1
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Alhosin M. Epigenetics Mechanisms of Honeybees: Secrets of Royal Jelly. Epigenet Insights 2023; 16:25168657231213717. [PMID: 38033464 PMCID: PMC10687967 DOI: 10.1177/25168657231213717] [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: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
Early diets in honeybees have effects on epigenome with consequences on their phenotype. Depending on the early larval diet, either royal jelly (RJ) or royal worker, 2 different female castes are generated from identical genomes, a long-lived queen with fully developed ovaries and a short-lived functionally sterile worker. To generate these prominent physiological and morphological differences between queen and worker, honeybees utilize epigenetic mechanisms which are controlled by nutritional input. These mechanisms include DNA methylation and histone post-translational modifications, mainly histone acetylation. In honeybee larvae, DNA methylation and histone acetylation may be differentially altered by RJ. This diet has biologically active ingredients with inhibitory effects on the de novo methyltransferase DNMT3A or the histone deacetylase 3 HDAC3 to create and maintain the epigenetic state necessary for developing larvae to generate a queen. DNMT and HDAC enzymes work together to induce the formation of a compacted chromatin structure, repressing transcription. Such dialog could be coordinated by their association with other epigenetic factors including the ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1 (UHRF1). Through its multiple functional domains, UHRF1 acts as an epigenetic reader of both DNA methylation patterns and histone marks. The present review discusses the epigenetic regulation of honeybee's chromatin and how the early diets in honeybees can affect the DNA/histone modifying types of machinery that are necessary to stimulate the larvae to turn into either queen or worker. The review also looks at future directions in epigenetics mechanisms of honeybees, mainly the potential role of UHRF1 in these mechanisms.
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Affiliation(s)
- Mahmoud Alhosin
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre for Artificial intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
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2
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Kucharski R, Ellis N, Jurkowski TP, Hurd PJ, Maleszka R. The PWWP domain and the evolution of unique DNA methylation toolkits in Hymenoptera. iScience 2023; 26:108193. [PMID: 37920666 PMCID: PMC10618690 DOI: 10.1016/j.isci.2023.108193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
DNMT3 in Hymenoptera has a unique duplication of the essential PWWP domain. Using GST-tagged PWWP fusion proteins and histone arrays we show that these domains have gained new properties and represent the first case of PWWP domains binding to H3K27 chromatin modifications, including H3K27me3, a key modification that is important during development. Phylogenetic analyses of 107 genomes indicate that the duplicated PWWP domains separated into two sister clades, and their distinct binding capacities are supported by 3D modeling. Other features of this unique DNA methylation system include variable copies, losses, and duplications of DNMT1 and DNMT3, and combinatorial generations of DNMT3 isoforms including variants missing the catalytic domain. Some of these losses and duplications of are found only in parasitic wasps. We discuss our findings in the context of the crosstalk between DNA methylation and histone methylation, and the expanded potential of epigenomic modifications in Hymenoptera to drive evolutionary novelties.
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Affiliation(s)
- Robert Kucharski
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Nancy Ellis
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Paul J. Hurd
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ryszard Maleszka
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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3
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Zhu W, Yang C, Liu Q, Peng M, Li Q, Wang H, Chen X, Zhang B, Feng P, Chen T, Zeng D, Zhao Y. Integrated Analysis of DNA Methylome and Transcriptome Reveals Epigenetic Regulation of Cold Tolerance in Litopenaeus vannamei. Int J Mol Sci 2023; 24:11573. [PMID: 37511332 PMCID: PMC10380378 DOI: 10.3390/ijms241411573] [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: 06/01/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is an important epigenetic modification that has been shown to be associated with responses to non-biological stressors. However, there is currently no research on DNA methylation in response to environmental signals in shrimp. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles and differentially expressed genes between two strains of Litopenaeus vannamei with significantly different cold tolerance through whole genome bisulfite sequencing (WGBS) and transcriptome sequencing. Between Lv-C and Lv-T (constant temperature of 28 °C and low temperatures of 18 °C and 10 °C) under cytosine-guanine (CG) environments, 39,100 differentially methylated regions (DMRs) were identified, corresponding to 9302 DMR-related genes (DMRGs). The DMRs were mainly located in the gene body (exons and introns). Gene Ontology (GO) analysis showed that these DMRGs were significantly enriched in cell parts, catalytic activity, and metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed significant enrichment of these DMRGs in pathways such as proteasome (ko03050), oxidative phosphorylation (ko00190), mTOR signaling pathway (ko04150), fatty acid metabolism (ko01212), and fatty acid degradation (ko00071). The comprehensive results suggested that L. vannamei mainly regulates gene expression in response to low temperatures through hypermethylation or demethylation of some genes involved in thermogenesis, glycolysis, the autophagy pathway, the peroxisome, and drug metabolism pathways. These results provide important clues for studying DNA methylation patterns and identifying cold tolerance genes in shrimp.
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Affiliation(s)
- Weilin Zhu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Tiancong Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
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4
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Jin MJ, Wang ZL, Wu ZH, He XJ, Zhang Y, Huang Q, Zhang LZ, Wu XB, Yan WY, Zeng ZJ. Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications. iScience 2023; 26:106308. [PMID: 36942051 PMCID: PMC10024153 DOI: 10.1016/j.isci.2023.106308] [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: 05/23/2022] [Revised: 01/12/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
Phenotypic dimorphism between queens and workers is an important biological characteristic of honeybees that has been the subject of intensive research. The enormous differences in morphology, lifespan, physiology, and behavior between queens and workers are caused by a complicated set of factors. Epigenetic modifications are considered to play an important role in this process. In this study, we analyzed the differences in chromosome interactions and H3K27ac and H3K4me1 modifications between the queens and workers using high-throughput chromosome conformation capture (Hi-C) and Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) technologies. We found that the queens contain more chromosome interactions and more unique H3K27ac modifications than workers; in contrast, workers have more H3K4me1 modifications than queens. Moreover, we identified Map3k15 as a potential caste gene in queen-worker differentiation. Our results suggest that chromosomal conformation and H3K27ac and H3K4me1 modifications are involved in regulating queen-worker differentiation, which reveals that the queen-worker phenotypic dimorphism is regulated by multiple epigenetic modifications.
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Affiliation(s)
- Meng Jie Jin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zhi Hao Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Yong Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Li Zhen Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
- Corresponding author
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5
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Marshall H, Nicholas MT, van Zweden JS, Wäckers F, Ross L, Wenseleers T, Mallon EB. DNA methylation is associated with codon degeneracy in a species of bumblebee. Heredity (Edinb) 2023; 130:188-195. [PMID: 36658299 PMCID: PMC10076500 DOI: 10.1038/s41437-023-00591-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
Social insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males, and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebee Bombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity, unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a targeted mutagen at these sites, providing substrate for selection via non-synonymous changes in the underlying genome. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.
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Affiliation(s)
- H Marshall
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK.
| | - M T Nicholas
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK
| | - J S van Zweden
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - F Wäckers
- Biobest Belgium N.V., Westerlo, Belgium
- The Lancaster Environmental Centre, University of Lancaster, Lancaster, UK
| | - L Ross
- The Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - T Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - E B Mallon
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK.
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6
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Nasrullah, Hussain A, Ahmed S, Rasool M, Shah AJ. DNA methylation across the tree of life, from micro to macro-organism. Bioengineered 2022; 13:1666-1685. [PMID: 34986742 PMCID: PMC8805842 DOI: 10.1080/21655979.2021.2014387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a process in which methyl (CH3) groups are added to the DNA molecule. The DNA segment does not change in the sequence, but DNA methylation could alter the action of DNA. Different enzymes like DNA methyltransferases (DNMTs) take part in methylation of cytosine/adenine nucleosides in DNA. In prokaryotes, DNA methylation is performed to prevent the attack of phage and also plays a role in the chromosome replication and repair. In fungi, DNA methylation is studied to see the transcriptional changes, as in insects, the DNA methylation is not that well-known, it plays a different role like other organisms. In mammals, the DNA methylation is related to different types of cancers and plays the most important role in the placental development and abnormal DNA methylation connected with diseases like cancer, autoimmune diseases, and rheumatoid arthritis.
