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Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martín-Zamora FM, Hurd PJ, de Mendoza A, Martín-Durán JM. Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria. Genome Biol 2024; 25:204. [PMID: 39090757 PMCID: PMC11292947 DOI: 10.1186/s13059-024-03346-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as "mosaic". Yet, the role and developmental dynamics of 5mC and how these explain interspecies differences in DNA methylation patterns remain poorly understood, especially in Spiralia, a large clade of invertebrates comprising nearly half of the animal phyla. RESULTS Here, we generate base-resolution methylomes for three species with distinct genomic features and phylogenetic positions in Annelida, a major spiralian phylum. All possible 5mC patterns occur in annelids, from typical invertebrate intermediate levels in a mosaic distribution to hypermethylation and methylation loss. GbM is common to annelids with 5mC, and methylation differences across species are explained by taxon-specific transcriptional dynamics or the presence of intronic TEs. Notably, the link between GbM and transcription decays during development, alongside a gradual and global, age-dependent demethylation in adult stages. Additionally, reducing 5mC levels with cytidine analogs during early development impairs normal embryogenesis and reactivates TEs in the annelid Owenia fusiformis. CONCLUSIONS Our study indicates that global epigenetic erosion during development and aging is an ancestral feature of bilateral animals. However, the tight link between transcription and gene body methylation is likely more important in early embryonic stages, and 5mC-mediated TE silencing probably emerged convergently across animal lineages.
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Affiliation(s)
- Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, 1030, Austria
| | - Luke A Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Lan Xu
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Altos Labs, Cambridge, UK
| | - Paul J Hurd
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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Zhang Z, Liu G, Zhou Z, Su Z, Gu X. Global level of methylation in the sea lamprey (jawless vertebrate) genome is intermediate between invertebrate and jawed vertebrate genomes. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:391-397. [PMID: 38497317 DOI: 10.1002/jez.b.23250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
In eukaryotes, cytosine methylation is a primary heritable epigenetic modification of the genome that regulates many cellular processes. In invertebrate, methylated cytosine generally located on specific genomic elements (e.g., gene bodies and silenced repetitive elements) to show a "mosaic" pattern. While in jawed vertebrate (teleost and tetrapod), highly methylated cytosine located genome-wide but only absence at regulatory regions (e.g., promoter and enhancer). Many studies imply that the evolution of DNA methylation reprogramming may have helped the transition from invertebrates to jawed vertebrates, but the detail remains largely elusive. In this study, we used the whole-genome bisulfite-sequencing technology to investigate the genome-wide methylation in three tissues (heart, muscle, and sperm) from the sea lamprey, an extant agnathan (jawless) vertebrate. Strikingly, we found that the methylation level of the sea lamprey is very similar to that in sea urchin (a deuterostome) and sea squirt (a chordate) invertebrates. In sum, the global pattern in sea lamprey is intermediate methylation level (around 30%), that is higher than methylation level in the genomes of pre-bilaterians and protostomes (1%-10%), but lower than methylation level appeared in jawed vertebrates (around 70%, teleost and tetrapod). We anticipate that, in addition to genetic dynamics such as genome duplications, epigenetic dynamics such as global methylation reprograming was also orchestrated toward the emergence and evolution of vertebrates.
