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Sarkies P, Westoby J, Kilner RM, Mashoodh R. Gene body methylation evolves during the sustained loss of parental care in the burying beetle. Nat Commun 2024; 15:6606. [PMID: 39098855 PMCID: PMC11298552 DOI: 10.1038/s41467-024-50359-0] [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: 01/15/2024] [Accepted: 06/27/2024] [Indexed: 08/06/2024] Open
Abstract
Epigenetic modifications, such as 5-methylcytosine (5mC), can sometimes be transmitted between generations, provoking speculation that epigenetic changes could play a role in adaptation and evolution. Here, we use experimental evolution to investigate how 5mC levels evolve in populations of biparental insect (Nicrophorus vespilloides) derived from a wild source population and maintained independently under different regimes of parental care in the lab. We show that 5mC levels in the transcribed regions of genes (gene bodies) diverge between populations that have been exposed to different levels of care for 30 generations. These changes in 5mC do not reflect changes in the levels of gene expression. However, the accumulation of 5mC within genes between populations is associated with reduced variability in gene expression within populations. Our results suggest that evolved change in 5mC could contribute to phenotypic evolution by influencing variability in gene expression in invertebrates.
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Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Rahia Mashoodh
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK.
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2
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Zetzsche J, Fallet M. To live or let die? Epigenetic adaptations to climate change-a review. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae009. [PMID: 39139701 PMCID: PMC11321362 DOI: 10.1093/eep/dvae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/05/2024] [Accepted: 07/03/2024] [Indexed: 08/15/2024]
Abstract
Anthropogenic activities are responsible for a wide array of environmental disturbances that threaten biodiversity. Climate change, encompassing temperature increases, ocean acidification, increased salinity, droughts, and floods caused by frequent extreme weather events, represents one of the most significant environmental alterations. These drastic challenges pose ecological constraints, with over a million species expected to disappear in the coming years. Therefore, organisms must adapt or face potential extinctions. Adaptations can occur not only through genetic changes but also through non-genetic mechanisms, which often confer faster acclimatization and wider variability ranges than their genetic counterparts. Among these non-genetic mechanisms are epigenetics defined as the study of molecules and mechanisms that can perpetuate alternative gene activity states in the context of the same DNA sequence. Epigenetics has received increased attention in the past decades, as epigenetic mechanisms are sensitive to a wide array of environmental cues, and epimutations spread faster through populations than genetic mutations. Epimutations can be neutral, deleterious, or adaptative and can be transmitted to subsequent generations, making them crucial factors in both long- and short-term responses to environmental fluctuations, such as climate change. In this review, we compile existing evidence of epigenetic involvement in acclimatization and adaptation to climate change and discuss derived perspectives and remaining challenges in the field of environmental epigenetics. Graphical Abstract.
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Affiliation(s)
- Jonas Zetzsche
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
| | - Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
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3
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Anka IZ, Uren Webster TM, Berbel-Filho WM, Hitchings M, Overland B, Weller S, Garcia de Leaniz C, Consuegra S. Microbiome and epigenetic variation in wild fish with low genetic diversity. Nat Commun 2024; 15:4725. [PMID: 38830879 PMCID: PMC11148108 DOI: 10.1038/s41467-024-49162-8] [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: 05/11/2023] [Accepted: 05/23/2024] [Indexed: 06/05/2024] Open
Abstract
Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.
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Affiliation(s)
- Ishrat Z Anka
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Department of Aquaculture, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Tamsyn M Uren Webster
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Waldir M Berbel-Filho
- Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Biology, University of West Florida, Pensacola, FL, USA
| | - Matthew Hitchings
- Institute of Life Science, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Benjamin Overland
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Sarah Weller
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Carlos Garcia de Leaniz
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Marine Research Centre (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Sofia Consuegra
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK.
- Grupo de Biotecnología Acuática, Departamento de Biotecnología y Acuicultura, Instituto de Investigacións Mariñas, IIM-CSIC, Vigo, Spain.
