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

Abstract

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.

Grafting based DNA methylation alteration of snoRNAs in upland cotton (Gossypium L.)

“…The numbers of m CG-DMCs with increased methylation levels in ungraft TK vs PT were higher than in ungraft TK vs TT (Table 4 ). This indicated that grafting affected methylation levels by influencing probably the activities of domains rearranged methyltransferase 1 (DRM1) and (DRM2) and directed by small interfering RNAs (siRNAs) (Erdmann and Picard 2020 ; Agius et al 2023 ). Differences in the numbers of m CG + m CHG-DMCs among three gene elements were studied, and results revealed that among the gene elements, UPS regions contained the highest numbers of m CG + m CHG-DMCs, followed by DWN regions but the lowest numbers were observed in GB regions (Table 4 ).…”

Comparative restriction enzyme analysis of methylation (CREAM) reveals methylome variability within a clonal in vitro cannabis population

“…It also utilizes two anchoring enzymes ( Nsi I and Pst I) to capture more diverse restriction fragments, therefore providing a better overview of methylation sites across the genome. While it provides interesting elements to the family of MSAP methods coupled with sequencing technologies, the CREAM approach also only focuses on CCGG sequences recognized by restriction enzymes, thus ignoring DNA methylation in CHG and CHH contexts, notably involved in the regulation of genes and transposons ( Agius et al., 2023 ).…”

Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops

“…These methods enable the identification of methylation patterns across the genome, elucidating how epigenetic modifications influence gene expression and contribute to biological diversity and complexity. Moreover, knowing the dynamics of DNA methylation helps in exploring the developmental processes, environmental adaptability, and evolutionary mechanisms of organisms to improve stress resistance and productivity of crop plants [33]. Thus, the development and refinement of DNA methylation detection technologies continues to be a cornerstone of epigenetic research, with broad implications for biology and medicine.…”