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Affiliation(s)
- Nasrullah
- Center for Advanced Studies in Vaccinology & Biotechnology (Casvab), University of Baluchistan, Quetta- Pakistan. E-mails:
| | - Abrar Hussain
- Department of Biotechnology, Faculty of Life Sciences, Buitems, Quetta-Pakistan. E-mails:
| | - Sagheer Ahmed
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan. E-mails:
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. E-mails:
| | - Abdul Jabbar Shah
- Department of Pharmaceutical Sciences, Comsats University, Abbottabad. E-mails:
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7
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Intergenerational Patterns of DNA Methylation in Procambarus clarkii Following Exposure to Genotoxicants: A Conjugation in Past Simple or Past Continuous? TOXICS 2021; 9:toxics9110271. [PMID: 34822662 PMCID: PMC8618669 DOI: 10.3390/toxics9110271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/31/2022]
Abstract
Epigenome is susceptible to modulation by environmental pressures—namely, through alterations in global DNA methylation, impacting the organism condition and, ultimately, reverberating on the phenotype of the subsequent generations. Hence, an intergenerational study was conducted, aiming to clarify the influence of genotoxicants on global DNA methylation of the crayfish Procambarus clarkii. Two subsequent generations were exposed to the herbicide penoxsulam (Px; 23 µg·L−1) and to the genotoxicant model ethyl methanesulfonate (EMS; 5 mg·L−1). Px did not induce changes in DNA methylation of adult crayfish (F0). However, the hypomethylation occurring in unexposed F1 juveniles demonstrated that the history of exposure per se can modulate epigenome. In F1 descendants of the Px-exposed group, methylome (hypermethylated) was more affected in males than in females. EMS-induced hypomethylation in adult females (F0), also showed gender specificity. In addition, hypomethylation was also observed in the unexposed F1 crayfish, indicating an intergenerational epigenetic effect. The modulatory role of past exposure to penoxsulam or to EMS also showed a dependency on the crayfish developmental stage. Overall, this research revealed that indirect experiences (events occurring in a predecessor generation) can have an impact even greater than direct experiences (present events) on the epigenetic dynamics.
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8
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Lucas C, Ben-Shahar Y. The foraging gene as a modulator of division of labour in social insects. J Neurogenet 2021; 35:168-178. [PMID: 34151702 DOI: 10.1080/01677063.2021.1940173] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The social ants, bees, wasps, and termites include some of the most ecologically-successful groups of animal species. Their dominance in most terrestrial environments is attributed to their social lifestyle, which enable their colonies to exploit environmental resources with remarkable efficiency. One key attribute of social insect colonies is the division of labour that emerges among the sterile workers, which represent the majority of colony members. Studies of the mechanisms that drive division of labour systems across diverse social species have provided fundamental insights into the developmental, physiological, molecular, and genomic processes that regulate sociality, and the possible genetic routes that may have led to its evolution from a solitary ancestor. Here we specifically discuss the conserved role of the foraging gene, which encodes a cGMP-dependent protein kinase (PKG). Originally identified as a behaviourally polymorphic gene that drives alternative foraging strategies in the fruit fly Drosophila melanogaster, changes in foraging expression and kinase activity were later shown to play a key role in the division of labour in diverse social insect species as well. In particular, foraging appears to regulate worker transitions between behavioural tasks and specific behavioural traits associated with morphological castes. Although the specific neuroethological role of foraging in the insect brain remains mostly unknown, studies in genetically tractable insect species indicate that PKG signalling plays a conserved role in the neuronal plasticity of sensory, cognitive and motor functions, which underlie behaviours relevant to division of labour, including appetitive learning, aggression, stress response, phototaxis, and the response to pheromones.
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Affiliation(s)
- Christophe Lucas
- Institut de Recherche sur la Biologie de l'Insecte (UMR7261), CNRS - University of Tours, Tours, France
| | - Yehuda Ben-Shahar
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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9
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Oldroyd BP, Yagound B. The role of epigenetics, particularly DNA methylation, in the evolution of caste in insect societies. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200115. [PMID: 33866805 PMCID: PMC8059649 DOI: 10.1098/rstb.2020.0115] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Eusocial insects can be defined as those that live in colonies and have distinct queens and workers. For most species, queens and workers arise from a common genome, and so caste-specific developmental trajectories must arise from epigenetic processes. In this review, we examine the epigenetic mechanisms that may be involved in the regulation of caste dimorphism. Early work on honeybees suggested that DNA methylation plays a causal role in the divergent development of queen and worker castes. This view has now been challenged by studies that did not find consistent associations between methylation and caste in honeybees and other species. Evidence for the involvement of methylation in modulating behaviour of adult workers is also inconsistent. Thus, the functional significance of DNA methylation in social insects remains equivocal. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Benjamin P. Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
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10
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Rastogi A, Lin X, Lombard B, Loew D, Tirichine L. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms. AIMS GENETICS 2021. [DOI: 10.3934/genet.2015.3.173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractRecent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epigenetic features found in mammals and plants suggesting their ancient origin. Phaeodactylum tricornutum and Thalassiosira pseudonana, pennate and centric diatoms, respectively, emerged as model species to address questions on the evolution of epigenetic phenomena such as what has been lost, retained or has evolved in contemporary species. In the present work, we will discuss how the study of non-model or emerging model organisms, such as diatoms, helps understand the evolutionary history of epigenetic mechanisms with a particular focus on DNA methylation and histone modifications.
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Affiliation(s)
- Achal Rastogi
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
| | - Xin Lin
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Leïla Tirichine
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
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11
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Dyson CJ, Goodisman MAD. Gene Duplication in the Honeybee: Patterns of DNA Methylation, Gene Expression, and Genomic Environment. Mol Biol Evol 2021; 37:2322-2331. [PMID: 32243528 DOI: 10.1093/molbev/msaa088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Gene duplication serves a critical role in evolutionary adaptation by providing genetic raw material to the genome. The evolution of duplicated genes may be influenced by epigenetic processes such as DNA methylation, which affects gene function in some taxa. However, the manner in which DNA methylation affects duplicated genes is not well understood. We studied duplicated genes in the honeybee Apis mellifera, an insect with a highly sophisticated social structure, to investigate whether DNA methylation was associated with gene duplication and genic evolution. We found that levels of gene body methylation were significantly lower in duplicate genes than in single-copy genes, implicating a possible role of DNA methylation in postduplication gene maintenance. Additionally, we discovered associations of gene body methylation with the location, length, and time since divergence of paralogous genes. We also found that divergence in DNA methylation was associated with divergence in gene expression in paralogs, although the relationship was not completely consistent with a direct link between DNA methylation and gene expression. Overall, our results provide further insight into genic methylation and how its association with duplicate genes might facilitate evolutionary processes and adaptation.