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4
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Ayano T, Yokosawa T, Oki M. GTP-dependent regulation of heterochromatin fluctuations at subtelomeric regions in Saccharomyces cerevisiae. Genes Cells 2024; 29:217-230. [PMID: 38229233 DOI: 10.1111/gtc.13094] [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: 10/13/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
In eukaryotes, single cells in a population display different transcriptional profiles. One of the factors regulating this heterogeneity is the chromatin state in each cell. However, the mechanisms of epigenetic chromatin regulation of specific chromosomal regions remain unclear. Therefore, we used single-cell tracking system to analyze IMD2. IMD2 is located at the subtelomeric region of budding yeast, and its expression is epigenetically regulated by heterochromatin fluctuations. Treatment with mycophenolic acid, an inhibitor of de novo GTP biosynthesis, triggered a decrease in GTP, which caused heterochromatin fluctuations at the IMD2 locus. Interestingly, within individually tracked cells, IMD2 expression state underwent repeated switches even though IMD2 is positioned within the heterochromatin region. We also found that 30% of the cells in a population always expressed IMD2. Furthermore, the addition of nicotinamide, a histone deacetylase inhibitor, or guanine, the GTP biosynthesis factor in salvage pathway of GTP biosynthesis, regulated heterogeneity, resulting in IMD2 expression being uniformly induced or suppressed in the population. These results suggest that gene expression heterogeneity in the IMD2 region is regulated by changes in chromatin structure triggered by slight decreases in GTP.
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Affiliation(s)
- Takahito Ayano
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Research Fellowships of Japan Society for the Promotion of Science for Young Scientists (JSPS), Tokyo, Japan
| | - Takuma Yokosawa
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
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5
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Webster AK, Phillips PC. Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation. G3 (BETHESDA, MD.) 2024; 14:jkad287. [PMID: 38113034 PMCID: PMC10849368 DOI: 10.1093/g3journal/jkad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/03/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Abstract
How genetic and phenotypic variation are maintained has long been one of the fundamental questions in population and quantitative genetics. A variety of factors have been implicated to explain the maintenance of genetic variation in some contexts (e.g. balancing selection), but the potential role of epigenetic regulation to influence population dynamics has been understudied. It is well recognized that epigenetic regulation, including histone methylation, small RNA expression, and DNA methylation, helps to define differences between cell types and facilitate phenotypic plasticity. In recent years, empirical studies have shown the potential for epigenetic regulation to also be heritable for at least a few generations without selection, raising the possibility that differences in epigenetic regulation can act alongside genetic variation to shape evolutionary trajectories. Heritable differences in epigenetic regulation that arise spontaneously are termed "epimutations." Epimutations differ from genetic mutations in 2 key ways-they occur at a higher rate and the loci at which they occur often revert back to their original state within a few generations. Here, we present an extension of the standard population genetic model with selection to incorporate epigenetic variation arising via epimutation. Our model assumes a diploid, sexually reproducing population with random mating. In addition to spontaneous genetic mutation, we included parameters for spontaneous epimutation and back-epimutation, allowing for 4 potential epialleles at a single locus (2 genetic alleles, each with 2 epigenetic states), each of which affect fitness. We then analyzed the conditions under which stable epialleles were maintained. Our results show that highly reversible epialleles can be maintained in long-term equilibrium under neutral conditions in a manner that depends on the epimutation and back-epimutation rates, which we term epimutation-back-epimutation equilibrium. On the other hand, epialleles that compensate for deleterious mutations cause deviations from the expectations of mutation-selection balance by a simple factor that depends on the epimutation and back-epimutation rates. We also numerically analyze several sets of fitness parameters for which large deviations from mutation-selection balance occur. Together, these results demonstrate that transient epigenetic regulation may be an important factor in the maintenance of both epigenetic and genetic variation in populations.
