1
|
Prabh N, Linnenbrink M, Jovicic M, Guenther A. Fast adjustment of pace-of-life and risk-taking to changes in food quality by altered gene expression in house mice. Ecol Lett 2023; 26:99-110. [PMID: 36366786 DOI: 10.1111/ele.14137] [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: 07/04/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022]
Abstract
The pace-of-life syndrome hypothesis provides a framework for the adaptive integration of behaviour, physiology and life history between and within species. It suggests that behaviours involving a risk of death or injury should co-vary with a higher allocation to fast reproduction. Empirical support for this hypothesis is mixed, presumably because important influencing factors such as environmental variation, are usually neglected. By experimentally manipulating food quality of wild mice living under semi-natural conditions for three generations, we show that individuals adjust their life history strategies and risk-taking behaviours as well as trait covariation (Nindividuals = 1442). These phenotypic differences are correlated to differences in transcriptomic gene expression of primary metabolic processes in the liver while no changes in gene frequencies occurred. Our discussion emphasises the need to integrate the role of environmental conditions and phenotypic plasticity in shaping relationships among behaviour, physiology and life history in response to changing environmental conditions.
Collapse
Affiliation(s)
- Neel Prabh
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Milan Jovicic
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Anja Guenther
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| |
Collapse
|
2
|
Epigenetic Drifts during Long-Term Intestinal Organoid Culture. Cells 2021; 10:cells10071718. [PMID: 34359888 PMCID: PMC8305684 DOI: 10.3390/cells10071718] [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: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 11/17/2022] Open
Abstract
Organoids retain the morphological and molecular patterns of their tissue of origin, are self-organizing, relatively simple to handle and accessible to genetic engineering. Thus, they represent an optimal tool for studying the mechanisms of tissue maintenance and aging. Long-term expansion under standard growth conditions, however, is accompanied by changes in the growth pattern and kinetics. As a potential explanation of these alterations, epigenetic drifts in organoid culture have been suggested. Here, we studied histone tri-methylation at lysine 4 (H3K4me3) and 27 (H3K27me3) and transcriptome profiles of intestinal organoids derived from mismatch repair (MMR)-deficient and control mice and cultured for 3 and 20 weeks and compared them with data on their tissue of origin. We found that, besides the expected changes in short-term culture, the organoids showed profound changes in their epigenomes also during the long-term culture. The most prominent were epigenetic gene activation by H3K4me3 recruitment to previously unmodified genes and by H3K27me3 loss from originally bivalent genes. We showed that a long-term culture is linked to broad transcriptional changes that indicate an ongoing maturation and metabolic adaptation process. This process was disturbed in MMR-deficient mice, resulting in endoplasmic reticulum (ER) stress and Wnt activation. Our results can be explained in terms of a mathematical model assuming that epigenetic changes during a long-term culture involve DNA demethylation that ceases if the metabolic adaptation is disturbed.
Collapse
|
3
|
Runge JN, Lindholm AK. Experiments confirm a dispersive phenotype associated with a natural gene drive system. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202050. [PMID: 34040786 PMCID: PMC8113913 DOI: 10.1098/rsos.202050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Meiotic drivers are genetic entities that increase their own probability of being transmitted to offspring, usually to the detriment of the rest of the organism, thus 'selfishly' increasing their fitness. In many meiotic drive systems, driver-carrying males are less successful in sperm competition, which occurs when females mate with multiple males in one oestrus cycle (polyandry). How do drivers respond to this selection? An observational study found that house mice carrying the t haplotype, a meiotic driver, are more likely to disperse from dense populations. This could help the t avoid detrimental sperm competition, because density is associated with the frequency of polyandry. However, no controlled experiments have been conducted to test these findings. Here, we confirm that carriers of the t haplotype are more dispersive, but we do not find this to depend on the local density. t-carriers with above-average body weight were particularly more likely to disperse than wild-type mice. t-carrying mice were also more explorative but not more active than wild-type mice. These results add experimental support to the previous observational finding that the t haplotype affects the dispersal phenotype in house mice, which supports the hypothesis that dispersal reduces the fitness costs of the t.
