Legume Genomics and Genetics 2025, Vol.16, No.5, 225-233 http://cropscipublisher.com/index.php/lgg 226 mechanisms play in the tumor formation process. At the same time, we will also identify some new trends in current research, especially potential regulatory pathways and key factors. Through these contents, perhaps some new perspectives can be provided for understanding how leguminous plants precisely control the symbiotic process with rhizobia. 2 Epigenetic Landscape in Legume Root Cells 2.1 DNA methylation and demethylation patterns When studying the regulation of gene expression in root cells of leguminous plants, DNA methylation is often an unavoidable topic. It mainly occurs at cytosine sites and is regarded as a "silencing" mechanism, sometimes also playing a role in stabilizing expression. However, methylation itself does not emerge out of thin air or exist permanently. Its formation and maintenance rely on DNA methyltransferase (DNMT), while the removal of these markers requires demethylase. The two are like a pair of switches, regulating the expression requirements of plants at different developmental stages (Cheng et al., 2019). It is worth noting that although we are more familiar with the role of these mechanisms in processes such as embryonic development or leaf differentiation, they may also play a decisive role in the formation of root nodules in leguminous plants. Some genes should have been activated to drive the development of root nodules, but they have become "silent" due to abnormal methylation. On the contrary, if the methyl groups at specific sites are removed, those pathways related to symbiosis may be activated. However, it should also be noted that these regulations are not fixed. Their specific effects depend on the environment, the stage of development, and the state of the genes themselves. 2.2 Histone modifications in nodule priming Not all regulation is accomplished through methylation. At the chromatin level, various "processing" methods of histones-such as methylation, acetylation, phosphorylation, ubiquitination, etc.-are also quietly influencing the on-off state of genes. Interestingly, certain histone modifications are almost always associated with gene activity, such as the methylation of H3K4 and H3K36; While others, such as methylation of H3K9 and H3K27, often predict gene silencing (Ramazi et al., 2023). Of course, histone modifications are not a solo effort. They usually rely on a complete set of enzyme systems for "writing", "erasing" and "reading" to operate in coordination. This regulatory mode is particularly important during the organogenesis stage of plant cells. Although research on the formation of root nodules in leguminous plants is still ongoing, there are already indications that such modifications may start to "warm up" the related expression programs long before the root cells initiate symbiosis. 2.3 Small RNAs and epigenetic silencing In addition to the regulation at the DNA and histone levels, there is another type of "minor role" that cannot be ignored-small Rnas, such as micrornas and small interfering RNAs. Although they are small in size, they have considerable influence. They can precisely identify target gene loci, guide methylation or histone modification, and thereby achieve the purpose of silencing certain genes. Sometimes they directly interfere with post-transcriptional expression, and sometimes they achieve regulation by influencing chromatin structure. Especially in plants, small Rnas have been found to be widely involved in responses to external signals and developmental changes. In other words, if leguminous plants are to form root nodules, their root cells are likely to use small Rnas to "adjust channels" to ensure that the relevant genes are turned on or off at the right time. 3 Epigenetic Regulation During Early Symbiotic Signaling 3.1 Nod factor recognition and signal cascade At the beginning, root cells do not respond to all external stimuli; only specific nodulation factors can be recognized. Once this recognition occurs, it is like pressing a switch, and a series of subsequent signals will be activated one after another, thereby driving the formation of the root tumor. However, signal transmission alone is not enough; cells also need to readjust which genes should be turned on and which should be turned off. And this often relies on rapid regulation at the epigenetic level. Operations like the removal of DNA methylation and the increase of histone acetylation are essentially "revising and modifying the instruction manual", temporarily making the chromatin structure more open and the genes easier to read. Importantly, these modifications are
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