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Affiliation(s)
- Zhao Zhang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Gangbiao Liu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhixi Su
- Singlera Genomics Ltd., Shanghai, China
| | - Xun Gu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
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Banousse G, Normandeau E, Semeniuk C, Bernatchez L, Audet C. Parental thermal environment controls the offspring phenotype in Brook charr (Salvelinus fontinalis): insights from a transcriptomic study. G3 (BETHESDA, MD.) 2024; 14:jkae051. [PMID: 38478598 PMCID: PMC11075542 DOI: 10.1093/g3journal/jkae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/01/2024] [Indexed: 05/08/2024]
Abstract
Brook charr is a cold-water species which is highly sensitive to increased water temperatures, such as those associated with climate change. Environmental variation can potentially induce phenotypic changes that are inherited across generations, for instance, via epigenetic mechanisms. Here, we tested whether parental thermal regimes (intergenerational plasticity) and offspring-rearing temperatures (within-generational plasticity) modify the brain transcriptome of Brook charr progeny (fry stage). Parents were exposed to either cold or warm temperatures during final gonad maturation and their progeny were reared at 5 or 8 °C during the first stages of development. Illumina Novaseq6000 was used to sequence the brain transcriptome at the yolk sac resorption stage. The number of differentially expressed genes was very low when comparing fry reared at different temperatures (79 differentially expressed genes). In contrast, 9,050 differentially expressed genes were significantly differentially expressed between fry issued from parents exposed to either cold or warm temperatures. There was a significant downregulation of processes related to neural and synaptic activity in fry originating from the warm parental group vs fry from the cold parental one. We also observed significant upregulation of DNA methylation genes and of the most salient processes associated with compensation to warming, such as metabolism, cellular response to stress, and adaptive immunity.
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Affiliation(s)
- Ghizlane Banousse
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, QC, Canada G5L 2Z9
| | - Eric Normandeau
- Plateforme de bio-informatique de l’IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada G1V 0A6
| | - Christina Semeniuk
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, Windsor, Ont, Canada N9C 1A2
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, QC, Canada G5L 2Z9
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4
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Skvortsova K, Bertrand S, Voronov D, Duckett PE, Ross SE, Magri MS, Maeso I, Weatheritt RJ, Gómez Skarmeta JL, Arnone MI, Escriva H, Bogdanovic O. Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins. SCIENCE ADVANCES 2022; 8:eabn2258. [PMID: 36459547 PMCID: PMC10936051 DOI: 10.1126/sciadv.abn2258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
DNA methylation [5-methylcytosine (5mC)] is a repressive gene-regulatory mark required for vertebrate embryogenesis. Genomic 5mC is tightly regulated through the action of DNA methyltransferases, which deposit 5mC, and ten-eleven translocation (TET) enzymes, which participate in its active removal through the formation of 5-hydroxymethylcytosine (5hmC). TET enzymes are essential for mammalian gastrulation and activation of vertebrate developmental enhancers; however, to date, a clear picture of 5hmC function, abundance, and genomic distribution in nonvertebrate lineages is lacking. By using base-resolution 5mC and 5hmC quantification during sea urchin and lancelet embryogenesis, we shed light on the roles of nonvertebrate 5hmC and TET enzymes. We find that these invertebrate deuterostomes use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes and show that the complement of identified 5hmC-regulated genes is conserved to vertebrates. This work demonstrates that active 5mC removal from regulatory regions is a common feature of deuterostome embryogenesis suggestive of an unexpected deep conservation of a major gene-regulatory module.
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Affiliation(s)
- Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Danila Voronov
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Paul E. Duckett
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
| | - Samuel E. Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 22, Australia
| | - Marta Silvia Magri
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Robert J. Weatheritt
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
- EMBL Australia, Garvan Institute of Medical Research, Sydney, Australia
| | - Jose Luis Gómez Skarmeta
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 22, Australia
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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Vogt G. Paradigm shifts in animal epigenetics: Research on non-model species leads to new insights into dependencies, functions and inheritance of DNA methylation. Bioessays 2022; 44:e2200040. [PMID: 35618444 DOI: 10.1002/bies.202200040] [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: 02/16/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022]
Abstract
