1
|
Viña-Feás A, Temes-Rodríguez J, Vidal-Capón A, Novas S, Rodríguez-Castro J, Pequeño-Valtierra A, Pasantes JJ, Tubío JMC, Garcia-Souto D. Unravelling epigenetic mechanisms in Cerastoderma edule genome: a comparison of healthy and neoplastic cockles. Mol Genet Genomics 2024; 299:58. [PMID: 38789628 PMCID: PMC11126487 DOI: 10.1007/s00438-024-02148-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: 12/12/2023] [Accepted: 04/28/2024] [Indexed: 05/26/2024]
Abstract
Cancer is a multifaceted genetic disease characterized by the acquisition of several essential hallmarks. Notably, certain cancers exhibit horizontal transmissibility, observed across mammalian species and diverse bivalves, the latter referred to as hemic neoplasia. Within this complex landscape, epigenetic mechanisms such as histone modifications and cytosine methylation emerge as fundamental contributors to the pathogenesis of these transmissible cancers. Our study delves into the epigenetic landscape of Cerastoderma edule, focusing on whole-genome methylation and hydroxymethylation profiles in heathy specimens and transmissible neoplasias by means of Nanopore long-read sequencing. Our results unveiled a global hypomethylation in the neoplastic specimens compared to their healthy counterparts, emphasizing the role of DNA methylation in these tumorigenic processes. Furthermore, we verified that intragenic CpG methylation positively correlated with gene expression, emphasizing its role in modulating transcription in healthy and neoplastic cockles, as also highlighted by some up-methylated oncogenic genes. Hydroxymethylation levels were significantly more elevated in the neoplastic samples, particularly within satellites and complex repeats, likely related to structural functions. Additionally, our analysis also revealed distinct methylation and activity patterns in retrotransposons, providing additional insights into bivalve neoplastic processes. Altogether, these findings contribute to understanding the epigenetic dynamics of bivalve neoplasias and shed light on the roles of DNA methylation and hydroxymethylation in tumorigenesis. Understanding these epigenetic alterations holds promise for advancing our broader understanding of cancer epigenetics.
Collapse
Affiliation(s)
- Alejandro Viña-Feás
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Javier Temes-Rodríguez
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Samuel Novas
- Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Jorge Rodríguez-Castro
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Ana Pequeño-Valtierra
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | | | - Jose M C Tubío
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel Garcia-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Department of Biological Sciences, School of Environment, Arts and Society, College of Arts, Sciences & Education (CASE), Florida International University, Miami, FL, USA.
| |
Collapse
|
2
|
Dang X, Lim YK, Li Y, Roberts SB, Li L, Thiyagarajan V. Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment. Mol Ecol 2023; 32:412-427. [PMID: 36314404 DOI: 10.1111/mec.16751] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/22/2022]
Abstract
For marine invertebrates with a pelagic-benthic life cycle, larval exposure to ocean acidification (OA) can affect adult performance in response to another environmental stressor. This carry-over effect has the potential to alter phenotypic traits. However, the molecular mechanisms that mediate "OA"-triggered carry-over effects have not been explored despite such information being key to improving species fitness and management strategies for aquafarming. This study integrated the genome-wide DNA methylome and transcriptome to examine epigenetic modification-mediated carry-over OA impacts on phenotypic traits of the ecologically and commercially important oyster species Crassostrea hongkongensis under field conditions. Larvae of C. hongkongensis were exposed to control pH 8.0 and low pH 7.4 conditions, mimicking near future OA scenario in their habitat, before being outplanted as post-metamorphic juveniles at two mariculture field sites with contrasting environmental stressors for 9 months. The larval carry-over OA effect was found to have persistent impacts on the growth and survival trade-off traits on the outplanted juveniles, although the beneficial or adverse effect depended on the environmental conditions at the outplanted sites. Site-specific plasticity was demonstrated with a diverse DNA methylation-associated gene expression profile, with signal transduction and the endocrine system being the most common and highly enriched functions. Highly methylated exons prevailed in the key genes related to general metabolic and endocytic responses and these genes are evolutionarily conserved in various marine invertebrates in response to OA. These results suggest that oysters with prior larval exposure history to OA had the ability to trigger rapid local adaptive responses via epigenetic modification to cope with multiple stressors in the field.
Collapse
Affiliation(s)
- Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.,School of Applied Science, Temasek Polytechnic, Singapore, Singapore
| | - Yang Li
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,The Joint Laboratory for Marine Ecology and Environmental Sciences (JLMEES), Institute of Oceanology, Chinese Acadamy of Sciences, Beijing, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.,The Joint Laboratory for Marine Ecology and Environmental Sciences (JLMEES), The Swire Institute of Marine Sciences, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
3
|
Zhao B, van Bodegom PM, Trimbos KB. Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA. Mol Ecol Resour 2023; 23:81-91. [PMID: 35899418 PMCID: PMC10087510 DOI: 10.1111/1755-0998.13691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments.
