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Patriota MSS, Bernd RB, de Souza ALX, de Melo LAMP, Scherwinski-Pereira JE. Quantification of DNA Methylation by ELISA in Epigenetic Studies in Plant Tissue Culture: A Theoretical-Practical Guide. Methods Mol Biol 2024; 2827:323-350. [PMID: 38985280 DOI: 10.1007/978-1-0716-3954-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
This chapter describes a step-by-step protocol for rapid serological quantification of global DNA methylation by enzyme-linked immunosorbent assay (ELISA) in plant tissue culture specimens. As a case study model, we used the coconut palm (Cocos nucifera), from which plumules were subjected to somatic embryogenesis followed by embryogenic calli multiplication. DNA methylation is one of the most common epigenetic markers in the regulation of gene expression. DNA methylation is generally associated with non-expressed genes, that is, gene silencing under certain conditions, and the degree of DNA methylation can be used as a marker of various physiological processes, both in plants and in animal cells. Methylation consists of adding a methyl radical to carbon 5 of the DNA cytosine base. Herein, the global DNA methylation was quantified by ELISA with antibodies against methylated cytosines using a commercial kit (Zymo-Research™). The method allowed the detection of methylation in total DNA extracts from coconut palm embryogenic calli (arising from somatic embryogenesis) cultivated in liquid or solid media by using antibodies against methylated cytosines and enzymatic development with a colorimetric substrate. Control samples of commercially provided Escherichia coli bacterial DNA with previously known methylation percentages were included in the ELISA test to construct an experimental methylation standard curve. The logarithmic regression of this E. coli standard curve allowed methylation quantification in coconut palm samples. The present ELISA methodology, applied to coconut palm tissue culture specimens, is promising for use in other plant species and botanical families. This chapter is presented in a suitable format for use as a step-by-step laboratory procedure manual, with theoretical introduction information, which makes it easy to apply the protocol in samples of any biological nature to evaluate DNA global methylation associated with any physiological process.
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Pan J, Li X, Liu H, Wang C, Xu S, Xu B, Deng Y, Yang T, Liu W. Exploring the molecular mechanisms underlie the endoplasmic reticulum stress-mediated methylmercury-induced neuronal developmental damage. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 245:114099. [PMID: 36152427 DOI: 10.1016/j.ecoenv.2022.114099] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/01/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Methylmercury (MeHg) is a ubiquitous environmental pollutant, which can cross the placenta and blood brain barrier, thus affecting fetal growth and development. Although previous studies have demonstrated that MeHg induces endoplasmic reticulum (ER) stress in rat cerebral cortex and primary neurons, the role of ER stress in MeHg-induced neurodevelopmental toxicity remains unclear. Here, we used ICR pregnant mice and hippocampal neurons cells (HT22 cells) to investigate the molecular mechanism by which MeHg exposure during pregnancy affects neurodevelopment. We found that prenatal MeHg exposure caused developmental delay in offspring, accompanied with ER stress, cell apoptosis, cell cycle arrest and abnormal DNA methylation. Then, we used ER stress specific inhibitor 4-PBA and CHOP siRNA to investigate the role of ER stress on HT22 cells damage caused by MeHg. The results showed that 4-PBA pretreatment restored MeHg-induced axonal shortening and alleviated apoptosis, cell cycle arrest and DNA methylation. At the same time, the activation of CHOP/c-Jun/GADD45A signaling pathway was inhibited, and the interaction between CHOP and c-Jun was weakened. In addition, CHOP siRNA reduced the expression of c-Jun and GADD45A, and relieved DNA methylation levels to some extent. In summary, our study suggested that ER stress induced by MeHg mediated cell apoptosis and cell cycle arrest, and may affect DNA methylation through activation of CHOP/c-Jun/GADD45A signaling pathway, thus leading to neuronal damage.
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Affiliation(s)
- Jingjing Pan
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Xiaoyang Li
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Haihui Liu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Chen Wang
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Si Xu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Tianyao Yang
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, China.
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Silva DMZA, Castro JP, Goes CAG, Utsunomia R, Vidal MR, Nascimento CN, Lasmar LF, Paim FG, Soares LB, Oliveira C, Porto-Foresti F, Artoni RF, Foresti F. B Chromosomes in Psalidodon scabripinnis (Characiformes, Characidae) Species Complex. Animals (Basel) 2022; 12:ani12172174. [PMID: 36077895 PMCID: PMC9454733 DOI: 10.3390/ani12172174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary For more than a century, B chromosomes have been investigated in several eukaryotic species. These supernumerary genomic elements behave as parasites or provide fitness benefits to the hosts. They are mostly composed of repetitive DNA, but they also have protein-coding genes. B chromosomes are associated with differential gene expression and phenotypic effects. This makes them one of the most interesting genomic elements to investigate. Fish species of the Psalidodon genus harbor a great diversity of B chromosomes. Recent studies showed they share a common ancestor, persisting in the genus for a long time and enduring speciation processes. In the Psalidodon scabripinnis species complex, B chromosomes express their own genes, mostly related to cell cycle and gonad differentiation. Moreover, these B chromosomes are associated with functional effects, e.g., cell cycle extension. Here, we review the current knowledge regarding these elements in the P. scabripinnis species complex and propose a chromosome speciation model facilitated by the B chromosome manipulation of the cell machinery. Abstract B chromosomes are extra-genomic components of cells found in individuals and in populations of some eukaryotic organisms. They have been described since the first observations of chromosomes, but several aspects of their biology remain enigmatic. Despite being present in hundreds of fungi, plants, and animal species, only a small number of B chromosomes have been investigated through high-throughput analyses, revealing the remarkable mechanisms employed by these elements to ensure their maintenance. Populations of the Psalidodon scabripinnis species complex exhibit great B chromosome diversity, making them a useful material for various analyses. In recent years, important aspects of their biology have been revealed. Here, we review these studies presenting a comprehensive view of the B chromosomes in the P. scabripinnis complex and a new hypothesis regarding the role of the B chromosome in the speciation process.
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Affiliation(s)
- Duílio M. Z. A. Silva
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
- Correspondence:
| | - Jonathan P. Castro
- Post-Graduate Program in Evolutionary Genetics and Molecular Biology, Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil
- Laboratory of Evolutionary Genetics, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Caio A. G. Goes
- Laboratory of Fish Genetics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru 17033-360, SP, Brazil
| | - Ricardo Utsunomia
- Laboratory of Fish Genetics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru 17033-360, SP, Brazil
- Laboratory of Fish Genetics, Department of Genetics, Institute of Biological Sciences and Health, Federal Rural University of Rio de Janeiro, Seropedica 23890-000, RJ, Brazil
| | - Mateus R. Vidal
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Cristiano N. Nascimento
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Lucas F. Lasmar
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Fabilene G. Paim
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Letícia B. Soares
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Claudio Oliveira
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Fábio Porto-Foresti
- Laboratory of Fish Genetics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru 17033-360, SP, Brazil
| | - Roberto F. Artoni
- Post-Graduate Program in Evolutionary Genetics and Molecular Biology, Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil
- Laboratory of Evolutionary Genetics, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Fausto Foresti
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
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