Recent investigations with non-model species and whole-genome approaches have challenged several paradigms in animal epigenetics. They revealed that epigenetic variation in populations is not the mere consequence of genetic variation, but is a semi-independent or independent source of phenotypic variation, depending on mode of reproduction. DNA methylation is not positively correlated with genome size and phylogenetic position as earlier believed, but has evolved differently between and within higher taxa. Epigenetic marks are usually not completely erased in the zygote and germ cells as generalized from mouse, but often persist and can be transgenerationally inherited, making them evolutionarily relevant. Gene body methylation and promoter methylation are similar in vertebrates and invertebrates with well methylated genomes but transposon silencing through methylation is variable. The new data also suggest that animals use epigenetic mechanisms to cope with rapid environmental changes and to adapt to new environments. The main benefiters are asexual populations, invaders, sessile taxa and long-lived species.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
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6
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L M, C H, V V, J L, M M, E Q, T C, M DN, F M. A plant-based diet differentially affects the global hepatic methylome in rainbow trout depending on genetic background. Epigenetics 2022; 17:1726-1737. [PMID: 35345978 PMCID: PMC9621033 DOI: 10.1080/15592294.2022.2058226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Replacing fish meal and oil in trout diets with plant-derived ingredients is a contemporary challenge to move towards more sustainable aquaculture practices. However, such dietary replacement causes hepatic metabolic changes that have not yet been elucidated. Here, we aimed to decipher the effect of a 100% plant-based diet on the hepatic global DNA methylation landscape in trout and assess whether changes depend on fish genetic background. We analysed the global methylome and the expression of DNA (de)methylation-related genes of three isogenic lines that exhibit similar growth when fed a marine resource-based diet (M diet), but differ in their responses to a plant-based diet (V diet). Our results revealed that the V diet induced a decrease in 5-cytosine combined with an increase in 5-hydroxymethylcytosine in two of the three analysed lines. For one of these 2 affected lines, when fed the M diet but at the same feed intake of the V diet (MR), no methylome differences were highlighted between M and MR or between MR and V-fed trout whereas for the other affected line, M fed trout displayed a divergent methylome profile from MR and V fed fish. DNA (de)methylation-related genes were also affected by the V or MR diets. Our findings showed that the global hepatic methylome of trout is affected by a V diet, depending on genetic background. This latter effect seems to be due to either a decreased feed intake alone or combined with the effect of the dietary composition per se.
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Affiliation(s)
- Marandel L
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Heraud C
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Véron V
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Laithier J
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Marchand M
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Quillet E
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Callet T
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Dupont-Nivet M
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Médale F
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
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7
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Liu J, Heraud C, Véron V, Laithier J, Burel C, Prézelin A, Panserat S, Marandel L. Hepatic Global DNA Hypomethylation Phenotype in Rainbow Trout Fed Diets Varying in Carbohydrate to Protein Ratio. J Nutr 2022; 152:29-39. [PMID: 34550380 DOI: 10.1093/jn/nxab343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/30/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A high carbohydrate-low protein diet can induce hepatic global DNA hypomethylation in trout. The mechanisms remain unclear. OBJECTIVES We aimed to investigate whether an increase in dietary carbohydrates (dHCs) or a decrease in dietary proteins (dLPs) can cause hepatic global DNA hypomethylation, as well as explore the underlying mechanisms in trout. METHODS Two feeding trials were conducted on juvenile males, both of which involved a 4-d fasting and 4-d refeeding protocol. In trial 1, trout were fed either a high protein-no carbohydrate [HP-NC, protein 60% dry matter (DM), carbohydrates 0% DM] or a moderate protein-high carbohydrate (MP-HC, protein 40% DM, carbohydrates 30% DM) diet. In trial 2, fish were fed either a moderate protein-no carbohydrate (MP-NC, protein 40% DM, carbohydrates 0% DM), an MP-HC (protein 40% DM, carbohydrates 30% DM), or a low protein-no carbohydrate (LP-NC, protein 20% DM, carbohydrates 0% DM) diet to separate the effects of dHCs and dLPs on the hepatic methylome. Global CmCGG methylation, DNA demethylation derivative concentrations, and mRNA expression of DNA (de)methylation-related genes were measured. Differences were tested by 1-factor ANOVA when data were normally distributed or by Kruskal-Wallis nonparametric test if not. RESULTS In both trials, global CmCGG methylation concentrations remained unaffected, but the hepatic 5-mdC content decreased after refeeding (1-3%). The MP-HC group had 3.4-fold higher hepatic 5-hmdC and a similar 5-mdC concentration compared with the HP-NC group in trial 1. Both MP-HC and LP-NC diets lowered the hepatic 5-mdC content (1-2%), but only the LP-NC group had a significantly lower 5-hmdC concentration (P < 0.01) compared with MP-NC group in trial 2. CONCLUSIONS dHC and dLP independently induced hepatic global DNA demethylation in trout. The alterations in other methylation derivative concentrations indicated the demethylation process was achieved through an active demethylation pathway and probably occurred at non-CmCGG sites.