Collapse
Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| |
Collapse
|
4
|
Baldanzi S, Saldías GS, Vargas CA, Porri F. Long term environmental variability modulates the epigenetics of maternal traits of kelp crabs in the coast of Chile. Sci Rep 2022; 12:18806. [PMID: 36335115 PMCID: PMC9637151 DOI: 10.1038/s41598-022-23165-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 10/26/2022] [Indexed: 11/08/2022] Open
Abstract
The methylation of DNA is an environmentally inducible epigenetic mechanism reflecting the short-term ecological and environmental background of populations. Marine invertebrate populations, which spread along a latitudinal cline, are particularly suitable for profiling DNA methylation, due to the heterogenous environmental conditions experienced. We used the MSAP (Methylation Sensitive Amplified Polymorphism) technique to investigate the natural variation in DNA methylation of different female's tissues (muscle, gonads, and gills) and early-stage eggs from five populations of the kelp crab Taliepus dentatus, distributed along a latitudinal cline in the coast of Chile. We assessed whether, (1) the distribution of DNA methylation profiles can be associated with the temporal variability of long term (18 years) climatologies (sea surface temperature, turbidity and productivity) and (2) the epigenetic diversity of eggs is related to the population-level phenotypic variability of several maternal investment traits (egg volume, egg weight, egg lipids and fecundity). The DNA methylation of eggs correlated positively and negatively with the long term variability in productivity and sea surface temperature, respectively. Furthermore, the diversity of DNA methylation of eggs correlated positively with the population-level phenotypic variability of several maternal investment traits, suggesting a key role of epigenetic mechanisms in generating phenotypic variability at population level for this species. We provide evidence of a strong link between the temporal variability of long term climatologies with the epigenetic profiles of key early ontogenetic traits associated with the maternal investment of kelp crabs. These modulating mechanisms can hence contribute early to phenotypic variability at population levels in response to local and past environmental fluctuation.
Collapse
Affiliation(s)
- Simone Baldanzi
- Laboratorio de Ecofisiologia y Ecologia evolutiva marinas (eCO2lab), Facultad de Ciencia del Mar y de Recursos Naturales, Universidad de Valparaíso, Av. Borgoño 16344, Viña del Mar, Chile.
- Centro de Observación Marino para Estudios de Riesgos del Ambiente Costero (COSTA-R), Universidad de Valparaíso, Valparaiso, Chile.
- South African Institute for Aquatic Biodiversity (SAIAB), Private Bag 1015, Makhanda, 6139, South Africa.
| | - Gonzalo S Saldías
- Instituto Milenio en Socio-Ecología Costera (SECOS), P. Universidad Católica de Chile, Santiago, Chile
- Departamento de Física, Facultad de Ciencias, Universidad del Bío-Bío, Concepción, Chile
| | - Cristian A Vargas
- Instituto Milenio en Socio-Ecología Costera (SECOS), P. Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Ecosistemas Costeros y Cambio Ambiental Global (ECCALab), Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro de Ciencias Ambientales EULA Chile, Universidad de Concepción, Concepción, Chile
| | - Francesca Porri
- South African Institute for Aquatic Biodiversity (SAIAB), Private Bag 1015, Makhanda, 6139, South Africa
- Department of Zoology and Entomology, Rhodes University, Makhanda, 6139, South Africa
| |
Collapse
|
5
|
Gerdol M, La Vecchia C, Strazzullo M, De Luca P, Gorbi S, Regoli F, Pallavicini A, D’Aniello E. Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.
Collapse
|
6
|
Fargeot L, Loot G, Prunier JG, Rey O, Veyssière C, Blanchet S. Patterns of Epigenetic Diversity in Two Sympatric Fish Species: Genetic vs. Environmental Determinants. Genes (Basel) 2021; 12:107. [PMID: 33467145 PMCID: PMC7830833 DOI: 10.3390/genes12010107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/05/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic components are hypothesized to be sensitive to the environment, which should permit species to adapt to environmental changes. In wild populations, epigenetic variation should therefore be mainly driven by environmental variation. Here, we tested whether epigenetic variation (DNA methylation) observed in wild populations is related to their genetic background, and/or to the local environment. Focusing on two sympatric freshwater fish species (Gobio occitaniae and Phoxinus phoxinus), we tested the relationships between epigenetic differentiation, genetic differentiation (using microsatellite and single nucleotide polymorphism (SNP) markers), and environmental distances between sites. We identify positive relationships between pairwise genetic and epigenetic distances in both species. Moreover, epigenetic marks better discriminated populations than genetic markers, especially in G. occitaniae. In G. occitaniae, both pairwise epigenetic and genetic distances were significantly associated to environmental distances between sites. Nonetheless, when controlling for genetic differentiation, the link between epigenetic differentiation and environmental distances was not significant anymore, indicating a noncausal relationship. Our results suggest that fish epigenetic variation is mainly genetically determined and that the environment weakly contributed to epigenetic variation. We advocate the need to control for the genetic background of populations when inferring causal links between epigenetic variation and environmental heterogeneity in wild populations.
