Exploring the crop epigenome: a comparison of DNA methylation profiling techniques.

Autor:	Agius DR; Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta.; Biology Department, Ġ.F.Abela Junior College, Msida, Malta., Kapazoglou A; Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece., Avramidou E; Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece., Baranek M; Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia., Carneros E; Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain., Caro E; Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain., Castiglione S; Department of Chemistry and Biology 'A. Zambelli', University of Salerno, Fisciano, Italy., Cicatelli A; Department of Chemistry and Biology 'A. Zambelli', University of Salerno, Fisciano, Italy., Radanovic A; Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia., Ebejer JP; Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta., Gackowski D; Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland., Guarino F; Department of Chemistry and Biology 'A. Zambelli', University of Salerno, Fisciano, Italy., Gulyás A; Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary., Hidvégi N; Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary., Hoenicka H; Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany., Inácio V; BioISI - BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal., Johannes F; Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany., Karalija E; Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina., Lieberman-Lazarovich M; Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel., Martinelli F; Department of Biology, University of Florence, Sesto Fiorentino, Italy., Maury S; Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d'Orléans, Orléans, France., Mladenov V; Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia., Morais-Cecílio L; Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal., Pecinka A; Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia., Tani E; Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece., Testillano PS; Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain., Todorov D; Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria., Valledor L; Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain., Vassileva V; Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria.
Jazyk:	angličtina
Zdroj:	Frontiers in plant science [Front Plant Sci] 2023 May 30; Vol. 14, pp. 1181039. Date of Electronic Publication: 2023 May 30 (Print Publication: 2023).
DOI:	10.3389/fpls.2023.1181039
Abstrakt:	Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Agius, Kapazoglou, Avramidou, Baranek, Carneros, Caro, Castiglione, Cicatelli, Radanovic, Ebejer, Gackowski, Guarino, Gulyás, Hidvégi, Hoenicka, Inácio, Johannes, Karalija, Lieberman-Lazarovich, Martinelli, Maury, Mladenov, Morais-Cecílio, Pecinka, Tani, Testillano, Todorov, Valledor and Vassileva.)
Databáze:	MEDLINE
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