigenetic regulation of environmental influences on child health across generations. Commun Biol 2021; 4:769. [PMID: 34158610 PMCID: PMC8219763 DOI: 10.1038/s42003-021-02316-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/03/2021] [Indexed: 02/08/2023] Open
Abstract
Environmental exposures, psychosocial stressors and nutrition are all potentially important influences that may impact health outcomes directly or via interactions with the genome or epigenome over generations. While there have been clear successes in large-scale human genetic studies in recent decades, there is still a substantial amount of missing heritability to be elucidated for complex childhood disorders. Mounting evidence, primarily in animals, suggests environmental exposures may generate or perpetuate altered health outcomes across one or more generations. One putative mechanism for these environmental health effects is via altered epigenetic regulation. This review highlights the current epidemiologic literature and supporting animal studies that describe intergenerational and transgenerational health effects of environmental exposures. Both maternal and paternal exposures and transmission patterns are considered, with attention paid to the attendant ethical, legal and social implications.
Collapse
Affiliation(s)
- Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Remy Landon
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Linda G Kahn
- Department of Pediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Michelle Bosquet Enlow
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alicia K Peterson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Theresa Bastain
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joseph Braun
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, USA
| | - Cristiane S Duarte
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Alison Hipwell
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hong Ji
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Rashelle Musci
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jonathan Posner
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Rebecca Schmidt
- Department of Public Health Sciences, UC Davis School of Medicine, Davis, CA, USA
| | | | - Irene Tung
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yeyi Zhu
- Division of Research, Kaiser Permanente Northern California and Department of Epidemiology and Biostatistics, University of California, San Francisco, Oakland, CA, USA
| | - Rebecca Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, UNC Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
49
|
Ow MC, Hall SE. piRNAs and endo-siRNAs: Small molecules with large roles in the nervous system. Neurochem Int 2021; 148:105086. [PMID: 34082061 DOI: 10.1016/j.neuint.2021.105086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/23/2021] [Accepted: 05/26/2021] [Indexed: 01/02/2023]
Abstract
Since their discovery, small non-coding RNAs have emerged as powerhouses in the regulation of numerous cellular processes. In addition to guarding the integrity of the reproductive system, small non-coding RNAs play critical roles in the maintenance of the soma. Accumulating evidence indicates that small non-coding RNAs perform vital functions in the animal nervous system such as restricting the activity of deleterious transposable elements, regulating nerve regeneration, and mediating learning and memory. In this review, we provide an overview of the current understanding of the contribution of two major classes of small non-coding RNAs, piRNAs and endo-siRNAs, to the nervous system development and function, and present highlights on how the dysregulation of small non-coding RNA pathways can assist in understanding the neuropathology of human neurological disorders.
Collapse
Affiliation(s)
- Maria C Ow
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| | - Sarah E Hall
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| |
Collapse
|
50
|
Robles P, Turner A, Zuco G, Adams S, Paganopolou P, Winton M, Hill B, Kache V, Bateson C, Pires-daSilva A. Parental energy-sensing pathways control intergenerational offspring sex determination in the nematode Auanema freiburgensis. BMC Biol 2021; 19:102. [PMID: 34001117 PMCID: PMC8130380 DOI: 10.1186/s12915-021-01032-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Environmental stimuli experienced by the parental generation influence the phenotype of subsequent generations (Demoinet et al., Proc Natl Acad Sci U S A 114:E2689-E2698, 2017; Burton et al., Nat Cell Biol 19:252-257, 2017; Agrawal et al., Nature 401:60-63, 1999). The effects of these stimuli on the parental generation may be passed through the germline, but the mechanisms at the basis of this non-Mendelian type of inheritance, their level of conservation, how they lead to adaptive vs non-adaptive, and intergenerational vs transgenerational inheritance are poorly understood. Here we show that modulation of nutrient-sensing pathways in the parental generation of the nematode Auanema freiburgensis regulates phenotypic plasticity of its offspring. RESULTS In response to con-specific pheromones indicative of stress, AMP-activated protein kinase (AMPK), mechanistic target of rapamycin complex 1 (mTORC1), and insulin signaling regulate stress resistance and sex determination across one generation, and these effects can be mimicked by pathway modulators. The effectors of these pathways are closely associated with the chromatin, and their regulation affects the chromatin acetylation status in the germline. CONCLUSION These results suggest that highly conserved metabolic sensors regulate phenotypic plasticity through regulation of subcellular localization of their effectors, leading to changes in chromatin acetylation and epigenetic status of the germline.
Collapse
Affiliation(s)
- Pedro Robles
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Anisa Turner
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Giusy Zuco
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Michael Winton
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Beth Hill
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Vikas Kache
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Christine Bateson
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Andre Pires-daSilva
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA.
| |
Collapse
|