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Affiliation(s)
- Jingwei Liu
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Cécile Heraud
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Vincent Véron
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Jésabel Laithier
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Christine Burel
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Audrey Prézelin
- Université Paris Saclay, UVSQ, INRAE, BREED, Jouy en Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Stéphane Panserat
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Lucie Marandel
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
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8
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Wellband K, Roth D, Linnansaari T, Curry RA, Bernatchez L. Environment-driven reprogramming of gamete DNA methylation occurs during maturation and is transmitted intergenerationally in Atlantic Salmon. G3 (BETHESDA, MD.) 2021; 11:jkab353. [PMID: 34849830 PMCID: PMC8664423 DOI: 10.1093/g3journal/jkab353] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 02/06/2023]
Abstract
An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally induced intergenerational effects, but solely in the context of early life environmental differences. Using whole-genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Some genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.
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Affiliation(s)
- Kyle Wellband
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - David Roth
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Tommi Linnansaari
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - R Allen Curry
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
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Effects of Cadmium Sulfate on the Brown Garden Snail Cornu aspersum: Implications for DNA Methylation. TOXICS 2021; 9:toxics9110306. [PMID: 34822697 PMCID: PMC8619149 DOI: 10.3390/toxics9110306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
An extensive literature exists regarding the cellular, physiological, and genetic effects of cadmium (Cd)—A highly toxic, but commonly used trace metal in modern industry. However, limited data are available on its epigenetic effects, especially for terrestrial sentinel invertebrates. We determined Cd retention, total DNA methylation, and the methylation status of 5′ end of the Cd-MT gene in the hepatopancreas of the brown garden snail, Cornu aspersum, fed Cd sulfate for four weeks. Bodyweight changes and survival were also measured. Hepatopancreas cadmium increased in a dose-dependent manner from the third-lowest dose onward, with very large amounts being found for the highest treatment group. However, no mortalities occurred, irrespective of dietary Cd dose. We identified significant genome-wide hypermethylation in specimens given the highest dose, which overlapped with a significant bodyweight decrease. The Cd-MT gene showed an unmethylated 5′ end of the Cd-MT gene and this status was not affected by cadmium exposure. Hepatopancreas DNA methylation is as sensitive as bodyweight to non-lethal concentrations of dietary Cd given as cadmium sulfate but less responsive than tissue accumulation. Such an exposure event, by contrast, does not affect the methylation status of the Cd-MT gene 5′ end.
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10
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Wang F, Qin Z, Li Z, Yang S, Gao T, Sun L, Wang D. Dnmt3aa but Not Dnmt3ab Is Required for Maintenance of Gametogenesis in Nile Tilapia ( Oreochromis niloticus). Int J Mol Sci 2021; 22:ijms221810170. [PMID: 34576333 PMCID: PMC8469005 DOI: 10.3390/ijms221810170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
Dnmt3a, a de novo methyltransferase, is essential for mammalian germ line DNA methylation. Only one Dnmt3a is identified in mammals, and homozygous mutants of Dnmt3a are lethal, while two Dnmt3a paralogs, dnmt3aa and dnmt3ab, are identified in teleosts due to the third round of genome duplication, and homozygous mutants of dnmt3aa and dnmt3ab are viable in zebrafish. The expression patterns and roles of dnmt3aa and dnmt3ab in gonadal development remain poorly understood in teleosts. In this study, we elucidated the precise expression patterns of dnmt3aa and dnmt3ab in tilapia gonads. Dnmt3aa was highly expressed in oogonia, phase I and II oocytes and granulosa cells in ovaries and spermatogonia and spermatocytes in testes, while dnmt3ab was mainly expressed in ovarian granulosa cells and testicular spermatocytes. The mutation of dnmt3aa and dnmt3ab was achieved by CRISPR/Cas9 in tilapia. Lower gonadosomatic index (GSI), increased apoptosis of oocytes and spermatocytes and significantly reduced sperm quality were observed in dnmt3aa−/− mutants, while normal gonadal development was observed in dnmt3ab−/− mutants. Consistently, the expression of apoptotic genes was significantly increased in dnmt3aa−/− mutants. In addition, the 5-methylcytosine (5-mC) level in dnmt3aa−/− gonads was decreased significantly, compared with that of dnmt3ab−/− and wild type (WT) gonads. Taken together, our results suggest that dnmt3aa, not dnmt3ab, plays important roles in maintaining gametogenesis in teleosts.