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Affiliation(s)
- Carl J Dyson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
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12
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Hurd PJ, Grübel K, Wojciechowski M, Maleszka R, Rössler W. Novel structure in the nuclei of honey bee brain neurons revealed by immunostaining. Sci Rep 2021; 11:6852. [PMID: 33767244 PMCID: PMC7994413 DOI: 10.1038/s41598-021-86078-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/10/2021] [Indexed: 11/08/2022] Open
Abstract
In the course of a screen designed to produce antibodies (ABs) with affinity to proteins in the honey bee brain we found an interesting AB that detects a highly specific epitope predominantly in the nuclei of Kenyon cells (KCs). The observed staining pattern is unique, and its unfamiliarity indicates a novel previously unseen nuclear structure that does not colocalize with the cytoskeletal protein f-actin. A single rod-like assembly, 3.7-4.1 µm long, is present in each nucleus of KCs in adult brains of worker bees and drones with the strongest immuno-labelling found in foraging bees. In brains of young queens, the labelling is more sporadic, and the rod-like structure appears to be shorter (~ 2.1 µm). No immunostaining is detectable in worker larvae. In pupal stage 5 during a peak of brain development only some occasional staining was identified. Although the cellular function of this unexpected structure has not been determined, the unusual distinctiveness of the revealed pattern suggests an unknown and potentially important protein assembly. One possibility is that this nuclear assembly is part of the KCs plasticity underlying the brain maturation in adult honey bees. Because no labelling with this AB is detectable in brains of the fly Drosophila melanogaster and the ant Camponotus floridanus, we tentatively named this antibody AmBNSab (Apis mellifera Brain Neurons Specific antibody). Here we report our results to make them accessible to a broader community and invite further research to unravel the biological role of this curious nuclear structure in the honey bee central brain.
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Affiliation(s)
- Paul J Hurd
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Kornelia Grübel
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Marek Wojciechowski
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ryszard Maleszka
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Wolfgang Rössler
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
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13
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Bain SA, Marshall H, de la Filia AG, Laetsch DR, Husnik F, Ross L. Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination. Mol Ecol 2021; 30:5687-5703. [PMID: 33629415 DOI: 10.1111/mec.15842] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/27/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022]
Abstract
Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate these expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, paternal genome elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. Planococcus citri has no sex chromosomes and both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. Here, we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole-genome bisulphite sequencing. We identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifest as more uniform low levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq, we identify extensive sex-specific gene expression and alternative splicing, but we find no correlation with cis-acting DNA methylation.
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Affiliation(s)
- Stevie A Bain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Hollie Marshall
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Filip Husnik
- Evolution, Cell Biology, and Symbiosis Unit, Okinawa Institute of Science and Technology, Kunigami-gun, Japan
| | - Laura Ross
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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14
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Hearn J, Plenderleith F, Little TJ. DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna. Epigenetics Chromatin 2021; 14:4. [PMID: 33407738 PMCID: PMC7789248 DOI: 10.1186/s13072-020-00379-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Patterns of methylation influence lifespan, but methylation and lifespan may also depend on diet, or differ between genotypes. Prior to this study, interactions between diet and genotype have not been explored together to determine their influence on methylation. The invertebrate Daphnia magna is an excellent choice for testing the epigenetic response to the environment: parthenogenetic offspring are identical to their siblings (making for powerful genetic comparisons), they are relatively short lived and have well-characterised inter-strain life-history trait differences. We performed a survival analysis in response to caloric restriction and then undertook a 47-replicate experiment testing the DNA methylation response to ageing and caloric restriction of two strains of D. magna. RESULTS Methylated cytosines (CpGs) were most prevalent in exons two to five of gene bodies. One strain exhibited a significantly increased lifespan in response to caloric restriction, but there was no effect of food-level CpG methylation status. Inter-strain differences dominated the methylation experiment with over 15,000 differently methylated CpGs. One gene, Me31b, was hypermethylated extensively in one strain and is a key regulator of embryonic expression. Sixty-one CpGs were differentially methylated between young and old individuals, including multiple CpGs within the histone H3 gene, which were hypermethylated in old individuals. Across all age-related CpGs, we identified a set that are highly correlated with chronological age. CONCLUSIONS Methylated cytosines are concentrated in early exons of gene sequences indicative of a directed, non-random, process despite the low overall DNA methylation percentage in this species. We identify no effect of caloric restriction on DNA methylation, contrary to our previous results, and established impacts of caloric restriction on phenotype and gene expression. We propose our approach here is more robust in invertebrates given genome-wide CpG distributions. For both strain and ageing, a single gene emerges as differentially methylated that for each factor could have widespread phenotypic effects. Our data showed the potential for an epigenetic clock at a subset of age positions, which is exciting but requires confirmation.
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Affiliation(s)
- Jack Hearn
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Fiona Plenderleith
- The James Hutton Institute, Craigiebuckler, Aberdeen, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom J. Little
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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15
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Yi Y, He XJ, Barron AB, Liu YB, Wang ZL, Yan WY, Zeng ZJ. Transgenerational accumulation of methylome changes discovered in commercially reared honey bee (Apis mellifera) queens. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 127:103476. [PMID: 33053387 DOI: 10.1016/j.ibmb.2020.103476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Whether a female honey bee (Apis mellifera) develops into a worker or a queen depends on her nutrition during development, which changes the epigenome to alter the developmental trajectory. Beekeepers typically exploit this developmental plasticity to produce queen bee by transplanting worker larvae into queen cells to be reared as queens, thus redirecting a worker developmental pathway to a queen developmental pathway. We studied the consequences of this manipulation for the queen phenotype and methylome over four generations. Queens reared from worker larvae consistently had fewer ovarioles than queens reared from eggs. Over four generations the methylomes of lines of queens reared from eggs and worker larvae diverged, accumulating increasing differences in exons of genes related to caste differentiation, growth and immunity. We discuss the consequences of these cryptic changes to the honey bee epigenome for the health and viability of honey bee stocks.
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Affiliation(s)
- Yao Yi
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, 330004, PR China
| | - Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China
| | - Andrew B Barron
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Yi Bo Liu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China.
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16
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Marshall H, Lonsdale ZN, Mallon EB. Methylation and gene expression differences between reproductive and sterile bumblebee workers. Evol Lett 2019; 3:485-499. [PMID: 31636941 PMCID: PMC6791180 DOI: 10.1002/evl3.129] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
Phenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with DNA methylation being explored to the greatest extent. DNA methylation is thought to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on its role in other bee species. In this study, we analyzed whole genome bisulfite sequencing and RNA-seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris. We found that genome-wide methylation in B. terrestris is similar to other holometabolous insects and does not differ between reproductive castes. We did, however, find differentially methylated genes between castes, which are enriched for multiple biological processes including reproduction. However, we found no relationship between differential methylation and differential gene expression or differential exon usage between castes. Our results also indicate high intercolony variation in methylation. These findings suggest that methylation is associated with caste differences but may serve an alternate function, other than direct caste determination in this species. This study provides the first insights into the nature of a bumblebee caste-specific methylome as well as its interaction with gene expression and caste-specific alternative splicing, providing greater understanding of the role of methylation in phenotypic plasticity within social bee species. Future experimental work is needed to determine the function of methylation and other epigenetic mechanisms in insects.
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Affiliation(s)
- Hollie Marshall
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
| | - Zoë N. Lonsdale
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
| | - Eamonn B. Mallon
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
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17
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Bebane PSA, Hunt BJ, Pegoraro M, Jones ARC, Marshall H, Rosato E, Mallon EB. The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris. Proc Biol Sci 2019; 286:20190718. [PMID: 31213186 PMCID: PMC6599982 DOI: 10.1098/rspb.2019.0718] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee Bombus terrestris workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid-treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.
