International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.2, 111-123 http://ecoevopublisher.com/index.php/ijmeb 114 Figure 2 Methylation sites inB. napus and its diploid parents have been identified and analyzed (Adopted from Hu et al., 2023) Image caption: (a) The percentage of methylated cytosine in B. rapa (AA), B. oleracea (CC), and B. napus (RAC); (b) Average CG, CHG, and CHH methylation levels inB. napus and its diploid parents; (c) Cisco map of methylation levels in B. napus and its diploid parents; GC content (green), gene density (red), CG methylation level (purple), CHG methylation level (orange), and CHH methylation level (light blue) are displayed sequentially from the outside in; The level or density is greater the darker the color is. The ordinate of Figure A indicates the proportion of methylated cytosine (e.g., mCG proportion = mCG/CG); Figure B shows the average methylation level of the whole genome (Adopted from Hu et al., 2023) 4.2 Regulatory network of histone modification In chromatin regulation, various histone modifications together constitute a complex and precise "code system". For example, H3K4me3 modification is often regarded as an activation sign, like a "green signal light" to guide transcription initiation; in contrast, H3K27me3 modification plays an inhibitory function, like a "red light" to prevent unnecessary gene expression (Li et al., 2021). During the microspore embryogenesis stage, histone acetylation levels can increase to three to five times the normal level, significantly accelerating the development of the embryo (Rodríguez-Sanz et al., 2014). Interestingly, when treated with histone deacetylase inhibitors, the originally silent rRNA genes will be "reactivated", suggesting that this regulatory mechanism has a high degree of plasticity and reversibility (Zj and Pikaard, 1997). In addition, in some genomic regions, both activation and inhibition modifications coexist, forming a "bivalent mark", which provides more flexible options for cell fate decisions (Zhang et al., 2020). 4.3 Regulatory role of non-coding RNA In gene regulation, small molecule RNA, especially siRNA, plays a role of precise navigation. They can effectively guide DNA methyltransferases to locate specific target sequences, thereby initiating or maintaining methylation silencing (Xiao et al., 2023). These small RNA molecules not only act alone, but also coordinate with histone modifications to jointly regulate gene expression, forming a highly coordinated regulatory system (Zhou, 2024). Although the study of non-coding RNA in rapeseed is still in its early stages, studies have shown that it has an important function in stress response. Taking drought as an example, the expression levels of some siRNAs change rapidly at the beginning of stress, which helps to adjust the expression of related genes, thereby improving the environmental adaptability of plants.
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