Collapse
Affiliation(s)
- Laura Fargeot
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d’Ecologie Théorique et Expérimentale, UMR 5321, F-09200 Moulis, France;
| | - Géraldine Loot
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse CEDEX 4, France; (G.L.); (C.V.)
- Université Paul Sabatier (UPS), Institut Universitaire de France (IUF), F-75231 Paris CEDEX 05, France
| | - Jérôme G. Prunier
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d’Ecologie Théorique et Expérimentale, UMR 5321, F-09200 Moulis, France;
| | - Olivier Rey
- CNRS, Interaction Hôtes-Parasites-Environnements (IHPE), UMR 5244, F-66860 Perpignan, France;
| | - Charlotte Veyssière
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse CEDEX 4, France; (G.L.); (C.V.)
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d’Ecologie Théorique et Expérimentale, UMR 5321, F-09200 Moulis, France;
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse CEDEX 4, France; (G.L.); (C.V.)
| |
Collapse
|
7
|
Sun H, Zhou Z, Dong Y, Yang A, Jiang J. Insights into the DNA methylation of sea cucumber Apostichopus japonicus in response to skin ulceration syndrome infection. FISH & SHELLFISH IMMUNOLOGY 2020; 104:155-164. [PMID: 32502611 DOI: 10.1016/j.fsi.2020.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/23/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is an important epigenetic modification that regulates gene expression in many biological processes, including immune response. In this study, whole-genome bisulfite sequencing (WGBS) was carried out on healthy body wall (HB) and skin ulceration syndrome (SUS) infected body wall (SFB) to gain insights into the epigenetic regulatory mechanism in sea cucumber Apostichopus japonicus. After comparison, a total of 116,522 differentially methylated regions (DMRs) were obtained including 67,269 hyper-methylated and 49,253 hypo-methylated DMRs (p < 0.05, FDR < 0.001). GO enrichment analysis indicated that regulation of DNA-templated transcription (GO: 0006355), where DNA methylation occurred, was the most significant term in the biology process. The integration of methylome and transcriptome analysis revealed that 10,499 DMRs were negatively correlated with 496 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEGs were enriched in the phosphoinositide 3-kinase-protein kinase B (PI3K/Akt)/mammalian target of rapamycin (mTOR) signaling pathway. Interestingly, two serine/threonine-protein kinases, nemo-like kinase (NLK) and mTOR, were highlighted after functional analysis. The variations of methylation in these two genes were associated with SUS infection and immune regulation. They regulated gene expression at different levels and showed interaction during response process. The validation of methylation sites showed high consistency between pyrosequencing and WGBS. WGBS analysis not only revealed the changes of DNA methylation, but also presented important information about the regulation of key genes after SUS infection in A. japonicus.
Collapse
Affiliation(s)
- Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| |
Collapse
|
8
|
Zhang J, Luo S, Gu Z, Deng Y, Jiao Y. Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:380-390. [PMID: 32140888 DOI: 10.1007/s10126-020-09957-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from Pinctada fucata martensii. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from P. f. martensii via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of P. f. martensii and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.
Collapse
Affiliation(s)
- Jiabin Zhang
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Shaojie Luo
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zefeng Gu
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yuewen Deng
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
- Pearl Breeding and Processing Engineering Technology Research Center of Guangdong Province, Zhanjiang, 524088, China
| | - Yu Jiao
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China.
- Pearl Breeding and Processing Engineering Technology Research Center of Guangdong Province, Zhanjiang, 524088, China.
| |
Collapse
|
9
|
Wang P, Wang J, Su Y, Liu Z, Mao Y. Air Exposure Affects Physiological Responses, Innate Immunity, Apoptosis and DNA Methylation of Kuruma Shrimp, Marsupenaeus japonicus. Front Physiol 2020; 11:223. [PMID: 32226395 PMCID: PMC7081841 DOI: 10.3389/fphys.2020.00223] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
Abstract
Air exposure stress is a common phenomenon for commercial crustacean species in aquaculture and during waterless transportation. However, the antioxidant responses to air exposure discussed in previous studies may be insufficient to present the complexities involved in this process. The comprehensive immune responses, especially considering the immune genes, cell apoptosis, and epigenetic changes, are still unknown. Accordingly, we investigated the multifaceted responses of Marsupenaeus japonicus to air exposure. The results showed that the expression profiles of the apoptosis genes (e.g., IAP, TXNIP, caspase, and caspase-3) and the hypoxia-related genes (e.g., hsp70, hif-1α, and HcY) were all dramatically induced in the hepatopancreas and gills of M. japonicus. Heart rates, T-AOC (total antioxidant capacity) and lactate contents showed time-dependent changes upon air exposure. Air exposure significantly induced apoptosis in hepatopancreas and gills. Compared with the control group, the apoptosis index (AI) of the 12.5 h experimental group increased significantly (p < 0.05) in the hepatopancreas and gills. Most individuals in the experimental group (EG, 12.5 h) had lower methylation ratios than the control group (CG). Air exposure markedly reduced the full-methylation and total-methylation ratios (31.39% for the CG and 26.46% for the EG). This study provided a comprehensive understanding of the antioxidant responses of M. japonicus considering its physiology, innate immunity, apoptosis, and DNA methylation levels, and provided theoretical guidance for waterless transportation.