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Affiliation(s)
- P. S. A. Bebane
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - B. J. Hunt
- School of Natural Sciences and Psychology, John Moores University Liverpool, Liverpool L3 3AF, UK
| | - M. Pegoraro
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - A. R. C Jones
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - H. Marshall
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - E. Rosato
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - E. B. Mallon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
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18
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Jones JC, Wallberg A, Christmas MJ, Kapheim KM, Webster MT. Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee. Mol Biol Evol 2019; 36:2277-2291. [DOI: 10.1093/molbev/msz130] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Abstract
Social insect genomes exhibit the highest rates of crossing over observed in plants and animals. The evolutionary causes of these extreme rates are unknown. Insight can be gained by comparing recombination rate variation across the genomes of related social and solitary insects. Here, we compare the genomic recombination landscape of the highly social honey bee, Apis mellifera, with the solitary alfalfa leafcutter bee, Megachile rotundata, by analyzing patterns of linkage disequilibrium in population-scale genome sequencing data. We infer that average recombination rates are extremely elevated in A. mellifera compared with M. rotundata. However, our results indicate that similar factors control the distribution of crossovers in the genomes of both species. Recombination rate is significantly reduced in coding regions in both species, with genes inferred to be germline methylated having particularly low rates. Genes with worker-biased patterns of expression in A. mellifera and their orthologs in M. rotundata have higher than average recombination rates in both species, suggesting that selection for higher diversity in genes involved in worker caste functions in social taxa is not the explanation for these elevated rates. Furthermore, we find no evidence that recombination has modulated the efficacy of selection among genes during bee evolution, which does not support the hypothesis that high recombination rates facilitated positive selection for new functions in social insects. Our results indicate that the evolution of sociality in insects likely entailed selection on modifiers that increased recombination rates genome wide, but that the genomic recombination landscape is determined by the same factors.
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Affiliation(s)
- Julia C Jones
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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19
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Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera. G3-GENES GENOMES GENETICS 2019; 9:1055-1063. [PMID: 30792192 PMCID: PMC6469410 DOI: 10.1534/g3.118.200857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA-seq has proven to be a powerful tool to unravel various aspects of the transcriptome, especially the quantification of alternative splicing (AS) that leads to isoform diversity. The honey bee (Apis mellifera) is an important model organism for studying the molecular underpinnings of behavioral plasticity and social behavior, and recent RNA-seq studies of honey bees have revealed AS patterns and their regulation by DNA methylation. However, tissue-specific AS patterns have not been fully explored. In this paper, we characterized AS patterns in two different honey bee tissue types, and also explored their conservation and regulation. We used the RNA-seq data from brain and fat body to improve the existing models of honey bee genes and identified tissue-specific AS patterns. We found that AS genes show high conservation between honey bee and Drosophila melanogaster. We also confirmed and extended previous findings of a correlation between gene body DNA methylation and AS patterns, providing further support for the role of DNA methylation in regulating AS. In addition, our analysis suggests distinct functional roles for tissue-specific alternatively spliced genes. Taken together, our work provides new insights into the conservation and dynamics of AS patterns across different tissue types.
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20
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Glastad KM, Hunt BG, Goodisman MAD. Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity. ANNUAL REVIEW OF ENTOMOLOGY 2019; 64:185-203. [PMID: 30285490 DOI: 10.1146/annurev-ento-011118-111914] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epigenetic inheritance is fundamentally important to cellular differentiation and developmental plasticity. In this review, we provide an introduction to the field of molecular epigenetics in insects. Epigenetic information is passed across cell divisions through the methylation of DNA, the modification of histone proteins, and the activity of noncoding RNAs. Much of our knowledge of insect epigenetics has been gleaned from a few model species. However, more studies of epigenetic information in traditionally nonmodel taxa will help advance our understanding of the developmental and evolutionary significance of epigenetic inheritance in insects. To this end, we also provide a brief overview of techniques for profiling and perturbing individual facets of the epigenome. Doing so in diverse cellular, developmental, and taxonomic contexts will collectively help shed new light on how genome regulation results in the generation of diversity in insect form and function.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, Georgia 30223, USA;
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
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21
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Faragalla KM, Chernyshova AM, Gallo AJ, Thompson GJ. From gene list to gene network: Recognizing functional connections that regulate behavioral traits. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:317-329. [DOI: 10.1002/jez.b.22829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/10/2018] [Indexed: 12/27/2022]
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22
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The effect of maternal care on gene expression and DNA methylation in a subsocial bee. Nat Commun 2018; 9:3468. [PMID: 30150650 PMCID: PMC6110825 DOI: 10.1038/s41467-018-05903-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
Developmental plasticity describes the influence of environmental factors on phenotypic variation. An important mediator of developmental plasticity in many animals is parental care. Here, we examine the consequences of maternal care on offspring after the initial mass provisioning of brood in the small carpenter bee, Ceratina calcarata. Removal of the mother during larval development leads to increased aggression and avoidance in adulthood. This corresponds with changes in expression of over one thousand genes, alternative splicing of hundreds of genes, and significant changes to DNA methylation. We identify genes related to metabolic and neuronal functions that may influence developmental plasticity and aggression. We observe no genome-wide association between differential DNA methylation and differential gene expression or splicing, though indirect relationships may exist between these factors. Our results provide insight into the gene regulatory context of DNA methylation in insects and the molecular avenues through which variation in maternal care influences developmental plasticity.
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23
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Glastad KM, Arsenault SV, Vertacnik KL, Geib SM, Kay S, Danforth BN, Rehan SM, Linnen CR, Kocher SD, Hunt BG. Variation in DNA Methylation Is Not Consistently Reflected by Sociality in Hymenoptera. Genome Biol Evol 2018; 9:1687-1698. [PMID: 28854636 PMCID: PMC5522706 DOI: 10.1093/gbe/evx128] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2017] [Indexed: 12/12/2022] Open
Abstract
Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of eusocial division of labor is associated with enhanced gene regulatory potential, which may include expansions in DNA methylation in the genomes of Hymenoptera (bees, ants, wasps, and sawflies). Recently, this hypothesis garnered support from analyses of a commonly used metric to estimate DNA methylation in silico, CpG content. Here, we test this hypothesis using direct, nucleotide-level measures of DNA methylation across nine species of Hymenoptera. In doing so, we generated new DNA methylomes for three species of interest, including one solitary and one facultatively eusocial halictid bee and a sawfly. We demonstrate that the strength of correlation between CpG content and DNA methylation varies widely among hymenopteran taxa, highlighting shortcomings in the utility of CpG content as a proxy for DNA methylation in comparative studies of taxa with sparse DNA methylomes. We observed strikingly high levels of DNA methylation in the sawfly relative to other investigated hymenopterans. Analyses of molecular evolution suggest the relatively distinct sawfly DNA methylome may be associated with positive selection on functional DNMT3 domains. Sawflies are an outgroup to all ants, bees, and wasps, and no sawfly species are eusocial. We find no evidence that either global expansions or variation within individual ortholog groups in DNA methylation are consistently associated with the evolution of social behavior.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania
| | | | | | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Sasha Kay
- Department of Entomology, University of Georgia
| | | | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire
| | | | - Sarah D Kocher
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
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24
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Trijau M, Asselman J, Armant O, Adam-Guillermin C, De Schamphelaere KAC, Alonzo F. Transgenerational DNA Methylation Changes in Daphnia magna Exposed to Chronic γ Irradiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:4331-4339. [PMID: 29486114 DOI: 10.1021/acs.est.7b05695] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Our aim was to investigate epigenetic changes in Daphnia magna after a 25-day chronic external γ irradiation (generation F0 exposed to 6.5 μGy·h-1 or 41.3 mGy·h-1) and their potential inheritance by subsequent recovering generations, namely, F2 (exposed as germline cells in F1 embryos) and F3 (the first truly unexposed generation). Effects on survival, growth, and reproduction were observed and DNA was extracted for whole-genome bisulfite sequencing in all generations. Results showed effects on reproduction in F0 but no effect in the subsequent generations F1, F2, and F3. In contrast, we observed significant methylation changes at specific CpG positions in every generation independent of dose rate, with a majority of hypomethylation. Some of these changes were shared between dose rates and between generations. Associated gene functions included gene families and genes that were previously shown to play roles during exposure to ionizing radiation. Common methylation changes detected between generations F2 and F3 clearly showed that epigenetic modifications can be transmitted to unexposed generations, most likely through the germline, with potential implications for environmental risk.