Collapse
Affiliation(s)
- Jan-Niklas Runge
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| |
Collapse
|
4
|
Hoffmann LB, Rae M, Marianno P, Pang TY, Hannan AJ, Camarini R. Preconceptual paternal environmental stimulation alters behavioural phenotypes and adaptive responses intergenerationally in Swiss mice. Physiol Behav 2020; 223:112968. [DOI: 10.1016/j.physbeh.2020.112968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/26/2020] [Accepted: 05/12/2020] [Indexed: 02/09/2023]
|
5
|
Gibert JM. [Phenotypic plasticity in insects]. Biol Aujourdhui 2020; 214:33-44. [PMID: 32773028 DOI: 10.1051/jbio/2020005] [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: 05/23/2020] [Indexed: 11/14/2022]
Abstract
Insects represent 85% of the animals. They have adapted to many environments and play a major role in ecosystems. Many insect species exhibit phenotypic plasticity. We here report on the mechanisms involved in phenotypic plasticity of different insects (aphids, migratory locust, map butterfly, honeybee) and also on the nutritional size plasticity in Drosophila and the plasticity of the wing eye-spots of the butterfly Bicyclus anynana. We also describe in more detail our work concerning the thermal plasticity of pigmentation in Drosophila. We have shown that the expression of the tan, yellow and Ddc genes, encoding enzymes of the melanin synthesis pathway, is modulated by temperature and that it is a consequence, at least in part, of the temperature-sensitive expression of the bab locus genes that repress them.
Collapse
Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), UMR7622, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement (IBPS-LBD), 75005 Paris, France
| |
Collapse
|
6
|
Miller RL, Zhang H, Jezioro J, De Planell Saguer M, Lovinsky-Desir S, Liu X, Perzanowski M, Divjan A, Phipatanakul W, Matsui EC. Reduced mouse allergen is associated with epigenetic changes in regulatory genes, but not mouse sensitization, in asthmatic children. ENVIRONMENTAL RESEARCH 2017; 156:619-624. [PMID: 28454014 PMCID: PMC5503684 DOI: 10.1016/j.envres.2017.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 03/06/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Chronic exposure to mouse allergen may contribute greatly to the inner-city asthma burden. We hypothesized that reducing mouse allergen exposure may modulate the immunopathology underlying symptomatic pediatric allergic asthma, and that this occurs through epigenetic regulation. To test this hypothesis, we studied a cohort of mouse sensitized, persistent asthmatic inner-city children undergoing mouse allergen-targeted integrated pest management (IPM) vs education in a randomized controlled intervention trial. We found that decreasing mouse allergen exposure, but not cockroach, was associated with reduced FOXP3 buccal DNA promoter methylation, but this was unrelated to mouse specific IgE production. This finding suggests that the environmental epigenetic regulation of an immunomodulatory gene may occur following changing allergen exposures in some highly exposed cohorts. Given the clinical and public health importance of inner-city pediatric asthma and the potential impact of environmental interventions, further studies will be needed to corroborate changes in epigenetic regulation following changing exposures over time, and determine their impact on asthma morbidity in susceptible children.
Collapse
Affiliation(s)
- Rachel L Miller
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA; Department of Environmental Health Sciences, Columbia University, 722 W 168th St, 11th Floor, New York City, NY, 10032, USA.
| | - Hanjie Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA
| | - Jacqueline Jezioro
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA
| | - Mariangels De Planell Saguer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA
| | - Stephanie Lovinsky-Desir
- Division of Pulmonary, Department of Pediatrics, Columbia University Medical Center, 3959 Broadway, CHC 7-701, New York City, NY 10032, USA
| | - Xinhua Liu
- Department of Biostatistics, Columbia University Medical Center, 722 W 168 St, 6 Floor, New York City, NY, 10032, USA
| | - Matthew Perzanowski
- Department of Environmental Health Sciences, Columbia University, 722 W 168th St, 11th Floor, New York City, NY, 10032, USA
| | - Adnan Divjan
- Department of Environmental Health Sciences, Columbia University, 722 W 168th St, 11th Floor, New York City, NY, 10032, USA
| | - Wanda Phipatanakul
- Division of Pediatric Allergy/Immunology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Elizabeth C Matsui
- Division of Pediatric Allergy/Immunology, Johns Hopkins School of Medicine, CMSC 1102, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| |
Collapse
|
7
|
Gibert JM, Mouchel-Vielh E, De Castro S, Peronnet F. Phenotypic Plasticity through Transcriptional Regulation of the Evolutionary Hotspot Gene tan in Drosophila melanogaster. PLoS Genet 2016; 12:e1006218. [PMID: 27508387 PMCID: PMC4980059 DOI: 10.1371/journal.pgen.1006218] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/02/2016] [Indexed: 11/18/2022] Open
Abstract
Phenotypic plasticity is the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. Phenotypic plasticity can be adaptive. Furthermore, it is thought to facilitate evolution. Although phenotypic plasticity is a widespread phenomenon, its molecular mechanisms are only beginning to be unravelled. Environmental conditions can affect gene expression through modification of chromatin structure, mainly via histone modifications, nucleosome remodelling or DNA methylation, suggesting that phenotypic plasticity might partly be due to chromatin plasticity. As a model of phenotypic plasticity, we study abdominal pigmentation of Drosophila melanogaster females, which is temperature sensitive. Abdominal pigmentation is indeed darker in females grown at 18°C than at 29°C. This phenomenon is thought to be adaptive as the dark pigmentation produced at lower temperature increases body temperature. We show here that temperature modulates the expression