Collapse
Affiliation(s)
- Panpan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yongquan Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixin Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| |
Collapse
|
10
|
Li Y, Zhang L, Li Y, Li W, Guo Z, Li R, Hu X, Bao Z, Wang S. Dynamics of DNA Methylation and DNMT Expression During Gametogenesis and Early Development of Scallop Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:196-205. [PMID: 30680591 DOI: 10.1007/s10126-018-09871-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
DNA methylation reprograms during gametogenesis and embryo development, which is essential for germ cell specification and genomic imprinting in mammals. Corresponding process remains poorly investigated in molluscs. Here, we examined global DNA methylation level in the gonads of scallop Patinopecten yessoensis during gametogenesis and in embryos/larvae at different stages. DNA methylation level fluctuates during gametogenesis and early development, peaking at proliferative stage of ovary, growing stage of testis, and in blastulae. To understand the mechanisms underlying these changes, we conducted genome-wide characterization of DNMT family and investigated their expression profiles based on transcriptomes and in situ hybridization. Three genes were identified, namely PyDNMT1, PyDNMT2, and PyDNMT3. Expression of PyDnmt3 agrees with DNA methylation level during oogenesis and early development, suggesting PyDNMT3 may participate in de novo DNA methylation that occurs mainly at proliferative stage of ovary and testis, and in blastulae and gastrulae. PyDnmt1 expression is positively correlated with DNA methylation level during spermatogenesis, and is higher at maturation stage of ovary and in 2-8 cell embryos than other stages, implying possible involvement of PyDNMT1 in DNA methylation maintenance during meiosis and embryonic development. This study will facilitate better understanding of the developmental epigenetic reprogramming in bivalve molluscs.
Collapse
Affiliation(s)
- Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Wanru Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Zhenyi Guo
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China.
| |
Collapse
|
11
|
Ardura A, Clusa L, Zaiko A, Garcia-Vazquez E, Miralles L. Stress related epigenetic changes may explain opportunistic success in biological invasions in Antipode mussels. Sci Rep 2018; 8:10793. [PMID: 30018391 PMCID: PMC6050280 DOI: 10.1038/s41598-018-29181-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023] Open
Abstract
Different environmental factors could induce epigenetic changes, which are likely involved in the biological invasion process. Some of these factors are driven by humans as, for example, the pollution and deliberate or accidental introductions and others are due to natural conditions such as salinity. In this study, we have analysed the relationship between different stress factors: time in the new location, pollution and salinity with the methylation changes that could be involved in the invasive species tolerance to new environments. For this purpose, we have analysed two different mussels' species, reciprocally introduced in antipode areas: the Mediterranean blue mussel Mytilus galloprovincialis and the New Zealand pygmy mussel Xenostrobus securis, widely recognized invaders outside their native distribution ranges. The demetylathion was higher in more stressed population, supporting the idea of epigenetic is involved in plasticity process. These results can open a new management protocols, using the epigenetic signals as potential pollution monitoring tool. We could use these epigenetic marks to recognise the invasive status in a population and determine potential biopollutants.
Collapse
Affiliation(s)
- Alba Ardura
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain.
| | - Laura Clusa
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
- Marine Research Institute, Klaipeda University, H. Manto 84, Klaipeda, 92294, Lithuania
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain
| | - Laura Miralles
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain
| |
Collapse
|
12
|
Clark MS, Thorne MAS, King M, Hipperson H, Hoffman JI, Peck LS. Life in the intertidal: Cellular responses, methylation and epigenetics. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13077] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Melody S. Clark
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
| | | | - Michelle King
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
| | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of Sheffield Sheffield UK
| | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of Bielefeld Bielefeld Germany
| | - Lloyd S. Peck
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
| |
Collapse
|
13
|
Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM. cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. Nucleic Acids Res 2017; 45:11559-11569. [PMID: 29036576 PMCID: PMC5714207 DOI: 10.1093/nar/gkx814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/04/2017] [Indexed: 11/14/2022] Open
Abstract
DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets.
