Agius Dolores Rita, Kapazoglou Aliki, Avramidou Evangelia, Baranek Miroslav, Carneros Elena, Caro Elena, Castiglione Stefano, Cicatelli Angela, Radanovic Aleksandra, Ebejer Jean-Paul, Gackowski Daniel, Guarino Francesco, Gulyás Andrea, Hidvégi Norbert, Hoenicka Hans, Inácio Vera, Johannes Frank, Karalija Erna, Lieberman-Lazarovich Michal, Martinelli Federico, Maury Stéphane, Mladenov Velimir, Morais-Cecílio Leonor, Pecinka Ales, Tani Eleni, Testillano Pilar S, Todorov Dimitar, Valledor Luis, Vassileva Valya
Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta.
Biology Department, Ġ.F.Abela Junior College, Msida, Malta.
Front Plant Sci. 2023 May 30;14:1181039. doi: 10.3389/fpls.2023.1181039. eCollection 2023.
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.
表观遗传修饰在维持基因组完整性和调控基因表达方面发挥着至关重要的作用。DNA甲基化作为表观遗传调控的关键机制之一，影响着包括植物在内的所有生物体的生长、发育、应激反应和适应性。检测DNA甲基化标记对于理解这些过程背后的机制以及制定提高作物生产力和抗逆性的策略至关重要。检测植物DNA甲基化有不同的方法，如亚硫酸氢盐测序、甲基化敏感扩增多态性、全基因组DNA甲基化分析、甲基化DNA免疫沉淀测序、简化代表性亚硫酸氢盐测序、质谱和基于免疫的技术。这些分析方法在许多方面存在差异，包括DNA输入量、分辨率、基因组区域覆盖范围和生物信息学分析。选择合适的甲基化筛选方法需要了解所有这些技术。本文综述了作物植物中DNA甲基化分析方法，并比较了这些技术在模式植物和作物植物之间的有效性。概述了每种方法的优缺点，并强调了考虑技术和生物学因素的重要性。此外，还介绍了在模式植物和作物物种中调节DNA甲基化的方法。总体而言，本文综述将帮助科学家在选择合适的DNA甲基化分析方法时做出明智的决策。