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Affiliation(s)
- Amy K Webster
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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6
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Bogan SN, Yi SV. Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations. Genome Biol Evol 2024; 16:evae022. [PMID: 38324384 PMCID: PMC10899001 DOI: 10.1093/gbe/evae022] [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: 07/13/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
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7
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Fallet M, Wilson R, Sarkies P. Cisplatin exposure alters tRNA-derived small RNAs but does not affect epimutations in C. elegans. BMC Biol 2023; 21:276. [PMID: 38031056 PMCID: PMC10688063 DOI: 10.1186/s12915-023-01767-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The individual lifestyle and environment of an organism can influence its phenotype and potentially the phenotype of its offspring. The different genetic and non-genetic components of the inheritance system and their mutual interactions are key mechanisms to generate inherited phenotypic changes. Epigenetic changes can be transmitted between generations independently from changes in DNA sequence. In Caenorhabditis elegans, epigenetic differences, i.e. epimutations, mediated by small non-coding RNAs, particularly 22G-RNAs, as well as chromatin have been identified, and their average persistence is three to five generations. In addition, previous research showed that some epimutations had a longer duration and concerned genes that were enriched for multiple components of xenobiotic response pathways. These results raise the possibility that environmental stresses might change the rate at which epimutations occur, with potential significance for adaptation. RESULTS In this work, we explore this question by propagating C. elegans lines either in control conditions or in moderate or high doses of cisplatin, which introduces genotoxic stress by damaging DNA. Our results show that cisplatin has a limited effect on global small non-coding RNA epimutations and epimutations in gene expression levels. However, cisplatin exposure leads to increased fluctuations in the levels of small non-coding RNAs derived from tRNA cleavage. We show that changes in tRNA-derived small RNAs may be associated with gene expression changes. CONCLUSIONS Our work shows that epimutations are not substantially altered by cisplatin exposure but identifies transient changes in tRNA-derived small RNAs as a potential source of variation induced by genotoxic stress.
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Affiliation(s)
- Manon Fallet
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182, Örebro, Sweden.
| | - Rachel Wilson
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Peter Sarkies
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
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8
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Ewe CK, Rechavi O. The third barrier to transgenerational inheritance in animals: somatic epigenetic resetting. EMBO Rep 2023; 24:e56615. [PMID: 36862326 PMCID: PMC10074133 DOI: 10.15252/embr.202256615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
After early controversy, it is now increasingly clear that acquired responses to environmental factors may perpetuate across multiple generations-a phenomenon termed transgenerational epigenetic inheritance (TEI). Experiments with Caenorhabditis elegans, which exhibits robust heritable epigenetic effects, demonstrated small RNAs as key factors of TEI. Here, we discuss three major barriers to TEI in animals, two of which, the "Weismann barrier" and germline epigenetic reprogramming, have been known for decades. These are thought to effectively prevent TEI in mammals but not to the same extent in C. elegans. We argue that a third barrier-that we termed "somatic epigenetic resetting"-may further inhibit TEI and, unlike the other two, restricts TEI in C. elegans as well. While epigenetic information can overcome the Weismann barrier and transmit from the soma to the germline, it usually cannot "travel back" directly from the germline to the soma in subsequent generations. Nevertheless, heritable germline memory may still influence the animal's physiology by indirectly modifying gene expression in somatic tissues.
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Affiliation(s)
- Chee Kiang Ewe
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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9
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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.
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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
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10
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González-Forero M. How development affects evolution. Evolution 2023; 77:562-579. [PMID: 36691368 DOI: 10.1093/evolut/qpac003] [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: 04/28/2022] [Revised: 09/14/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023]
Abstract
Natural selection acts on developmentally constructed phenotypes, but how does development affect evolution? This question prompts a simultaneous consideration of development and evolution. However, there has been a lack of general mathematical frameworks mechanistically integrating the two, which may have inhibited progress on the question. Here, we use a new mathematical framework that mechanistically integrates development into evolution to analyse how development affects evolution. We show that, while selection pushes genotypic and phenotypic evolution up the fitness landscape, development determines the admissible evolutionary pathway, such that evolutionary outcomes occur at path peaks rather than landscape peaks. Changes in development can generate path peaks, triggering genotypic or phenotypic diversification, even on constant, single-peak landscapes. Phenotypic plasticity, niche construction, extra-genetic inheritance, and developmental bias alter the evolutionary path and hence the outcome. Thus, extra-genetic inheritance can have permanent evolutionary effects by changing the developmental constraints, even if extra-genetically acquired elements are not transmitted to future generations. Selective development, whereby phenotype construction points in the adaptive direction, may induce adaptive or maladaptive evolution depending on the developmental constraints. Moreover, developmental propagation of phenotypic effects over age enables the evolution of negative senescence. Overall, we find that development plays a major evolutionary role.
