Cotton Genomics and Genetics 2025, Vol.16, No.3, 107-116 http://cropscipublisher.com/index.php/cgg 109 cell wall synthesis, and response to external pressure. These regulatory proteins together form a very complex network responsible for regulating various aspects of fiber development (Prasad et al., 2022; You et al., 2023). 2.3 Role of non-coding RNAs (e.g., lncRNAs, miRNAs) in post-transcriptional regulation Although transcription factors are often mentioned, non-coding RNA is not idle either. In the development of cotton fiber, "behind-the-scenes roles" such as lncRNA and siRNA also participate in regulation. Studies have found that there are thousands of lncRNA transcripts with different expression patterns at different stages, indicating that they are not "spectators" during the fiber initiation and elongation stages (Zou et al., 2016). More interestingly, some small RNAs are derived from natural antisense transcripts (NAT), which can directly cut mRNA and thus change gene expression. For example, GhMML3_A12 itself will be regulated by an siRNA, which is equivalent to a "self-pruning" operation (Wan et al., 2016). These findings show that post-transcriptional regulation is also a link that cannot be ignored, and its role is not necessarily less than that of transcription factors. 3 Epigenomic Regulation in Cotton Fiber Cells 3.1 DNA methylation patterns and their correlation with fiber-specific gene expression During the development of cotton fiber, DNA methylation, especially CHH type methylation, will gradually increase. This change is related to the differentiation of fiber cells and the expression of related genes. This methylation process is mainly completed through a pathway called H3K9me2, not through RNA-guided DNA methylation (RdDM). At the same time, this methylation is also related to the synthesis of lipid substances and the regulation of gene expression of reactive oxygen species, both of which are very important for fiber differentiation. 3.2 Histone modifications (e.g., H3K4me3, H3K27ac) and chromatin accessibility During the development of fiber cells, histone modification and chromatin openness are critical. By studying the distribution of nucleosomes, scientists found that during the maturation of fiber cells, chromatin changes from a more active state to a less active state, and this change also affects the location of methylation on DNA, thereby affecting gene expression. "Active" marks such as H3K9me2 are associated with enhanced DNA methylation and the regulation of fiber-related gene expression (Wang et al., 2016). Through single-cell ATAC-seq technology, researchers have discovered some regulatory regions that only work in fiber cells, such as TCP pattern sequences, which can bind to transcription factors to regulate the rhythm of gene expression and metabolic activity during fiber growth. 3.3 Chromatin remodeling and the 3D genome organization in fiber developmental stages Chromatin is not always the same. Especially at different stages of cotton fiber cell development, it will become more open, or on the contrary, more compact. There are actually many details behind this. For example, the position of nucleosomes is not fixed, but moves at certain key time points, so that chromatin gradually changes from the "on" state to the "off" state. But this structural change is not just a physical swing, it is often related to some deeper regulatory mechanisms-such as the establishment of DNA methylation patterns, and those gene expression programs that control cell differentiation and fiber elongation will also be affected. However, not all changes can be seen directly. After analyzing the openness of chromatin and gene expression data together, the study found that those special regulatory regions in the three-dimensional structure actually play a very critical role in regulating "when and where" genes are activated (Wang et al., 2023). In other words, these regions are like switch boxes. If they are not turned on, genes may remain silent. DNA methylation, histone modification, chromatin structure adjustment-they work separately and cooperate with each other. These epigenetic mechanisms are built up layer by layer, jointly determining which genes should play a role and which genes should be temporarily "dormant" during the development of fibroblasts. Overall, the regulation is rhythmic and hierarchical, rather than random. 4 Integrated Transcriptome-Epigenome Analysis 4.1 Correlating differentially expressed genes with epigenetic landscapes Analyzing transcriptome data and epigenomic data together can more clearly show the relationship between changes in gene expression and some epigenetic modifications (such as DNA methylation and chromatin
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