Collapse
Affiliation(s)
- Daniel E Martin-Herranz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Thomas M Stubbs
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| |
Collapse
|
14
|
Huang X, Li S, Ni P, Gao Y, Jiang B, Zhou Z, Zhan A. Rapid response to changing environments during biological invasions: DNA methylation perspectives. Mol Ecol 2017; 26:6621-6633. [PMID: 29057612 DOI: 10.1111/mec.14382] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 10/01/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Abstract
Dissecting complex interactions between species and their environments has long been a research hot spot in the fields of ecology and evolutionary biology. The well-recognized Darwinian evolution has well-explained long-term adaptation scenarios; however, "rapid" processes of biological responses to environmental changes remain largely unexplored, particularly molecular mechanisms such as DNA methylation that have recently been proposed to play crucial roles in rapid environmental adaptation. Invasive species, which have capacities to successfully survive rapidly changing environments during biological invasions, provide great opportunities to study molecular mechanisms of rapid environmental adaptation. Here, we used the methylation-sensitive amplified polymorphism (MSAP) technique in an invasive model ascidian, Ciona savignyi, to investigate how species interact with rapidly changing environments at the whole-genome level. We detected quite rapid DNA methylation response: significant changes of DNA methylation frequency and epigenetic differentiation between treatment and control groups occurred only after 1 hr of high-temperature exposure or after 3 hr of low-salinity challenge. In addition, we detected time-dependent hemimethylation changes and increased intragroup epigenetic divergence induced by environmental stresses. Interestingly, we found evidence of DNA methylation resilience, as most stress-induced DNA methylation variation maintained shortly (~48 hr) and quickly returned back to the control levels. Our findings clearly showed that invasive species could rapidly respond to acute environmental changes through DNA methylation modifications, and rapid environmental changes left significant epigenetic signatures at the whole-genome level. All these results provide fundamental background to deeply investigate the contribution of DNA methylation mechanisms to rapid contemporary environmental adaptation.
Collapse
Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
15
|
Farias ND, de Oliveira NFP, da Silva PM. Perkinsus infection is associated with alterations in the level of global DNA methylation of gills and gastrointestinal tract of the oyster Crassostrea gasar. J Invertebr Pathol 2017; 149:76-81. [PMID: 28800971 DOI: 10.1016/j.jip.2017.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
Abstract
Bivalves are filter feeders that obtain food from seawater that may contain infectious agents, such as the protozoan parasites Perkinsus marinus and P. olseni that are associated with massive mortalities responsible for losses in the aquaculture industry. Despite all physical and chemical barriers, microorganisms cross epithelia and infect host tissues to cause pathologies. Epigenetics mechanisms play important roles in a variety of human processes, from embryonic development to cell differentiation and growth. It is currently emerging as crucial mechanism involved in modulation of host-parasite interactions and pathogenesis, promoting discovery of targets for drug treatment. In bivalves, little is known about epigenetic mechanism in host parasite interactions. The objective of the present study was to evaluate the effect of Perkinsus sp. infections on DNA methylation levels in tissues of Crassostrea gasar oysters. Samples were collected in 2015 and 2016 in the Mamanguape River estuary (PB). Oyster gills were removed and used for Perkinsus sp. DIAGNOSIS Gills (G) and gastrointestinal tract (GT), as well as cultured P. marinus trophozoites were preserved in 95% ethanol for DNA extractions. DNA methylation levels were estimated from G and GT tissues of uninfected (n=60) and infected oysters (n=60), and from P. marinus trophozoites, by ELISA assays. Results showed that the mean prevalence of Perkinsus sp. infections was high (87.3%) in 2015 and moderate (59.6%) in 2016. DNA methylation levels of G and GT tissues were significantly lower in infected oyster than in uninfected oysters, suggesting that infections are associated with hypomethylation. Methylation level was significantly higher in G than in GT tissues, indicating a likely tissue-specific mechanism. P. marinus trophozoites showed 33% methylation. This was the first study that confirms alterations of DNA methylation in two tissues of C. gasar oysters in association with Perkinsus sp. infections.
Collapse
Affiliation(s)
- Natanael Dantas Farias
- Laboratório de Imunologia e Patologia de Invertebrados, Departamento de Biologia Molecular, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil.
| | - Naila Francis Paulo de Oliveira
- Laboratório de Genética Molecular Humana, Departamento de Biologia Molecular, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil.
| | - Patricia Mirella da Silva
- Laboratório de Imunologia e Patologia de Invertebrados, Departamento de Biologia Molecular, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil.