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11
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Liontis T, Verma K, Grishok A. DOT-1.1 (DOT1L) deficiency in C. elegans leads to small RNA-dependent gene activation. BBA ADVANCES 2023; 3:100080. [PMID: 37082252 PMCID: PMC10074844 DOI: 10.1016/j.bbadva.2023.100080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Methylation of histone H3 at lysine 79 (H3K79) is conserved from yeast to humans and is accomplished by Dot1 (disruptor of telomeric silencing-1) methyltransferases. The C. elegans enzyme DOT-1.1 and its interacting partners are similar to the mammalian DOT1L (Dot1-like) complex. The C. elegans DOT-1.1 complex has been functionally connected to RNA interference. Specifically, we have previously shown that embryonic and larval lethality of dot-1.1 mutant worms deficient in H3K79 methylation was suppressed by mutations in the RNAi pathway genes responsible for generation (rde-4) and function (rde-1) of primary small interfering RNAs (siRNAs). This suggests that dot-1.1 mutant lethality is dependent on the enhanced production of some siRNAs. We have also found that this lethality is suppressed by a loss-of-function of CED-3, a conserved apoptotic protease. Here, we describe a comparison of gene expression and primary siRNA production changes between control and dot-1.1 deletion mutant embryos. We found that elevated antisense siRNA production occurred more often at upregulated than downregulated genes. Importantly, gene expression changes were dependent on RDE-4 in both instances. Moreover, the upregulated group, which is potentially activated by ectopic siRNAs, was enriched in protease-coding genes. Our findings are consistent with a model where in the absence of H3K79 methylation there is a small RNA-dependent activation of protease genes, which leads to embryonic and larval lethality. DOT1 enzymes' conservation suggests that the interplay between H3K79 methylation and small RNA pathways may exist in higher organisms.
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12
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Karin O, Miska EA, Simons BD. Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition. Cell Syst 2023; 14:24-40.e11. [PMID: 36657390 PMCID: PMC7614883 DOI: 10.1016/j.cels.2022.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/05/2022] [Accepted: 12/12/2022] [Indexed: 01/19/2023]
Abstract
Biological systems can maintain memories over long timescales, with examples including memories in the brain and immune system. It is unknown how functional properties of memory systems, such as memory persistence, can be established by biological circuits. To address this question, we focus on transgenerational epigenetic inheritance in Caenorhabditis elegans. In response to a trigger, worms silence a target gene for multiple generations, resisting strong dilution due to growth and reproduction. Silencing may also be maintained indefinitely upon selection according to silencing levels. We show that these properties imply the fine-tuning of biochemical rates in which the silencing system is positioned near the transition to bistability. We demonstrate that this behavior is consistent with a generic mechanism based on competition for synthesis resources, which leads to self-organization around a critical state with broad silencing timescales. The theory makes distinct predictions and offers insights into the design principles of long-term memory systems.
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Affiliation(s)
- Omer Karin
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, CB3 0WA, UK; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Mathematics, Imperial College London, London, SW7 2AZ, UK.