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Affiliation(s)
- Marie Trijau
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
| | - Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology , Ghent University , Ghent 9000 , Belgium
| | - Olivier Armant
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
| | | | - Frédéric Alonzo
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
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25
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Li B, Hou L, Zhu D, Xu X, An S, Wang X. Identification and caste-dependent expression patterns of DNA methylation associated genes in Bombus terrestris. Sci Rep 2018; 8:2332. [PMID: 29402971 PMCID: PMC5799256 DOI: 10.1038/s41598-018-20831-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/24/2018] [Indexed: 11/09/2022] Open
Abstract
DNA methylation has been proposed to play critical roles in caste fate and behavioral plasticity in bumblebees, however, there is little information on its regulatory mechanisms. Here, we identified six important genes mediating the modification of DNA methylation and determined their expression patterns in the bumblebee Bombus terrestris. There is a complete functional DNA methylation system, including four DNA methyltransferases (DNMT1a, DNMT1b, DNMT2, and DNMT3), a DNA demethylase (Ten-eleven translocation), and a methyl-CpG-binding domain protein in B. terrestris. Most of these genes were highly expressed in fat bodies and gonads but lowly expressed in antennae and brains of bumblebee adults. Besides, these genes exhibited caste-specific expression patterns in bumblebees, with higher transcription levels in queens than workers and drones. Whereas their expression levels showed no remarkable difference in queenright and queenless workers. These results suggested potential roles of DNA methylation-related genes in caste differentiation in bumblebees.
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Affiliation(s)
- Beibei Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Li Hou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dan Zhu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xilian Xu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shiheng An
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xianhui Wang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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26
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Hemimetabolous genomes reveal molecular basis of termite eusociality. Nat Ecol Evol 2018; 2:557-566. [PMID: 29403074 PMCID: PMC6482461 DOI: 10.1038/s41559-017-0459-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/19/2017] [Indexed: 11/25/2022]
Abstract
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.
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27
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Sumner S, Bell E, Taylor D. A molecular concept of caste in insect societies. CURRENT OPINION IN INSECT SCIENCE 2018; 25:42-50. [PMID: 29602361 DOI: 10.1016/j.cois.2017.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 05/20/2023]
Abstract
The term 'caste' is used to describe the division of reproductive labour that defines eusocial insect societies. The definition of 'caste' has been debated over the last 50 years, specifically with respect to the simplest insect societies; this raises the question of whether a simple categorisation of social behaviour by reproductive state alone is helpful. Gene-level analyses of behaviours of individuals in hymenopteran social insect societies now provide a new empirical base-line for defining caste and understanding the evolution and maintenance of a reproductive division of labour. We review this literature to identify a set of potential molecular signatures that, combined with behavioural, morphological and physiological data, help define caste more precisely; these signatures vary with the type of society, and are likely to be influenced by ecology, life-history, and stage in the colony cycle. We conclude that genomic approaches provide us with additional ways to help quantify and categorise caste, and behaviour in general.
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Affiliation(s)
- Seirian Sumner
- Centre for Biodiversity and Environmental Research, Medawar Building, University College London, Gower Street, London WC1E 6BT, UK.
| | - Emily Bell
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Daisy Taylor
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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Wang W, Ashby R, Ying H, Maleszka R, Forêt S. Contrasting Sex-and Caste-Dependent piRNA Profiles in the Transposon Depleted Haplodiploid Honeybee Apis mellifera. Genome Biol Evol 2018; 9:1341-1356. [PMID: 28472327 PMCID: PMC5452642 DOI: 10.1093/gbe/evx087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 12/12/2022] Open
Abstract
Protecting genome integrity against transposable elements is achieved by intricate molecular mechanisms involving PIWI proteins, their associated small RNAs (piRNAs), and epigenetic modifiers such as DNA methylation. Eusocial bees, in particular the Western honeybee, Apis mellifera, have one of the lowest contents of transposable elements in the animal kingdom, and, unlike other animals with a functional DNA methylation system, appear not to methylate their transposons. This raises the question of whether the PIWI machinery has been retained in this species. Using comparative genomics, mass spectrometry, and expressional profiling, we present seminal evidence that the piRNA system is conserved in honeybees. We show that honey bee piRNAs contain a 2'-O-methyl modification at the 3' end, and have a bias towards a 5' terminal U, which are signature features of their biogenesis. Both piRNA repertoire and expression levels are greater in reproductive individuals than in sterile workers. Haploid males, where the detrimental effects of transposons are dominant, have the greatest piRNA levels, but surprisingly, the highest expression of transposons. These results show that even in a transposon-depleted species, the piRNA system is required to guard the vulnerable haploid genome and reproductive castes against transposon-associated genomic instability. This also suggests that dosage plays an important role in the regulation of transposons and piRNAs expression in haplo-diploid systems.
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Affiliation(s)
- Weiwen Wang
- Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Regan Ashby
- Research School of Biology, Australian National University, Acton, ACT, Australia.,Centre for Research in Therapeutic Solutions, Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, ACT, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Ryszard Maleszka
- Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Acton, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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Kucharski R, Maleszka J, Maleszka R. A possible role of DNA methylation in functional divergence of a fast evolving duplicate gene encoding odorant binding protein 11 in the honeybee. Proc Biol Sci 2017; 283:rspb.2016.0558. [PMID: 27358363 DOI: 10.1098/rspb.2016.0558] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/09/2016] [Indexed: 12/26/2022] Open
Abstract
Although gene duplication is seen as the main path to evolution of new functions, molecular mechanisms by which selection favours the gain versus loss of newly duplicated genes and minimizes the fixation of pseudo-genes are not well understood. Here, we investigate in detail a duplicate honeybee gene obp11 belonging to a fast evolving insect gene family encoding odorant binding proteins (OBPs). We report that obp11 is expressed only in female bees in rare antennal sensilla basiconica in contrast to its tandem partner obp10 that is expressed in the brain in both females and males (drones). Unlike all other obp genes in the honeybee, obp11 is methylated suggesting that functional diversification of obp11 and obp10 may have been driven by an epigenetic mechanism. We also show that increased methylation in drones near one donor splice site that correlates with higher abundance of a transcript variant encoding a truncated OBP11 protein is one way of controlling its contrasting expression. Our data suggest that like in mammals and plants, DNA methylation in insects may contribute to functional diversification of proteins produced from duplicated genes, in particular to their subfunctionalization by generating complementary patterns of expression.
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Affiliation(s)
- R Kucharski
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - J Maleszka
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - R Maleszka
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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Welsh L, Maleszka R, Foret S. Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170248. [PMID: 28989734 PMCID: PMC5627074 DOI: 10.1098/rsos.170248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/07/2017] [Indexed: 05/12/2023]
Abstract
Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here, we have applied a novel approach to examine whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, a social insect with a high level of epigenetically driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics, we show that rare asymmetrically methylated CpGs can be unambiguously detected in the honeybee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric.
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31
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Welsh L, Maleszka R, Foret S. Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170248. [PMID: 28989734 DOI: 10.5061/dryad.7nb8q] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/07/2017] [Indexed: 05/26/2023]
Abstract
Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here, we have applied a novel approach to examine whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, a social insect with a high level of epigenetically driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics, we show that rare asymmetrically methylated CpGs can be unambiguously detected in the honeybee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric.