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Affiliation(s)
| | | | | | | | | | - Lina Sun
- Correspondence: (L.S.); (D.W.); Tel.: +86-23-6825-3702 (D.W.)
| | - Deshou Wang
- Correspondence: (L.S.); (D.W.); Tel.: +86-23-6825-3702 (D.W.)
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11
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Planques A, Kerner P, Ferry L, Grunau C, Gazave E, Vervoort M. DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii. BMC Biol 2021; 19:148. [PMID: 34340707 PMCID: PMC8330077 DOI: 10.1186/s12915-021-01074-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/16/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Methylation of cytosines in DNA (5mC methylation) is a major epigenetic modification that modulates gene expression and constitutes the basis for mechanisms regulating multiple aspects of embryonic development and cell reprogramming in vertebrates. In mammals, 5mC methylation of promoter regions is linked to transcriptional repression. Transcription regulation by 5mC methylation notably involves the nucleosome remodeling and deacetylase complex (NuRD complex) which bridges DNA methylation and histone modifications. However, less is known about regulatory mechanisms involving 5mC methylation and their function in non-vertebrate animals. In this paper, we study 5mC methylation in the marine annelid worm Platynereis dumerilii, an emerging evolutionary and developmental biology model capable of regenerating the posterior part of its body post-amputation. RESULTS Using in silico and experimental approaches, we show that P. dumerilii displays a high level of DNA methylation comparable to that of mammalian somatic cells. 5mC methylation in P. dumerilii is dynamic along the life cycle of the animal and markedly decreases at the transition between larval to post-larval stages. We identify a full repertoire of mainly single-copy genes encoding the machinery associated with 5mC methylation or members of the NuRD complex in P. dumerilii and show that this repertoire is close to the one inferred for the last common ancestor of bilaterians. These genes are dynamically expressed during P. dumerilii development and regeneration. Treatment with the DNA hypomethylating agent Decitabine impairs P. dumerilii larval development and regeneration and has long-term effects on post-regenerative growth. CONCLUSIONS Our data reveal high levels of 5mC methylation in the annelid P. dumerilii, highlighting that this feature is not specific to vertebrates in the bilaterian clade. Analysis of DNA methylation levels and machinery gene expression during development and regeneration, as well as the use of a chemical inhibitor of DNA methylation, suggest an involvement of 5mC methylation in P. dumerilii development and regeneration. We also present data indicating that P. dumerilii constitutes a promising model to study biological roles and mechanisms of DNA methylation in non-vertebrate bilaterians and to provide new knowledge about evolution of the functions of this key epigenetic modification in bilaterian animals.