| | - Eric A Miska
- Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Benjamin D Simons
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, CB3 0WA, UK; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
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13
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Gajic Z, Kaur D, Ni J, Zhu Z, Zhebrun A, Gajic M, Kim M, Hong J, Priyadarshini M, Frøkjær-Jensen C, Gu S. Target-dependent suppression of siRNA production modulates the levels of endogenous siRNAs in the Caenorhabditis elegans germline. Development 2022; 149:dev200692. [PMID: 35876680 PMCID: PMC9481970 DOI: 10.1242/dev.200692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/14/2022] [Indexed: 08/24/2023]
Abstract
Despite the prominent role of endo-siRNAs in transposon silencing, their expression is not limited to these 'nonself' DNA elements. Transcripts of protein-coding genes ('self' DNA) in some cases also produce endo-siRNAs in yeast, plants and animals. How cells distinguish these two populations of siRNAs to prevent unwanted silencing of active genes in animals is not well understood. To address this question, we inserted various self-gene or gfp fragments into an LTR retrotransposon that produces abundant siRNAs and examined the propensity of these gene fragments to produce ectopic siRNAs in the Caenorhabditis elegans germline. We found that fragments of germline genes are generally protected from production of ectopic siRNAs. This phenomenon, which we termed 'target-directed suppression of siRNA production' (or siRNA suppression), is dependent on the germline expression of target mRNA and requires germline P-granule components. We found that siRNA suppression can also occur in naturally produced endo-siRNAs. We suggest that siRNA suppression plays an important role in regulating siRNA expression and preventing self-genes from aberrant epigenetic silencing. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Zoran Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Diljeet Kaur
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Julie Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zhaorong Zhu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Anna Zhebrun
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Maria Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Matthew Kim
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Julia Hong
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Monika Priyadarshini
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Kingdom of Saudi Arabia
| | - Christian Frøkjær-Jensen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Kingdom of Saudi Arabia
| | - Sam Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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14
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Greenspoon PB, Spencer HG, M'Gonigle LK. Epigenetic induction may speed up or slow down speciation with gene flow. Evolution 2022; 76:1170-1182. [PMID: 35482931 PMCID: PMC9321097 DOI: 10.1111/evo.14494] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 03/09/2022] [Indexed: 01/21/2023]
Abstract
Speciation is less likely to occur when there is gene flow between nascent species. Natural selection can oppose gene flow and promote speciation if there is variation in ecological conditions among the nascent species' locations. Previous theory on ecological speciation with gene flow has focused primarily on the role of genetic variation in ecological traits, largely neglecting the role of nongenetic inheritance or transgenerational plasticity. Here, we build and analyze models incorporating both genetic and epigenetic inheritance, the latter representing a form of nongenetic inheritance. We investigate the rate of speciation for a population that inhabits two patches connected by migration, and find that adaptively biased epigenetic induction can speed up or slow down speciation, depending on the form of the map from genotype and epigenotype to phenotype. While adaptively relevant epigenetic variation can speed up speciation by reducing the fitness of migrants and hybrids, it can also slow down speciation. This latter effect occurs when the epialleles are able to achieve adaptation faster than the genetic alleles, thereby weakening selection on the latter.
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15
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Conradsen C, Blows MW, McGuigan K. Causes of variability in estimates of mutational variance from mutation accumulation experiments. Genetics 2022; 221:6569838. [PMID: 35435211 PMCID: PMC9157167 DOI: 10.1093/genetics/iyac060] [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: 02/25/2022] [Accepted: 04/08/2022] [Indexed: 11/15/2022] Open
Abstract
Characteristics of the new phenotypic variation introduced via mutation have broad implications in evolutionary and medical genetics. Standardized estimates of this mutational variance, VM, span 2 orders of magnitude, but the causes of this remain poorly resolved. We investigated estimate heterogeneity using 2 approaches. First, meta-analyses of ∼150 estimates of standardized VM from 37 mutation accumulation studies did not support a difference among taxa (which differ in mutation rate) but provided equivocal support for differences among trait types (life history vs morphology, predicted to differ in mutation rate). Notably, several experimental factors were confounded with taxon and trait, and further empirical data are required to resolve their influences. Second, we analyzed morphological data from an experiment in Drosophila serrata to determine the potential for unintentional heterogeneity among environments in which phenotypes were measured (i.e. among laboratories or time points) or transient segregation of mutations within mutation accumulation lines to affect standardized VM. Approximating the size of an average mutation accumulation experiment, variability among repeated estimates of (accumulated) mutational variance was comparable to variation among published estimates of standardized VM. This heterogeneity was (partially) attributable to unintended environmental variation or within line segregation of mutations only for wing size, not wing shape traits. We conclude that sampling error contributed substantial variation within this experiment, and infer that it will also contribute substantially to differences among published estimates. We suggest a logistically permissive approach to improve the precision of estimates, and consequently our understanding of the dynamics of mutational variance of quantitative traits.
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Affiliation(s)
- Cara Conradsen
- School of Biological Sciences; The University of Queensland; St. Lucia, Queensland, Australia 4072
| | - Mark W Blows
- School of Biological Sciences; The University of Queensland; St. Lucia, Queensland, Australia 4072
| | - Katrina McGuigan
- School of Biological Sciences; The University of Queensland; St. Lucia, Queensland, Australia 4072
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16
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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.
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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
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17
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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.