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Affiliation(s)
- Laura Welsh
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ryszard Maleszka
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Sylvain Foret
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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32
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Lucas ER, Romiguier J, Keller L. Gene expression is more strongly influenced by age than caste in the ant Lasius niger. Mol Ecol 2017; 26:5058-5073. [DOI: 10.1111/mec.14256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Eric R. Lucas
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
- Department of Vector Biology; Liverpool School of Tropical Medicine; Liverpool UK
| | - Jonathan Romiguier
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
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Trapp J, McAfee A, Foster LJ. Genomics, transcriptomics and proteomics: enabling insights into social evolution and disease challenges for managed and wild bees. Mol Ecol 2017; 26:718-739. [DOI: 10.1111/mec.13986] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Judith Trapp
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
| | - Alison McAfee
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
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Kilaso M, Tipgomut C, Sanguankiattichai N, Teerapakpinyo C, Chanchao C. Expression and DNA methylation of phospholipase A2 in Thai native honeybees (Hymenoptera: Apidae). Russ J Dev Biol 2016. [DOI: 10.1134/s1062360416030024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Woestmann L, Saastamoinen M. The importance of trans-generational effects in Lepidoptera. Curr Zool 2016; 62:489-499. [PMID: 29491938 PMCID: PMC5804281 DOI: 10.1093/cz/zow029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/16/2016] [Indexed: 12/03/2022] Open
Abstract
The importance of trans-generational effects in shaping an individuals’ phenotype and fitness, and consequently even impacting population dynamics is increasingly apparent. Most of the research on trans-generational effects still focuses on plants, mammals, and birds. In the past few years, however, increasing number of studies, especially on maternal effects, have highlighted their importance also in many insect systems. Lepidoptera, specifically butterflies, have been used as model systems for studying the role of phenotypic plasticity within generations. As ectotherms, they are highly sensitive to environmental variation, and indeed many butterflies show adaptive phenotypic plasticity in response to environmental conditions. Here, we synthesize what is known about trans-generational effects in Lepidoptera, compile evidence for different environmental cues that are important drivers of trans-generational effects, and point out which offspring traits are mainly impacted. Finally, we emphasize directions for future research that are needed for better understanding of the adaptive nature of trans-generational effects in Lepidoptera in particular, but potentially also in other organisms.
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Affiliation(s)
- Luisa Woestmann
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Finland
| | - Marjo Saastamoinen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Finland
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Abstract
Many exciting studies have begun to elucidate the genetics of the morphological and physiological diversity of ants, but as yet few studies have investigated the genetics of ant behavior directly. Ant genomes are marked by extreme rates of gene turnover, especially in gene families related to olfactory communication, such as the synthesis of cuticular hydrocarbons and the perception of environmental semiochemicals. Transcriptomic and epigenetic differences are apparent between reproductive and sterile females, males and females, and workers that differ in body size. Quantitative genetic approaches suggest heritability of task performance, and population genetic studies indicate a genetic association with reproductive status in some species. Gene expression is associated with behavior including foraging, response to queens attempting to join a colony, circadian patterns of task performance, and age-related changes of task. Ant behavioral genetics needs further investigation of the feedback between individual-level physiological changes and socially mediated responses to environmental conditions.
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Affiliation(s)
- D A Friedman
- Department of Biology, Stanford University, Stanford, California 94305-5020;
| | - D M Gordon
- Department of Biology, Stanford University, Stanford, California 94305-5020;
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37
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Kesäniemi JE, Heikkinen L, Knott KE. DNA Methylation and Potential for Epigenetic Regulation in Pygospio elegans. PLoS One 2016; 11:e0151863. [PMID: 27008314 PMCID: PMC4805255 DOI: 10.1371/journal.pone.0151863] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/04/2016] [Indexed: 01/24/2023] Open
Abstract
Transitions in developmental mode are common evolutionarily, but how and why they occur is not understood. Developmental mode describes larval phenotypes, including morphology, ecology and behavior of larvae, which typically are generalized across different species. The polychaete worm Pygospio elegans is one of few species polymorphic in developmental mode, with multiple larval phenotypes, providing a possibility to examine the potential mechanisms allowing transitions in developmental mode. We investigated the presence of DNA methylation in P. elegans, and, since maternal provisioning is a key factor determining eventual larval phenotype, we compared patterns of DNA methylation in females during oogenesis in this species. We demonstrate that intragenic CpG site DNA methylation and many relevant genes necessary for DNA methylation occur in P. elegans. Methylation-sensitive AFLP analysis showed that gravid females with offspring differing in larval developmental mode have significantly different methylation profiles and that the females with benthic larvae and non-reproductive females from the same location also differ in their epigenetic profiles. Analysis of CpG sites in transcriptome data supported our findings of DNA methylation in this species and showed that CpG observed/expected ratios differ among females gravid with embryos destined to different developmental modes. The differences in CpG site DNA methylation patterns seen among the samples suggest a potential for epigenetic regulation of gene expression (through DNA methylation) in this species.
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Affiliation(s)
- Jenni E. Kesäniemi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- * E-mail:
| | - Liisa Heikkinen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - K. Emily Knott
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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Remnant EJ, Ashe A, Young PE, Buchmann G, Beekman M, Allsopp MH, Suter CM, Drewell RA, Oldroyd BP. Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation. BMC Genomics 2016; 17:226. [PMID: 26969617 PMCID: PMC4788913 DOI: 10.1186/s12864-016-2506-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes. RESULTS We compared genome-wide methylation patterns of sexually-produced, diploid embryos laid by a queen, with parthenogenetically-produced diploid embryos laid by her daughters. Thelytokous embryos inheriting two maternal genomes had fewer hypermethylated genes compared to fertilized embryos, supporting the prediction that fertilized embryos have increased methylation due to inheritance of a paternal genome. However, bisulfite PCR and sequencing of a differentially methylated gene, Stan (GB18207) showed strong allele-specific methylation that was maintained in both fertilized and thelytokous embryos. For this gene, methylation was associated with haplotype, not parent of origin. CONCLUSIONS The results of our study are consistent with predictions from the kin theory of genomic imprinting. However, our demonstration of allele-specific methylation based on sequence shows that genome-wide differential methylation studies can potentially confound imprinting and allele-specific methylation. It further suggests that methylation patterns are heritable or that specific sequence motifs are targets for methylation in some genes.
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Affiliation(s)
- Emily J. Remnant
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Alyson Ashe
- />School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006 Australia
| | - Paul E. Young
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Gabriele Buchmann
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Madeleine Beekman
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Michael H. Allsopp
- />Honey Bee Research Section, ARC-Plant Protection Research Institute, Private Bag X5017, Stellenbosch, South Africa
| | - Catherine M. Suter
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Robert A. Drewell
- />Biology Department, Clark University, 950 Main Street, Worcester, MA 01610 USA
| | - Benjamin P. Oldroyd
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
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Lockett GA, Almond EJ, Huggins TJ, Parker JD, Bourke AFG. Gene expression differences in relation to age and social environment in queen and worker bumble bees. Exp Gerontol 2016; 77:52-61. [PMID: 26883339 DOI: 10.1016/j.exger.2016.02.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/24/2016] [Accepted: 02/12/2016] [Indexed: 02/03/2023]
Abstract
Eusocial insects provide special insights into the genetic pathways influencing aging because of their long-lived queens and flexible aging schedules. Using qRT-PCR in the primitively eusocial bumble bee Bombus terrestris (Linnaeus), we investigated expression levels of four candidate genes associated with taxonomically widespread age-related pathways (coenzyme Q biosynthesis protein 7, COQ7; DNA methyltransferase 3, Dnmt3; foraging, for; and vitellogenin, vg). In Experiment 1, we tested how expression changes with queen relative age and productivity. We found a significant age-related increase in COQ7 expression in queen ovary. In brain, all four genes showed higher expression with increasing female (queen plus worker) production, with this relationship strengthening as queen age increased, suggesting a link with the positive association of fecundity and longevity found in eusocial insect queens. In Experiment 2, we tested effects of relative age and social environment (worker removal) in foundress queens and effects of age and reproductive status in workers. In this experiment, workerless queens showed significantly higher for expression in brain, as predicted if downregulation of for is associated with the cessation of foraging by foundress queens following worker emergence. Workers showed a significant age-related increase in Dnmt3 expression in fat body, suggesting a novel association between aging and methylation in B. terrestris. Ovary activation was associated with significantly higher vg expression in fat body and, in younger workers, in brain, consistent with vitellogenin's ancestral role in regulating egg production. Overall, our findings reveal a mixture of novel and conserved features in age-related genetic pathways under primitive eusociality.