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Affiliation(s)
- Anabelle Planques
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Pierre Kerner
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Laure Ferry
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75006, Paris, France
| | - Christoph Grunau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, F-66860, Perpignan, France
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
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12
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Callet T, Li H, Coste P, Glise S, Heraud C, Maunas P, Mercier Y, Turonnet N, Zunzunegui C, Panserat S, Bolliet V, Marandel L. Modulation of Energy Metabolism and Epigenetic Landscape in Rainbow Trout Fry by a Parental Low Protein/High Carbohydrate Diet. BIOLOGY 2021; 10:biology10070585. [PMID: 34202225 PMCID: PMC8301017 DOI: 10.3390/biology10070585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/17/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary While the effects of parental diets on their progeny have been highly described in mammals, such studies are lacking in fish. To explore such a question in a high trophic level teleost fish, two-year old male and female rainbow trout were fed either a control diet (0% carbohydrate and 63.89% protein) or a high-carbohydrate diet (35% carbohydrate and 42.96% protein), for a complete reproductive cycle for females and for a period of 5 months for males. Neither the maternal nor the paternal high-carbohydrate diet alone had induced significant effects on their progeny. Nevertheless, when both parents were fed the high-carbohydrate diet, the energy metabolism and mitochondrial dynamics of their progeny were altered. Moreover, the epigenetic landscape was also highly affected. Even though, offspring growth was only slightly affected at the early stage of life; the effect of parental high-carbohydrate diet should be explored over the long term. Abstract It is now recognized that parental diets could highly affect offspring metabolism and growth. Studies in fish are, however, lacking. In particular, the effect of a parental diet high in carbohydrate (HC) and low in protein (LP) on progeny has never been examined in higher trophic level teleost fish. Thus, two-year old male and female rainbow trout (Oncorhynchus mykiss) were fed either a control diet (0% carbohydrate and 63.89% protein) or a diet containing 35% carbohydrate and 42.96% protein (HC/LP) for a complete reproductive cycle for females and over a 5-month period for males. Cross-fertilizations were then carried out. To evaluate the effect of the parental diet on their offspring, different phenotypic and metabolic traits were recorded for offspring before their first feeding and again three weeks later. When considering the paternal and maternal HC/LP nutrition independently, fry phenotypes and transcriptomes were only slightly affected. The combination of the maternal and paternal HC/LP diets altered the energy metabolism and mitochondrial dynamics of their progeny, demonstrating the existence of a synergistic effect. The global DNA methylation of whole fry was also highly affected by the HC/LP parental diet, indicating that it could be one of the fundamental mechanisms responsible for the effects of nutritional programming.
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Affiliation(s)
- Thérèse Callet
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Hongyan Li
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Pascale Coste
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, ECOBIOP, 64310 Saint-Pée-sur-Nivelle, France; (P.C.); (S.G.); (V.B.)
| | - Stéphane Glise
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, ECOBIOP, 64310 Saint-Pée-sur-Nivelle, France; (P.C.); (S.G.); (V.B.)
| | - Cécile Heraud
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Patrick Maunas
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Yvan Mercier
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Nicolas Turonnet
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Chloé Zunzunegui
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Stéphane Panserat
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Valérie Bolliet
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, ECOBIOP, 64310 Saint-Pée-sur-Nivelle, France; (P.C.); (S.G.); (V.B.)
| | - Lucie Marandel
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
- Correspondence:
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13
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Kyger R, Luzuriaga-Neira A, Layman T, Milkewitz Sandberg TO, Singh D, Huchon D, Peri S, Atkinson SD, Bartholomew JL, Yi SV, Alvarez-Ponce D. Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation. Mol Biol Evol 2021; 38:393-404. [PMID: 32898240 PMCID: PMC7826176 DOI: 10.1093/molbev/msaa214] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.
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Affiliation(s)
- Ryan Kyger
- Department of Biology, University of Nevada, Reno, NV
| | | | - Thomas Layman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | | | - Devika Singh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Dorothée Huchon
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel.,The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Sateesh Peri
- Department of Biology, University of Nevada, Reno, NV
| | | | | | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
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14
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The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol 2021; 5:369-378. [PMID: 33462491 PMCID: PMC7116863 DOI: 10.1038/s41559-020-01371-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
Mammalian brains feature exceptionally high levels of non-CpG DNA methylation alongside the canonical form of CpG methylation. Non-CpG methylation plays a critical regulatory role in cognitive function, which is mediated by the binding of MeCP2, the transcriptional regulator that when mutated causes Rett syndrome. However, it is unclear whether the non-CpG neural methylation system is restricted to mammalian species with complex cognitive abilities or has deeper evolutionary origins. To test this, we investigated brain DNA methylation across 12 distantly related animal lineages, revealing that non-CpG methylation is restricted to vertebrates. We discovered that in vertebrates, non-CpG methylation is enriched within a highly conserved set of developmental genes transcriptionally repressed in adult brains, indicating that it demarcates a deeply conserved regulatory program. We also found that the writer of non-CpG methylation, DNMT3A, and the reader, MeCP2, originated at the onset of vertebrates as a result of the ancestral vertebrate whole-genome duplication. Together, we demonstrate how this novel layer of epigenetic information assembled at the root of vertebrates and gained new regulatory roles independent of the ancestral form of the canonical CpG methylation. This suggests that the emergence of non-CpG methylation may have fostered the evolution of sophisticated cognitive abilities found in the vertebrate lineage.