of tan (t), a pigmentation gene involved in melanin production. t is expressed 7 times more at 18°C than at 29°C in female abdominal epidermis. Genetic experiments show that modulation of t expression by temperature is essential for female abdominal pigmentation plasticity. Temperature modulates the activity of an enhancer of t without modifying compaction of its chromatin or level of the active histone mark H3K27ac. By contrast, the active mark H3K4me3 on the t promoter is strongly modulated by temperature. The H3K4 methyl-transferase involved in this process is likely Trithorax, as we show that it regulates t expression and the H3K4me3 level on the t promoter and also participates in female pigmentation and its plasticity. Interestingly, t was previously shown to be involved in inter-individual variation of female abdominal pigmentation in Drosophila melanogaster, and in abdominal pigmentation divergence between Drosophila species. Sensitivity of t expression to environmental conditions might therefore give more substrate for selection, explaining why this gene has frequently been involved in evolution of pigmentation. Environmental conditions can strongly modulate the phenotype produced by a particular genotype. This process, called phenotypic plasticity, has major implications in medicine and agricultural sciences, and is thought to facilitate evolution. Phenotypic plasticity is observed in many animals and plants but its mechanisms are only partially understood. As a model of phenotypic plasticity, we study the effect of temperature on female abdominal pigmentation in the fruit fly Drosophila melanogaster. Here we show that temperature affects female abdominal pigmentation by modulating the expression of tan (t), a gene involved in melanin production, in female abdominal epidermis. This effect is mediated at least partly by a particular regulatory sequence of t, the t_MSE enhancer. However we detected no modulation of chromatin structure of t_MSE by temperature. By contrast, the level of the active chromatin mark H3K4me3 on the t promoter is strongly increased at lower temperature. We show that the H3K4 methyl-transferase Trithorax is involved in female abdominal pigmentation and its plasticity and regulates t expression and H3K4me3 level on the t promoter. Several studies have linked t to pigmentation evolution within and between Drosophila species. Our results suggest that sensitivity of t expression to temperature might facilitate its role in pigmentation evolution.
Collapse
Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, Equipe “Contrôle épigénétique de l’homéostasie et de la plasticité du développement”, Paris, France
- * E-mail: (JMG); (EMV)
| | - Emmanuèle Mouchel-Vielh
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, Equipe “Contrôle épigénétique de l’homéostasie et de la plasticité du développement”, Paris, France
- * E-mail: (JMG); (EMV)
| | - Sandra De Castro
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, Equipe “Contrôle épigénétique de l’homéostasie et de la plasticité du développement”, Paris, France
| | - Frédérique Peronnet
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, Equipe “Contrôle épigénétique de l’homéostasie et de la plasticité du développement”, Paris, France
| |
Collapse
|
8
|
Changes in Methionine Metabolism and Histone H3 Trimethylation Are Linked to Mitochondrial Defects in Multiple Sclerosis. J Neurosci 2016; 35:15170-86. [PMID: 26558787 DOI: 10.1523/jneurosci.4349-14.2015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Mitochondrial changes, including decreased expression of electron transport chain subunit genes and impaired energetic, have been reported in multiple sclerosis (MS), but the mechanisms involved in these changes are not clear. To determine whether epigenetic mechanisms are involved, we measured the concentrations of methionine metabolites by liquid chromatography tandem mass spectrometry, histone H3 methylation patterns, and markers of mitochondrial respiration in gray matter from postmortem MS and control cortical samples. We found decreases in respiratory markers as well as decreased concentrations of the methionine metabolites S-adenosylmethionine, betaine, and cystathionine in MS gray matter. We also found expression of the enzyme betaine homocysteine methyltransferase in cortical neurons. This enzyme catalyzes the remethylation of homocysteine to methionine, with betaine as the methyl donor, and has previously been thought to be restricted to liver and kidney in the adult human. Decreases in the concentration of the methyl donor betaine were correlated with decreases in histone H3 trimethylation (H3K4me3) in NeuN+ neuronal nuclei in MS cortex compared with controls. Mechanistic studies demonstrated that H3K4me3 levels and mitochondrial respiration were reduced in SH-SY5Y cells after exposure to the nitric oxide donor sodium nitroprusside, and betaine was able to rescue H3K4me3 levels and respiratory capacity in these cells. Chromatin immunoprecipitation experiments showed that betaine regulates metabolic genes in human SH-SY5Y neuroblastoma cells. These data suggest that changes to methionine metabolism may be mechanistically linked to changes in neuronal energetics in MS cortex. SIGNIFICANCE STATEMENT For decades, it has been observed that vitamin B12 deficiency and multiple sclerosis (MS) share certain pathological changes, including conduction disturbances. In the present study, we have found that vitamin B12-dependent methionine metabolism is dysregulated in the MS brain. We found that concentrations of the methyl donor betaine are decreased in MS cortex and are correlated with reduced levels of the histone H3 methyl mark H3K4me3 in neurons. Cell culture and chromatin immunoprecipitation-seq data suggest that these changes may lead to defects in mitochondria and impact neuronal energetics. These data have uncovered a novel pathway linking methionine metabolism with mitochondrial respiration and have important implications for understanding mechanisms involved in neurodegeneration in MS.