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Affiliation(s)
- Gabrielle A Lockett
- School of Biological Sciences, University of Southampton, Life Sciences Building, Highfield Campus, Southampton SO17 1BJ, UK
| | - Edward J Almond
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Timothy J Huggins
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Joel D Parker
- School of Biological Sciences, University of Southampton, Life Sciences Building, Highfield Campus, Southampton SO17 1BJ, UK
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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40
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Abstract
The cellular mechanisms employed by some organisms to produce contrasting morphological and reproductive phenotypes from the same genome remains one of the key unresolved issues in biology. Honeybees (Apis mellifera) use differential feeding and a haplodiploid sex determination system to generate three distinct organismal outcomes from the same genome. Here we investigate the honeybee female and male caste-specific microRNA and transcriptomic molecular signatures during a critical time of larval development. Both previously undetected and novel miRNAs have been discovered, expanding the inventory of these genomic regulators in invertebrates. We show significant differences in the microRNA and transcriptional profiles of diploid females relative to haploid drone males as well as between reproductively distinct females (queens and workers). Queens and drones show gene enrichment in physio-metabolic pathways, whereas workers show enrichment in processes associated with neuronal development, cell signalling and caste biased structural differences. Interestingly, predicted miRNA targets are primarily associated with non-physio-metabolic genes, especially neuronal targets, suggesting a mechanistic disjunction from DNA methylation that regulates physio-metabolic processes. Accordingly, miRNA targets are under-represented in methylated genes. Our data show how a common set of genetic elements are differentially harnessed by an organism, which may provide the remarkable level of developmental flexibility required.
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Wedd L, Maleszka R. DNA Methylation and Gene Regulation in Honeybees: From Genome-Wide Analyses to Obligatory Epialleles. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:193-211. [DOI: 10.1007/978-3-319-43624-1_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Ronai I, Vergoz V, Oldroyd B. The Mechanistic, Genetic, and Evolutionary Basis of Worker Sterility in the Social Hymenoptera. ADVANCES IN THE STUDY OF BEHAVIOR 2016. [DOI: 10.1016/bs.asb.2016.03.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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43
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Keller TE, Han P, Yi SV. Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary. Mol Biol Evol 2015; 33:1019-28. [PMID: 26715626 PMCID: PMC4776710 DOI: 10.1093/molbev/msv345] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expression, its role in invertebrate gene regulation has been little explored. Instead, gene body DNA methylation is associated with expression of invertebrate genes. However, the evolutionary steps leading to the differentiation of invertebrate and vertebrate genomic DNA methylation remain unresolved. Here we analyzed experimentally determined DNA methylation maps of several species across the invertebrate–vertebrate boundary, to elucidate how vertebrate gene methylation has evolved. We show that, in contrast to the prevailing idea, a substantial number of promoters in an invertebrate basal chordate Ciona intestinalis are methylated. Moreover, gene expression data indicate significant, epigenomic context-dependent associations between promoter methylation and expression in C. intestinalis. However, there is no evidence that promoter methylation in invertebrate chordate has been evolutionarily maintained across the invertebrate–vertebrate boundary. Rather, body-methylated invertebrate genes preferentially obtain hypo-methylated promoters among vertebrates. Conversely, promoter methylation is preferentially found in lineage- and tissue-specific vertebrate genes. These results provide important insights into the evolutionary origin of epigenetic regulation of vertebrate gene expression.
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Affiliation(s)
| | | | - Soojin V Yi
- School of Biology, Georgia Institute of Technology
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44
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Wedd L, Kucharski R, Maleszka R. Differentially methylated obligatory epialleles modulate context-dependent LAM gene expression in the honeybee Apis mellifera. Epigenetics 2015; 11:1-10. [PMID: 26507253 DOI: 10.1080/15592294.2015.1107695] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Differential intragenic methylation in social insects has been hailed as a prime mover of environmentally driven organismal plasticity and even as evidence for genomic imprinting. However, very little experimental work has been done to test these ideas and to prove the validity of such claims. Here we analyze in detail differentially methylated obligatory epialleles of a conserved gene encoding lysosomal α-mannosidase (AmLAM) in the honeybee. We combined genotyping of progenies derived from colonies founded by single drone inseminated queens, ultra-deep allele-specific bisulfite DNA sequencing, and gene expression to reveal how sequence variants, DNA methylation, and transcription interrelate. We show that both methylated and non-methylated states of AmLAM follow Mendelian inheritance patterns and are strongly influenced by polymorphic changes in DNA. Increased methylation of a given allele correlates with higher levels of context-dependent AmLAM expression and appears to affect the transcription of an antisense long noncoding RNA. No evidence of allelic imbalance or imprinting involved in this process has been found. Our data suggest that by generating alternate methylation states that affect gene expression, sequence variants provide organisms with a high level of epigenetic flexibility that can be used to select appropriate responses in various contexts. This study represents the first effort to integrate DNA sequence variants, gene expression, and methylation in a social insect to advance our understanding of their relationships in the context of causality.
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Affiliation(s)
| | | | - Ryszard Maleszka
- a Research School of Biology, The Australian National University , Canberra , ACT , Australia
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45
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EGFR gene methylation is not involved in Royalactin controlled phenotypic polymorphism in honey bees. Sci Rep 2015; 5:14070. [PMID: 26358539 PMCID: PMC4566103 DOI: 10.1038/srep14070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/17/2015] [Indexed: 12/16/2022] Open
Abstract
The 2011 highly publicised Nature paper by Kamakura on honeybee phenotypic dimorphism, (also using Drosophila as an experimental surrogate), claims that a single protein in royal jelly, Royalactin, essentially acts as a master “on-off” switch in development via the epidermal growth factor receptor (AmEGFR), to seal the fate of queen or worker. One mechanism proposed in that study as important for the action of Royalactin is differential amegfr methylation in alternate organismal outcomes. According to the author differential methylation of amegfr was experimentally confirmed and shown in a supportive figure. Here we have conducted an extensive analysis of the honeybee egfr locus and show that this gene is never methylated. We discuss several lines of evidence casting serious doubts on the amegfr methylation result in the 2011 paper and consider possible origins of the author’s statement. In a broader context, we discuss the implication of our findings for contrasting context-dependent regulation of EGFR in three insect species, Apis mellifera, D. melanogaster and the carpenter ant, Camponotus floridanus, and argue that more adequate methylation data scrutiny measures are needed to avoid unwarranted conclusions.
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Ernst UR, Van Hiel MB, Depuydt G, Boerjan B, De Loof A, Schoofs L. Epigenetics and locust life phase transitions. ACTA ACUST UNITED AC 2015; 218:88-99. [PMID: 25568455 DOI: 10.1242/jeb.107078] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Insects are one of the most successful classes on Earth, reflected in an enormous species richness and diversity. Arguably, this success is partly due to the high degree to which polyphenism, where one genotype gives rise to more than one phenotype, is exploited by many of its species. In social insects, for instance, larval diet influences the development into distinct castes; and locust polyphenism has tricked researchers for years into believing that the drastically different solitarious and gregarious phases might be different species. Solitarious locusts behave much as common grasshoppers. However, they are notorious for forming vast, devastating swarms upon crowding. These gregarious animals are shorter lived, less fecund and transmit their phase characteristics to their offspring. The behavioural gregarisation occurs within hours, yet the full display of gregarious characters takes several generations, as does the reversal to the solitarious phase. Hormones, neuropeptides and neurotransmitters influence some of the phase traits; however, none of the suggested mechanisms can account for all the observed differences, notably imprinting effects on longevity and fecundity. This is why, more recently, epigenetics has caught the interest of the polyphenism field. Accumulating evidence points towards a role for epigenetic regulation in locust phase polyphenism. This is corroborated in the economically important locust species Locusta migratoria and Schistocerca gregaria. Here, we review the key elements involved in phase transition in locusts and possible epigenetic regulation. We discuss the relative role of DNA methylation, histone modification and small RNA molecules, and suggest future research directions.