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15
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Mallona I, Ilie IM, Karemaker ID, Butz S, Manzo M, Caflisch A, Baubec T. Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Res 2021; 49:145-157. [PMID: 33290556 PMCID: PMC7797059 DOI: 10.1093/nar/gkaa1168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/22/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences result from structural differences in the catalytic domains of the two de novo DNMTs and are not a consequence of differential recruitment to the genome. Molecular dynamics simulations suggest that, in case of human DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. By exchanging arginine to a lysine, the corresponding side chain in DNMT3B, the sequence preference is reversed, confirming the requirement for arginine at this position. This context-dependent enzymatic activity provides additional insights into the complex regulation of DNA methylation patterns.
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Affiliation(s)
- Izaskun Mallona
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich 8057, Switzerland
| | - Ioana Mariuca Ilie
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Ino Dominiek Karemaker
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
| | - Stefan Butz
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
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16
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Merlo MA, Portela-Bens S, Rodríguez ME, García-Angulo A, Cross I, Arias-Pérez A, García E, Rebordinos L. A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858). Genes (Basel) 2020; 12:genes12010049. [PMID: 33396249 PMCID: PMC7824234 DOI: 10.3390/genes12010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species’ chromosome dynamics and evolution.
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17
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Ross SE, Angeloni A, Geng FS, de Mendoza A, Bogdanovic O. Developmental remodelling of non-CG methylation at satellite DNA repeats. Nucleic Acids Res 2020; 48:12675-12688. [PMID: 33271598 PMCID: PMC7736785 DOI: 10.1093/nar/gkaa1135] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, remodelled during mid-blastula transition, and re-established during gastrulation in all embryonic layers. Moreover, we identify DNA methyltransferase 3ba (Dnmt3ba) as the primary enzyme responsible for the deposition of this mCH mark. Finally, we observe that TGCT-methylated repeats are specifically associated with H3K9me3-marked heterochromatin suggestive of a functional interplay between these two gene-regulatory marks. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases.
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Affiliation(s)
- Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Allegra Angeloni
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Fan-Suo Geng
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Alex de Mendoza
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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18
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Fu R, Huang X, Zhan A. Identification of DNA (de)methylation-related genes and their transcriptional response to environmental challenges in an invasive model ascidian. Gene 2020; 768:145331. [PMID: 33278554 DOI: 10.1016/j.gene.2020.145331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 10/26/2020] [Accepted: 11/27/2020] [Indexed: 01/07/2023]
Abstract
Marine invasive species are constantly challenged by acute or recurring environmental stresses during their range expansions. DNA methylation-mediated stress memory has been proposed to effectively affect species' response and enhance their overall performance in recurring environmental challenges. In order to further test this proposal in marine invasive species, we identified genes in the DNA methylation and demethylation processes in the highly invasive model species, Ciona robusta, and subsequently investigated the expression patterns of these genes under recurring salinity stresses. After a genome-wide comprehensive survey, we found a total of six genes, including two genes of DNA methyltransferase 3a (DNMT3a1 and DNMT3a2), and one gene of DNA methyltransferase 1 (DNMT1), methyl-CpG-binding domain protein 2 (MBD2), methyl-CpG-binding domain protein 4 (MBD4) and ten-eleven-translocation protein 1 (TET1). Phylogenetic reconstruction and domain arrangement analyses showed that the deduced proteins of the identified genes were evolutionarily conserved and functionally similar with their orthologs. All genes were constitutively expressed in all four tested tissues. Interestingly, we found time-dependent and stress-specific gene expression patterns under high and low salinity stresses. Under the recurring high salinity stresses, DNMT3a1 and TET1 conformed to the definition of memory genes, while under the recurring low salinity stresses, two DNMT3a paralogues were identified as the memory genes. Altogether, our results clearly showed that the transcriptional patterns of (de)methylation-related genes were significantly influenced by environmental stresses, and the transcriptional memory of some (de)methylation-related genes should play crucial roles in DNA methylation-mediated stress memory during the process of biological invasions.
