Maize Genomics and Genetics 2025, Vol.16, No.6, 325-333 http://cropscipublisher.com/index.php/mgg 327 Figure 1 Effect of salt stress on the isoenzyme composition of GDH in maize leaves. PAGE electropherogram of GDH from maize leaves under salt stress: 0, 1, 6, 12, 24-incubation time in the NaCl solution (hours); P1, P2-protein bands representing native GDH protein molecules (isoenzymes) stained by the tetrazolium method; and F-dye front (Adopted from Eprintsev et al., 2024) 3 Types, Functions, and Detection Methods of Plant DNA Methylation 3.1 Distribution characteristics and biological functions of CG, CHG, and CHH methylation In plants, DNA methylation is not immutable. It occurs in three sequence environments: CG, CHG and CHH (H stands for A, T or C). Although CG methylation is the most common and widely distributed, including the genome and transposition factor (TE), it does not mean that other types are unimportant. This type is mainly maintained by MET1. In contrast, CHG methylation is more prevalent around centromeres and in heterochromatin, maintained by enzymes such as CMT3, and it plays a more prominent role in silencing TE. The methylation of CHH is more volatile and is mostly established by the RdDM pathway and CMT2. It is particularly common in monocotyledonous plants such as corn, and is also frequently distributed at the edges of gene-dense chromatin regions. Some people believe that in certain regulatory scenarios, the role of CHG is even stronger than that of CG (Domb et al., 2020). The methylation levels and distributions vary significantly among different plant species, tissues, and even different developmental stages of the same plant, which reflects the diversity of its regulatory functions (Bartels et al., 2018). 3.2 Overview of plant DNA methylation techniques (e.g., WGBS, MeDIP-seq) There is no single method that can solve all methylation problems in one go. Which technology to use really depends on what kind of scientific research problem you plan to solve. WGBS is currently the most "comprehensive" solution, capable of being precise to a single base, with data as detailed as it can be. It is highly suitable for species with large and complex genomes like corn (Li et al., 2018; Garcia-Garcia et al., 2024). However, this method is not easy to master. Not only is the cost high, but the amount of data processing in the later stage is also quite large. Research groups with insufficient budgets often choose MeDIP-seq - although its resolution is slightly lower, the antibody enrichment strategy makes it quite efficient in screening (Beck et al., 2021). Small but precise methods like RRBS, which focus on regions rich in CpG, can provide details and are suitable for teams that want to conduct in-depth research on specific sites. In recent years, there has been a new technology called EM-seq, which bypasses the traditional bisulfite treatment process and is particularly suitable for the detection of non-CG methylation, with good accuracy and stability. In conclusion, different problems may require completely different methods. There is no such thing as "who is the best". More realistically, it depends on your goals and conditions to determine your choice.
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