| |
Collapse
|
16
|
García-Fernández P, García-Souto D, Almansa E, Morán P, Gestal C. Epigenetic DNA Methylation Mediating Octopus vulgaris Early Development: Effect of Essential Fatty Acids Enriched Diet. Front Physiol 2017; 8:292. [PMID: 28559849 PMCID: PMC5432645 DOI: 10.3389/fphys.2017.00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022] Open
Abstract
The common octopus, Octopus vulgaris, is a good candidate for aquaculture but a sustainable production is still unviable due to an almost total mortality during the paralarvae stage. DNA methylation regulates gene expression in the eukaryotic genome, and has been shown to exhibit plasticity throughout O. vulgaris life cycle, changing profiles from paralarvae to adult stages. This pattern of methylation could be sensitive to small alterations in nutritional and environmental conditions during the species early development, thus impacting on its health, growth and survival. In this sense, a full understanding of the epigenetic mechanisms operating during O. vulgaris development would contribute to optimizing the culture conditions for this species. Paralarvae of O. vulgaris were cultured over 28 days post-hatching (dph) using two different Artemia sp. based diets: control and a long chain polyunsaturated fatty acids (LC-PUFA) enriched diet. The effect of the diets on the paralarvae DNA global methylation was analyzed by Methyl-Sensitive Amplification Polymorphism (MSAP) and global 5-methylcytosine enzyme-linked immunosorbent assay (ELISA) approaches. The analysis of different methylation states over the time revealed a global demethylation phenomena occurring along O. vulgaris early development being directly driven by the age of the paralarvae. A gradual decline in methylated loci (hemimethylated, internal cytosine methylated, and hypermethylated) parallel to a progressive gain in non-methylated (NMT) loci toward the later sampling points was verified regardless of the diet provided and demonstrate a pre-established and well-defined demethylation program during its early development, involving a 20% of the MSAP loci. In addition, a differential behavior between diets was also observed at 20 dph, with a LC-PUFA supplementation effect over the methylation profiles. The present results show significant differences on the paralarvae methylation profiles during its development and a diet effect on these changes. It is characterized by a process of demethylation of the genome at the paralarvae stage and the influence of diet to favor this methylation loss.
Collapse
Affiliation(s)
- Pablo García-Fernández
- Aquatic Molecular Pathobiology Group, Instituto de Investigaciones Marinas (Consejo Superior de Investigaciones Científicas)Vigo, Spain.,Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Danie García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Eduardo Almansa
- Instituto Español de Oceanografía, Centro Oceanográfico de CanariasTenerife, Spain
| | - Paloma Morán
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Camino Gestal
- Aquatic Molecular Pathobiology Group, Instituto de Investigaciones Marinas (Consejo Superior de Investigaciones Científicas)Vigo, Spain
| |
Collapse
|
17
|
Geyer KK, Niazi UH, Duval D, Cosseau C, Tomlinson C, Chalmers IW, Swain MT, Cutress DJ, Bickham-Wright U, Munshi SE, Grunau C, Yoshino TP, Hoffmann KF. The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005246. [PMID: 28510608 PMCID: PMC5433704 DOI: 10.1371/journal.pntd.0005246] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions. Firstly, methyl-CpG binding domain protein (Bgmbd2/3) and DNA methyltransferase 1 (Bgdnmt1) genes are transcriptionally enriched in gonadal compared to somatic tissues with 5-azacytidine (5-AzaC) treatment significantly inhibiting oviposition. Secondly, elevated levels of 5-methyl cytosine (5mC), DNA methyltransferase activity and 5mC binding in pigmented hybrid- compared to inbred (NMRI)- B. glabrata populations indicate a role for the snail's DNA methylation machinery in maintaining hybrid vigour or heterosis. Thirdly, locus-specific detection of 5mC by bisulfite (BS)-PCR revealed 5mC within an exonic region of a housekeeping protein-coding gene (Bg14-3-3), supporting previous in silico predictions and whole genome BS-Seq analysis of this species' genome. Finally, we provide preliminary evidence for parasite-mediated host epigenetic reprogramming in the schistosome/snail system, as demonstrated by the increase in Bgdnmt1 and Bgmbd2/3 transcript abundance following Bge (B. glabrata embryonic cell line) exposure to parasite larval transformation products (LTP). CONCLUSIONS/SIGNIFICANCE The presence of a functional DNA methylation machinery in B. glabrata as well as the modulation of these gene products in response to schistosome products, suggests a vital role for DNA methylation during snail development/oviposition and parasite interactions. Further deciphering the role of this epigenetic process during Biomphalaria/Schistosoma co-evolutionary biology may reveal key factors associated with disease transmission and, moreover, enable the discovery of novel lifecycle intervention strategies.