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Affiliation(s)
- Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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19
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Lallias D, Bernard M, Ciobotaru C, Dechamp N, Labbé L, Goardon L, Le Calvez JM, Bideau M, Fricot A, Prézelin A, Charles M, Moroldo M, Cousin X, Bouchez O, Roulet A, Quillet E, Dupont-Nivet M. Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background. Epigenetics 2020; 16:1031-1052. [PMID: 33126823 DOI: 10.1080/15592294.2020.1834924] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Phenotypic plasticity is a key component of the ability of organisms to respond to changing environmental conditions. In this study, we aimed to study the establishment of DNA methylation marks in response to an environmental stress in rainbow trout and to assess whether these marks depend on the genetic background. The environmental stress chosen here was temperature, a known induction factor of epigenetic marks in fish. To disentangle the role of epigenetic mechanisms such as DNA methylation in generating phenotypic variations, nine rainbow trout isogenic lines with no genetic variability within a line were used. For each line, half of the eggs were incubated at standard temperature (11°C) and the other half at high temperature (16°C), from eyed-stage to hatching. In order to gain a first insight into the establishment of DNA methylation marks in response to an early temperature regime (control 11°C vs. heated 16°C), we have studied the expression of 8 dnmt3 (DNA methyltransferase) genes, potentially involved in de novo methylation, and analysed global DNA methylation in the different rainbow trout isogenic lines using LUMA (LUminometric Methylation Assay). Finally, finer investigation of genome-wide methylation patterns was performed using EpiRADseq, a reduced-representation library approach based on the ddRADseq (Double Digest Restriction Associated DNA) protocol, for six rainbow trout isogenic lines. We have demonstrated that thermal history during embryonic development alters patterns of DNA methylation, but to a greater or lesser extent depending on the genetic background.
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Affiliation(s)
- Delphine Lallias
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Maria Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Céline Ciobotaru
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | | | | | | | - Alexandre Fricot
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Mathieu Charles
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Marco Moroldo
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Xavier Cousin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Alain Roulet
- INRAE, GeT PlaGe, 31326, Castanet-Tolosan, France
| | - Edwige Quillet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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20
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Adrian-Kalchhauser I, Sultan SE, Shama LNS, Spence-Jones H, Tiso S, Keller Valsecchi CI, Weissing FJ. Understanding 'Non-genetic' Inheritance: Insights from Molecular-Evolutionary Crosstalk. Trends Ecol Evol 2020; 35:1078-1089. [PMID: 33036806 DOI: 10.1016/j.tree.2020.08.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022]
Abstract
Understanding the evolutionary and ecological roles of 'non-genetic' inheritance (NGI) is daunting due to the complexity and diversity of epigenetic mechanisms. We draw on insights from molecular and evolutionary biology perspectives to identify three general features of 'non-genetic' inheritance systems: (i) they are functionally interdependent with, rather than separate from, DNA sequence; (ii) precise mechanisms vary phylogenetically and operationally; and (iii) epigenetic elements are probabilistic, interactive regulatory factors and not deterministic 'epialleles' with defined genomic locations and effects. We discuss each of these features and offer recommendations for future empirical and theoretical research that implements a unifying inherited gene regulation (IGR) approach to studies of 'non-genetic' inheritance.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Centre for Fish and Wildlife Health, Department for Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland.
| | - Sonia E Sultan
- Biology Department, Wesleyan University, Middletown, CT 06459, USA
| | - Lisa N S Shama
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, Hafenstrasse 43, 25992 List, Germany
| | - Helen Spence-Jones
- Centre for Biological Diversity, School of Biology, University of St Andrews, St. Andrews, UK
| | - Stefano Tiso
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | | | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
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