Collapse
|
9
|
Krause L, Haubold B, Börsch-Haubold AG. Social exclusion changes histone modifications H3K4me3 and H3K27ac in liver tissue of wild house mice. PLoS One 2015; 10:e0133988. [PMID: 26267652 PMCID: PMC4534140 DOI: 10.1371/journal.pone.0133988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 07/05/2015] [Indexed: 11/18/2022] Open
Abstract
Wild house mice form social hierarchies with aggressive males defending territories, in which females, young mice and submissive adult males share nests. In contrast, socially excluded males are barred from breeding groups, have numerous bite wounds and patches of thinning fur. Since their feeding times are often disrupted, we investigated whether social exclusion leads to changes in epigenetic marks of metabolic genes in liver tissue. We used chromatin immunoprecipitation and quantitative PCR to measure enrichment of two activating histone marks at 15 candidate loci. The epigenetic profiles of healthy males sampled from nest boxes differed significantly from the profiles of ostracized males caught outside of nests and showing bite wounds indicative of social exclusion. Enrichment of histone-3 lysine-4 trimethylation (H3K4me3) changed significantly at genes Cyp4a14, Gapdh, Nr3c1, Pck1, Ppara, and Sqle. Changes at histone-3 lysine-27 acetylation (H3K27ac) marks were detected at genes Fasn, Nr3c1, and Plin5. A principal components analysis separated the socialized from the ostracized mice. This was independent of body weight for the H3K4me3 mark, and partially dependent for H3K27ac. There was no separation, however, between healthy males that had been sampled from two different nests. A hierarchical cluster analysis also separated the two phenotypes, which was independent of body weight for both markers. Our study shows that a period of social exclusion during adult life leads to quantitative changes in histone modification patterns in mouse liver tissue. Similar epigenetic changes might occur during the development of stress-induced metabolic disorders in humans.
Collapse
Affiliation(s)
- Linda Krause
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bernhard Haubold
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Angelika G. Börsch-Haubold
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| |
Collapse
|
10
|
Pezer Ž, Harr B, Teschke M, Babiker H, Tautz D. Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions. Genome Res 2015; 25:1114-24. [PMID: 26149421 PMCID: PMC4509996 DOI: 10.1101/gr.187187.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 06/05/2015] [Indexed: 11/29/2022]
Abstract
Copy number variation represents a major source of genetic divergence, yet the evolutionary dynamics of genic copy number variation in natural populations during differentiation and adaptation remain unclear. We applied a read depth approach to genome resequencing data to detect copy number variants (CNVs) ≥1 kb in wild-caught mice belonging to four populations of Mus musculus domesticus. We complemented the bioinformatics analyses with experimental validation using droplet digital PCR. The specific focus of our analysis is CNVs that include complete genes, as these CNVs could be expected to contribute most directly to evolutionary divergence. In total, 1863 transcription units appear to be completely encompassed within CNVs in at least one individual when compared to the reference assembly. Further, 179 of these CNVs show population-specific copy number differences, and 325 are subject to complete deletion in multiple individuals. Among the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns that suggest involvement in local adaptations. We found that genes that overlap with large segmental duplications are generally more copy-number variable. These genes encode proteins that are relevant for environmental and behavioral interactions, such as vomeronasal and olfactory receptors, as well as major urinary proteins and several proteins of unknown function. The overall analysis shows that genic CNVs contribute more to population differentiation in mice than in humans and may promote and speed up population divergence.
Collapse
Affiliation(s)
- Željka Pezer
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Bettina Harr
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Meike Teschke
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Hiba Babiker
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| |
Collapse
|