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Affiliation(s)
- Ulrich R Ernst
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Matthias B Van Hiel
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Geert Depuydt
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Bart Boerjan
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Arnold De Loof
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics Lab, KU Leuven, Naamsestraat 59, bus 2465, B-3000 Leuven, Belgium
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Isaksson C. Urbanization, oxidative stress and inflammation: a question of evolving, acclimatizing or coping with urban environmental stress. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12477] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Szarc vel Szic K, Declerck K, Vidaković M, Vanden Berghe W. From inflammaging to healthy aging by dietary lifestyle choices: is epigenetics the key to personalized nutrition? Clin Epigenetics 2015; 7:33. [PMID: 25861393 PMCID: PMC4389409 DOI: 10.1186/s13148-015-0068-2] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 03/09/2015] [Indexed: 01/12/2023] Open
Abstract
The progressively older population in developed countries is reflected in an increase in the number of people suffering from age-related chronic inflammatory diseases such as metabolic syndrome, diabetes, heart and lung diseases, cancer, osteoporosis, arthritis, and dementia. The heterogeneity in biological aging, chronological age, and aging-associated disorders in humans have been ascribed to different genetic and environmental factors (i.e., diet, pollution, stress) that are closely linked to socioeconomic factors. The common denominator of these factors is the inflammatory response. Chronic low-grade systemic inflammation during physiological aging and immunosenescence are intertwined in the pathogenesis of premature aging also defined as ‘inflammaging.’ The latter has been associated with frailty, morbidity, and mortality in elderly subjects. However, it is unknown to what extent inflammaging or longevity is controlled by epigenetic events in early life. Today, human diet is believed to have a major influence on both the development and prevention of age-related diseases. Most plant-derived dietary phytochemicals and macro- and micronutrients modulate oxidative stress and inflammatory signaling and regulate metabolic pathways and bioenergetics that can be translated into stable epigenetic patterns of gene expression. Therefore, diet interventions designed for healthy aging have become a hot topic in nutritional epigenomic research. Increasing evidence has revealed that complex interactions between food components and histone modifications, DNA methylation, non-coding RNA expression, and chromatin remodeling factors influence the inflammaging phenotype and as such may protect or predispose an individual to many age-related diseases. Remarkably, humans present a broad range of responses to similar dietary challenges due to both genetic and epigenetic modulations of the expression of target proteins and key genes involved in the metabolism and distribution of the dietary constituents. Here, we will summarize the epigenetic actions of dietary components, including phytochemicals, and macro- and micronutrients as well as metabolites, that can attenuate inflammaging. We will discuss the challenges facing personalized nutrition to translate highly variable interindividual epigenetic diet responses to potential individual health benefits/risks related to aging disease.
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Affiliation(s)
- Katarzyna Szarc vel Szic
- Lab Protein Science, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Ken Declerck
- Lab Protein Science, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Melita Vidaković
- Department of Molecular Biology, Institute for Biological Research, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
| | - Wim Vanden Berghe
- Lab Protein Science, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Galbraith DA, Yang X, Niño EL, Yi S, Grozinger C. Parallel epigenomic and transcriptomic responses to viral infection in honey bees (Apis mellifera). PLoS Pathog 2015; 11:e1004713. [PMID: 25811620 PMCID: PMC4374888 DOI: 10.1371/journal.ppat.1004713] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/28/2015] [Indexed: 01/07/2023] Open
Abstract
Populations of honey bees are declining throughout the world, with US beekeepers losing 30% of their colonies each winter. Though multiple factors are driving these colony losses, it is increasingly clear that viruses play a major role. However, information about the molecular mechanisms mediating antiviral immunity in honey bees is surprisingly limited. Here, we examined the transcriptional and epigenetic (DNA methylation) responses to viral infection in honey bee workers. One-day old worker honey bees were fed solutions containing Israeli Acute Paralysis Virus (IAPV), a virus which causes muscle paralysis and death and has previously been associated with colony loss. Uninfected control and infected, symptomatic bees were collected within 20-24 hours after infection. Worker fat bodies, the primary tissue involved in metabolism, detoxification and immune responses, were collected for analysis. We performed transcriptome- and bisulfite-sequencing of the worker fat bodies to identify genome-wide gene expression and DNA methylation patterns associated with viral infection. There were 753 differentially expressed genes (FDR<0.05) in infected versus control bees, including several genes involved in epigenetic and antiviral pathways. DNA methylation status of 156 genes (FDR<0.1) changed significantly as a result of the infection, including those involved in antiviral responses in humans. There was no significant overlap between the significantly differentially expressed and significantly differentially methylated genes, and indeed, the genomic characteristics of these sets of genes were quite distinct. Our results indicate that honey bees have two distinct molecular pathways, mediated by transcription and methylation, that modulate protein levels and/or function in response to viral infections.
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Affiliation(s)
- David A. Galbraith
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Xingyu Yang
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Elina Lastro Niño
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Soojin Yi
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Christina Grozinger
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
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Chapman NC, Beekman M, Allsopp MH, Rinderer TE, Lim J, Oxley PR, Oldroyd BP. Inheritance of thelytoky in the honey bee Apis mellifera capensis. Heredity (Edinb) 2015; 114:584-92. [PMID: 25585920 DOI: 10.1038/hdy.2014.127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/27/2014] [Accepted: 12/03/2014] [Indexed: 01/31/2023] Open
Abstract
Asexual reproduction via thelytokous parthenogenesis is widespread in the Hymenoptera, but its genetic underpinnings have been described only twice. In the wasp Lysiphlebus fabarum and the Cape honey bee Apis mellifera capensis the origin of thelytoky have each been traced to a single recessive locus. In the Cape honey bee it has been argued that thelytoky (th) controls the thelytoky phenotype and that a deletion of 9 bp in the flanking intron downstream of exon 5 (tae) of the gemini gene switches parthenogenesis from arrhenotoky to thelytoky. To further explore the mode of inheritance of thelytoky, we generated reciprocal backcrosses between thelytokous A. m. capensis and the arrhenotokous A. m. scutellata. Ten genetic markers were used to identify 108 thelytokously produced offspring and 225 arrhenotokously produced offspring from 14 colonies. Patterns of appearance of thelytokous parthenogenesis were inconsistent with a single locus, either th or tae, controlling thelytoky. We further show that the 9 bp deletion is present in the arrhenotokous A. m. scutellata population in South Africa, in A. m. intermissa in Morocco and in Africanized bees from Brazil and Texas, USA, where thelytoky has not been reported. Thus the 9 p deletion cannot be the cause of thelytoky. Further, we found two novel tae alleles. One contains the previously described 9 bp deletion and an additional deletion of 7 bp nearby. The second carries a single base insertion with respect to the wild type. Our data are consistent with the putative th locus increasing reproductive capacity.
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Affiliation(s)
- N C Chapman
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - M Beekman
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - M H Allsopp
- ARC-Plant Protection Research Institute, Stellenbosch, South Africa
| | - T E Rinderer
- Honey Bee Breeding, Genetics and Physiology Research Laboratory, USDA-ARS, Baton Rouge, LA, USA
| | - J Lim
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - P R Oxley
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - B P Oldroyd
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
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