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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.
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18
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Shukla A, Perales R, Kennedy S. piRNAs coordinate poly(UG) tailing to prevent aberrant and perpetual gene silencing. Curr Biol 2021; 31:4473-4485.e3. [PMID: 34428467 DOI: 10.1016/j.cub.2021.07.076] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/03/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Noncoding RNAs have emerged as mediators of transgenerational epigenetic inheritance (TEI) in a number of organisms. A robust example of such RNA-directed TEI is the inheritance of gene-silencing states following RNA interference (RNAi) in the metazoan C. elegans. During RNAi inheritance, gene silencing is transmitted by a self-perpetuating cascade of siRNA-directed poly(UG) tailing of mRNA fragments (pUGylation), followed by siRNA synthesis from poly(UG)-tailed mRNA templates (termed pUG RNA/siRNA cycling). Despite the self-perpetuating nature of pUG RNA/siRNA cycling, RNAi inheritance is finite, suggesting that systems likely exist to prevent indefinite RNAi-triggered gene silencing. Here we show that, in the absence of Piwi-interacting RNAs (piRNAs), an animal-specific class of small noncoding RNA, RNAi-based gene silencing can become essentially permanent, lasting at near 100% penetrance for more than 5 years and hundreds of generations. This perpetual gene silencing is mediated by continuous pUG RNA/siRNA cycling. Further, we find that piRNAs coordinate endogenous RNAi pathways to prevent germline-expressed genes, which are not normally subjected to TEI, from entering a state of continual and irreversible epigenetic silencing also mediated by continuous maintenance of pUG RNA/siRNA cycling. Together, our results show that one function of C. elegans piRNAs is to insulate germline-expressed genes from aberrant and runaway inactivation by the pUG RNA/siRNA epigenetic inheritance system.
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Affiliation(s)
- Aditi Shukla
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Roberto Perales
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA; Shape Therapeutics, Seattle, WA 98109, USA
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
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19
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Perez MF, Shamalnasab M, Mata-Cabana A, Della Valle S, Olmedo M, Francesconi M, Lehner B. Neuronal perception of the social environment generates an inherited memory that controls the development and generation time of C. elegans. Curr Biol 2021; 31:4256-4268.e7. [PMID: 34358445 DOI: 10.1016/j.cub.2021.07.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 12/31/2022]
Abstract
An old and controversial question in biology is whether information perceived by the nervous system of an animal can "cross the Weismann barrier" to alter the phenotypes and fitness of their progeny. Here, we show that such intergenerational transmission of sensory information occurs in the model organism, C. elegans, with a major effect on fitness. Specifically, that perception of social pheromones by chemosensory neurons controls the post-embryonic timing of the development of one tissue, the germline, relative to others in the progeny of an animal. Neuronal perception of the social environment thus intergenerationally controls the generation time of this animal.
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Affiliation(s)
- Marcos Francisco Perez
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Mehrnaz Shamalnasab
- Université de Lyon, ENS de Lyon, Université de Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, Site Jacques Monod, 69007 Lyon, France
| | - Alejandro Mata-Cabana
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Simona Della Valle
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - María Olmedo
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mirko Francesconi
- Université de Lyon, ENS de Lyon, Université de Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, Site Jacques Monod, 69007 Lyon, France.
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain.