Collapse
Affiliation(s)
- Kathrin K. Geyer
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Umar H. Niazi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David Duval
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Céline Cosseau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Chad Tomlinson
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Martin T. Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David J. Cutress
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Utibe Bickham-Wright
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Sabrina E. Munshi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Christoph Grunau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Timothy P. Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| |
Collapse
|
18
|
Liu X, Li X, Zhang C, Dai C, Zhou J, Ren C, Zhang J. Phosphoenolpyruvate carboxylase regulation in C4-PEPC-expressing transgenic rice during early responses to drought stress. PHYSIOLOGIA PLANTARUM 2017; 159:178-200. [PMID: 27592839 DOI: 10.1111/ppl.12506] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/14/2016] [Accepted: 08/05/2016] [Indexed: 05/11/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) has important functions in C4 photosynthesis and biosynthesis of intermediate metabolites. In this study, the drought resistance of C4-PEPC-expressing transgenic rice (Oryza sativa, line PC) plants was assessed using simulated drought conditions [i.e. polyethylene glycol (PEG)-6000 treatment]. The dry weight of PC plants was higher than that of wild-type (WT) plants following treatment with 15% PEG-6000 for 16 days. Furthermore, the water use efficiency, relative water content and proline content in PC plants were higher than those of WT plants, as were C4-PEPC activity and transcript levels following treatment with 5% PEG-6000 for 2 h. The protein kinase activities and transcript levels of sucrose non-fermenting-1-related protein kinases (SnRKs) genes, such as SnRK1a, OsK24 and OsK35 were also higher in PC plants than in WT plants following treatment with 5% PEG-6000 for 2 h. Additionally, phosphoenolpyruvate carboxylase kinase (PPCK, EC 4.1.1.32) activities and transcript levels (e.g. PPCK1 and PPCK2) increased following drought treatment. These changes were regulated by signaling molecules, such as calcium, nitric oxide and hydrogen peroxide. Furthermore, the -1095 to -416 region of the C4-PEPC promoter in PC plants was demethylated following exposure to drought conditions for 1 h. The demethylation coincided with an increase in C4-PEPC expression. Our data suggest that the demethylation of the C4-PEPC promoter and the phosphorylation catalyzed by PPCK have key roles in conferring drought tolerance to the transgenic rice plants.
Collapse
Affiliation(s)
- Xiaolong Liu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xia Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Chen Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jiayu Zhou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chenggang Ren
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Jinfei Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| |
Collapse
|
19
|
Baldanzi S, Watson R, McQuaid CD, Gouws G, Porri F. Epigenetic variation among natural populations of the South African sandhopper Talorchestia capensis. Evol Ecol 2016. [DOI: 10.1007/s10682-016-9877-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
20
|
Suarez-Ulloa V, Gonzalez-Romero R, Eirin-Lopez JM. Environmental epigenetics: A promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates. MARINE POLLUTION BULLETIN 2015; 98:5-13. [PMID: 26088539 DOI: 10.1016/j.marpolbul.2015.06.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/04/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
Environmental epigenetics investigates the cause-effect relationships between specific environmental factors and the subsequent epigenetic modifications triggering adaptive responses in the cell. Given the dynamic and potentially reversible nature of the different types of epigenetic marks, environmental epigenetics constitutes a promising venue for developing fast and sensible biomonitoring programs. Indeed, several epigenetic biomarkers have been successfully developed and applied in traditional model organisms (e.g., human and mouse). Nevertheless, the lack of epigenetic knowledge in other ecologically and environmentally relevant organisms has hampered the application of these tools in a broader range of ecosystems, most notably in the marine environment. Fortunately, that scenario is now changing thanks to the growing availability of complete reference genome sequences along with the development of high-throughput DNA sequencing and bioinformatic methods. Altogether, these resources make the epigenetic study of marine organisms (and more specifically marine invertebrates) a reality. By building on this knowledge, the present work provides a timely perspective highlighting the extraordinary potential of environmental epigenetic analyses as a promising source of rapid and sensible tools for pollution biomonitoring, using marine invertebrates as sentinel organisms. This strategy represents an innovative, groundbreaking approach, improving the conservation and management of natural resources in the oceans.
Collapse
Affiliation(s)
- Victoria Suarez-Ulloa
- CHROMEVOL Group, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Rodrigo Gonzalez-Romero
- CHROMEVOL Group, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Jose M Eirin-Lopez
- CHROMEVOL Group, Department of Biological Sciences, Florida International University, Miami, FL, USA.
| |
Collapse
|
21
|
The use of -omic tools in the study of disease processes in marine bivalve mollusks. J Invertebr Pathol 2015; 131:137-54. [PMID: 26021714 DOI: 10.1016/j.jip.2015.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/09/2015] [Accepted: 05/05/2015] [Indexed: 01/01/2023]
Abstract
Our understanding of disease processes and host-pathogen interactions in model species has benefited greatly from the application of medium and high-throughput genomic, metagenomic, epigenomic, transcriptomic, and proteomic analyses. The rate at which new, low-cost, high-throughput -omic technologies are being developed has also led to an expansion in the number of studies aimed at gaining a better understanding of disease processes in bivalves. This review provides a catalogue of the genetic and -omic tools available for bivalve species and examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis. The analysis of bivalve genomes and transcriptomes has revealed that many immune and stress-related gene families are expanded in the bivalve taxa examined thus far. In addition, the analysis of proteomes confirms that responses to infection are influenced by epigenetic, post-transcriptional, and post-translational modifications. The few studies performed in bivalves show that epigenetic modifications are non-random, suggesting a role for epigenetics in regulating the interactions between bivalves and their environments. Despite the progress -omic tools have enabled in the field of marine bivalve disease processes, there is much more work to be done. To date, only three bivalve genomes have been sequenced completely, with assembly status at different levels of completion. Transcriptome datasets are relatively easy and inexpensive to generate, but their interpretation will benefit greatly from high quality genome assemblies and improved data analysis pipelines. Finally, metagenomic, epigenomic, proteomic, and metabolomic studies focused on bivalve disease processes are currently limited but their expansion should be facilitated as more transcriptome datasets and complete genome sequences become available for marine bivalve species.
