Legume Genomics and Genetics 2025, Vol.16, No.5, 225-233 http://cropscipublisher.com/index.php/lgg 227 reversible. Once the external signal stops, they can also be "revoked", which ensures the flexibility and controllability of the entire process. However, which genes are activated and which remain silent depend on the signal strength, the time point, and the state of the root cells themselves. 3.2 Root hair curling and infection thread formation Not all cells will "accept" rhizobia. Root hair cells are the earliest type to react, and this reaction is often manifested as the curling of root hair and the formation of infected filaments. Behind such morphological changes lies a series of gene expression regulations that are precisely coordinated in time and space. Interestingly, this regulation is not as mechanical as simply turning genes on or off. Modifications such as histone acetylation can help activate genes related to cytoskeletal remodeling and cell wall changes; On the contrary, certain infection suppressants are "suppressed" due to DNA methylation at specific sites (Sadida et al., 2023). Overall, this epigenetic mechanism acts like a "fine-tuner", enabling root hairs to respond quickly to signals without overreacting. 3.3 Transcriptional reprogramming in cortical cells Once the infection enters the inner layer, it's the turn of the cortical cells to take the stage. These cells do not immediately show visible changes, but in fact, they are undergoing a "major shift in gene expression" inside. In order to cooperate with the formation of root nodules, they need to rearrange the working sequence of a large number of genes in a short period of time. This cannot be accomplished independently by any single mechanism. DNA demethylation opens the expression window of some developmental regulatory factors, histone modification helps maintain their activity, and small Rnas "screen" in the background which pathways should continue and which should be shut down. Not every pathway is allowed to operate. Only those genes that are useful for symbiosis are retained and activated, while the irrelevant ones are put on hold. It is precisely this multi-level coordination that enables ordinary cortical cells to gradually transform into root tumor cells with symbiotic functions. 4 Chromatin Modifications in Nodule Organogenesis 4.1 Chromatin accessibility at key regulatory loci When it comes to gene regulation, whether chromatin is "open" or "locked" has a very significant impact. But this is not a one-off deal; its accessibility is often in a state of dynamic change. Epigenetic modifications such as DNA methylation or histone acetylation are precisely the key means to regulate this "lock". Whether a transcription factor can enter a certain regulatory site depends not only on its own activity but also on whether the chromatin is willing to "open the door". There are many participants here. The enzymes commonly known as "writers", "erasers" and "readers" are the ones responsible for adding, interpreting or removing these modification markers (Gu et al., 2024). In the development of root nodules, the degree of openness of key promoter regions often affects whether certain specific genes can be activated. Especially in the early stage of organogenesis, if chromatin cannot be opened, these key genes will have difficulty functioning. 4.2 Histone code in nodule meristem maintenance The switch of genes is not always as simple as switching between the two states of "on" and "off". There are many "gray areas" in between. Among them, the so-called "histone code" has played a significant role. It is actually a combination of a series of modifications in the histone tail, such as acetylation, methylation, phosphorylation, etc. These combination patterns jointly affect the tightness of chromatin and the expressibility of genes. For instance, in the root tumor meristem, if modifications like H3K4me3 occur at certain locations, it often indicates that these genes are active (Figure 1) (Wang et al., 2020). On the contrary, modifications like H3K27me3 usually indicate that the gene has been suppressed. What is more complicated is that these modifications do not exist in isolation. It is the synergy and balance among histone acetyltransferase (HAT), deacetylase (HDAC), methyltransferase and demethylase that truly determine the stability maintenance ability of meristem and the direction of cell differentiation.
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