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20
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Stajic D, Jansen LET. Empirical evidence for epigenetic inheritance driving evolutionary adaptation. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200121. [PMID: 33866813 DOI: 10.1098/rstb.2020.0121] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The cellular machinery that regulates gene expression can be self-propagated across cell division cycles and even generations. This renders gene expression states and their associated phenotypes heritable, independently of genetic changes. These phenotypic states, in turn, can be subject to selection and may influence evolutionary adaptation. In this review, we will discuss the molecular basis of epigenetic inheritance, the extent of its transmission and mechanisms of evolutionary adaptation. The current work shows that heritable gene expression can facilitate the process of adaptation through the increase of survival in a novel environment and by enlarging the size of beneficial mutational targets. Moreover, epigenetic control of gene expression enables stochastic switching between different phenotypes in populations that can potentially facilitate adaptation in rapidly fluctuating environments. Ecological studies of the variation of epigenetic markers (e.g. DNA methylation patterns) in wild populations show a potential contribution of this mode of inheritance to local adaptation in nature. However, the extent of the adaptive contribution of the naturally occurring variation in epi-alleles compared to genetic variation remains unclear. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Dragan Stajic
- Department of Zoology, University of Stockholm, 106 91 Stockholm, Sweden
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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21
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Frolows N, Ashe A. Small RNAs and chromatin in the multigenerational epigenetic landscape of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200112. [PMID: 33866817 DOI: 10.1098/rstb.2020.0112] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
For decades, it was thought that the only heritable information transmitted from one individual to another was that encoded in the DNA sequence. However, it has become increasingly clear that this is not the case and that the transmission of molecules from within the cytoplasm of the gamete also plays a significant role in heritability. The roundworm, Caenorhabditis elegans, has emerged as one of the leading model organisms in which to study the mechanisms of transgenerational epigenetic inheritance (TEI). Collaborative efforts over the past few years have revealed that RNA molecules play a critical role in transmitting transgenerational responses, but precisely how they do so is as yet uncertain. In addition, the role of histone modifications in epigenetic inheritance is increasingly apparent, and RNA and histones interact in a way that we do not yet fully understand. Furthermore, both exogenous and endogenous RNA molecules, as well as other environmental triggers, are able to induce heritable epigenetic changes that affect transcription across the genome. In most cases, these epigenetic changes last only for a handful of generations, but occasionally can be maintained much longer: perhaps indefinitely. In this review, we discuss the current understanding of the role of RNA and histones in TEI, as well as making clear the gaps in our knowledge. We also speculate on the evolutionary implications of epigenetic inheritance, particularly in the context of a short-lived, clonally propagating species. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Natalya Frolows
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia.,CSIRO Health and Biosecurity, Sydney, New South Wales, 2113, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
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22
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Bergthorsson U, Sheeba CJ, Konrad A, Belicard T, Beltran T, Katju V, Sarkies P. Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression. BMC Biol 2020; 18:162. [PMID: 33158445 PMCID: PMC7646084 DOI: 10.1186/s12915-020-00897-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
Background Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood. Results Here, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Conclusions Our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.
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Affiliation(s)
- Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA
| | - Caroline J Sheeba
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA.,Present Address: Intituto Gulbenkian de Ciencia, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Tony Belicard
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Toni Beltran
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK.,Present Address: Centre for Genomic Regulation, PRBB Building, 08003, Barcelona, Spain
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA.
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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23
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Johnson LM, Smith OJ, Hahn DA, Baer CF. Short-term heritable variation overwhelms 200 generations of mutational variance for metabolic traits in Caenorhabditis elegans. Evolution 2020; 74:2451-2464. [PMID: 32989734 DOI: 10.1111/evo.14104] [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: 05/11/2020] [Revised: 08/05/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Metabolic disorders have a large heritable component, and have increased markedly in human populations over the past few generations. Genome-wide association studies of metabolic traits typically find a substantial unexplained fraction of total heritability, suggesting an important role of spontaneous mutation. An alternative explanation is that epigenetic effects contribute significantly to the heritable variation. Here, we report a study designed to quantify the cumulative effects of spontaneous mutation on adenosine metabolism in the nematode Caenorhabditis elegans, including both the activity and concentration of two metabolic enzymes and the standing pools of their associated metabolites. The only prior studies on the effects of mutation on metabolic enzyme activity, in Drosophila melanogaster, found that total enzyme activity presents a mutational target similar to that of morphological and life-history traits. However, those studies were not designed to account for short-term heritable effects. We find that the short-term heritable variance for most traits is of similar magnitude as the variance among MA lines. This result suggests that the potential heritable effects of epigenetic variation in metabolic disease warrant additional scrutiny.
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Affiliation(s)
- Lindsay M Johnson
- Department of Biology, University of Florida, Gainesville, Florida, 32611.,Ology Bioservices, Inc., Alachua, Florida, 32615
| | - Olivia J Smith
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - Daniel A Hahn
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, 32611.,University of Florida Genetics Institute, Gainesville, Florida, 32611
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, Florida, 32611.,University of Florida Genetics Institute, Gainesville, Florida, 32611
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