Maize Genomics and Genetics 2025, Vol.16, No.4, 182-201 http://cropscipublisher.com/index.php/mgg 193 such as MRP1 (Myb-related protein 1, specifying transfer cell fate) had a sharp increase in accessibility in the basal endosperm region right after fertilization. MRP1 binds to downstream target gene promoters to initiate transfer cell differentiation; our data show accessible sites in those target promoters (the so-called BETL genes) correspondingly present. We noted that gene sets associated with differentiation (like “regulation of meristem development” or “cell fate specification”) were enriched in early development clusters of OCR-linked genes. Another example is the set of WOX (WUSCHEL-related homeobox) genes, which control embryo patterning and meristem formation. ZmWOX2 and ZmWOX5 (involved in the apical and root pole of the embryo, respectively) are expressed very early; interestingly, ZmWOX2 was predicted as a target of ABI19 in our network and has promoter RY elements. We observed its promoter is indeed accessible in the early embryo, likely reflecting its activation and importance in the first cell divisions of the zygote. The enrichment of differentiation processes among OCR genes underscores that establishing new cell identities – which requires turning on specific sets of genes while turning off others – is accompanied by deliberate remodeling of chromatin at those gene loci. This ensures that lineage-specific genes (e.g. aleurone-specific or embryo shoot-specific) become accessible to transcription machinery only in the correct context. Plants use different hormones to control the growth of seeds. At first, auxin and cytokinin played a more important role. Afterwards, as the seeds mature and are ready to enter a dormant state, hormones such as abolic acid (ABA) and gibberellin (GA) become even more important. In our research, we found that many genes that respond to auxin - such as those from the Aux/IAA family and the GH3 enzyme - are close to open chromatin spots at an early stage. The promoters of some Aux/IAA genes open just a few days after pollination. This time coincides very well with the early leap in auxin activity during seed development. The Aux/IAA protein helps control how plants process auxin. They achieve this by working in synergy with ARF (enhanced growth Factor), a protein that helps transmit auxin signals. These obstructions emerged quite early. They may be involved in shaping the way embryos and endosperm form. We found that their promoters opened shortly after pollination. This point in time is in line with the view that auxin takes effect rapidly and uses these repressors to build feedback loops. For abscisic acid (ABA), which becomes more active in the later stage, we studied the LEA gene, especially the genes of the Em family. These genes are known targets of ABA and are usually activated by transcription factors such as ABI3 and VP1. At first, their promoter regions did not show too many ATAC-seq signals. But later, these regions opened up, indicating that as the level of abscisic acid rose, these genes were activated. We also found that the GO terms for many genes with late-opening OCR are "response to abscisic acid" and "response to drying". This is in line with the role of abscisic acid in helping seeds dry out and maintain dormancy. A gene related to gibberellin (GA), GA 2-oxidase, also has a late-opening promoter (Du et al., 2023). This gene helps break down gibberellin, which supports the view that an increase in abalic acid levels will reduce gibberellin, thereby preventing early germination. 5.3 Dynamics of pathway activities across development By tracking the accessibility of chromatin and the changes in gene expression over time, we outline how different biological pathways alter their activity during seed development. In the early stage, from fertilization to a few days after pollination (DAP), genes related to cell growth and basic biosynthetic requirements are particularly active. Our ATAC-seq and RNA-seq data show that the signals of DNA replication and cell cycle genes (including the gene of histone H4) are strong, and histone H4 supports the formation of new chromatin in rapidly dividing nuclei. At the same time, we noticed brief activity in hormone-related pathways, especially auxin and cytokinin. Several genes induced by auxin showed early transcription and accessible promoters, while type-A cytokinin response regulators also briefly opened up. These patterns match the idea that hormones give a short boost to early seed development, especially for launching endosperm formation. In contrast, ABA-related genes remained mostly inactive in this period—both in terms of expression and chromatin openness—consistent with the low ABA levels before seed maturation begins (Bernardi et al., 2019).
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