Collapse
|
22
|
Wang X, Li Q, Lian J, Li L, Jin L, Cai H, Xu F, Qi H, Zhang L, Wu F, Meng J, Que H, Fang X, Guo X, Zhang G. Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation. BMC Genomics 2014; 15:1119. [PMID: 25514978 PMCID: PMC4378273 DOI: 10.1186/1471-2164-15-1119] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 12/09/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Studies of DNA methylomes in a wide range of eukaryotes have revealed both conserved and divergent characteristics of DNA methylation among phylogenetic groups. However, data on invertebrates particularly molluscs are limited, which hinders our understanding of the evolution of DNA methylation in metazoa. The sequencing of the Pacific oyster Crassostrea gigas genome provides an opportunity for genome-wide profiling of DNA methylation in this model mollusc. RESULTS Homologous searches against the C. gigas genome identified functional orthologs for key genes involved in DNA methylation: DNMT1, DNMT2, DNMT3, MBD2/3 and UHRF1. Whole-genome bisulfite sequencing (BS-seq) of the oyster's mantle tissues revealed that more than 99% methylation modification was restricted to cytosines in CpG context and methylated CpGs accumulated in the bodies of genes that were moderately expressed. Young repeat elements were another major targets of CpG methylation in oysters. Comparison with other invertebrate methylomes suggested that the 5'-end bias of gene body methylation and the negative correlation between gene body methylation and gene length were the derived features probably limited to the insect lineage. Interestingly, phylostratigraphic analysis showed that CpG methylation preferentially targeted genes originating in the common ancestor of eukaryotes rather than the oldest genes originating in the common ancestor of cellular organisms. CONCLUSIONS Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ximing Guo
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | | |
Collapse
|
23
|
Zhao Y, Chen M, Storey KB, Sun L, Yang H. DNA methylation levels analysis in four tissues of sea cucumber Apostichopus japonicus based on fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) during aestivation. Comp Biochem Physiol B Biochem Mol Biol 2014; 181:26-32. [PMID: 25461675 DOI: 10.1016/j.cbpb.2014.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/04/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
DNA methylation plays an important role in regulating transcriptional change in response to environmental stimuli. In the present study, DNA methylation levels of tissues of the sea cucumber Apostichopus japonicus were analyzed by the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique over three stages of the aestivation cycle. Overall, a total of 26,963 fragments were amplified including 9112 methylated fragments among four sea cucumber tissues using 18 pairs of selective primers. Results indicated an average DNA methylation level of 33.79% for A. japonicus. The incidence of DNA methylation was different across tissue types in the non-aestivation stage: intestine (30.16%), respiratory tree (27.61%), muscle (27.94%) and body wall (56.25%). Our results show that hypermethylation accompanied deep-aestivation in A. japonicus, which suggests that DNA methylation may have an important role in regulating global transcriptional suppression during aestivation. Further analysis indicated that the main DNA modification sites were focused on intestine and respiratory tree tissues and that full-methylation but not hemi-methylation levels exhibited significant increases in the deep-aestivation stage.
Collapse
Affiliation(s)
- Ye Zhao
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Muyan Chen
- Fisheries College, Ocean University of China, Qingdao 266003, PR China.
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada, K1S 5B6
| | - Lina Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Hongsheng Yang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.
| |
Collapse
|
24
|
Olson CE, Roberts SB. Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes. Front Physiol 2014; 5:224. [PMID: 24987376 PMCID: PMC4060414 DOI: 10.3389/fphys.2014.00224] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/28/2014] [Indexed: 01/21/2023] Open
Abstract
DNA methylation patterns and functions are variable across invertebrate taxa. In order to provide a better understanding of DNA methylation in the Pacific oyster (Crassostrea gigas), we characterized the genome-wide DNA methylation profile in male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was performed to examine the relationship between DNA methylation and transcript expression. Methylation status of over 7.6 million CpG dinucleotides was described with a majority of methylated regions occurring among intragenic regions. Overall, 15% of the CpG dinucleotides were determined to be methylated and the mitochondrial genome lacked DNA methylation. Integrative analysis of DNA methylation and RNA-Seq data revealed a positive association between methylation status, both in gene bodies and putative promoter regions, and expression. This study provides a comprehensive characterization of the distribution of DNA methylation in the oyster male gamete tissue and suggests that DNA methylation is involved in gene regulatory activity.
Collapse
Affiliation(s)
- Claire E Olson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| |
Collapse
|