Genomics and Applied Biology 2024, Vol.15, No.3, 120-131 http://bioscipublisher.com/index.php/gab 124 6 Case Studies of Integrated Networks in Cold Stress Response 6.1 Specific MiRNA-target interactions and their functional implications MiRNAs play crucial roles in the regulation of gene expression under cold stress in rice. One notable example is Osa-miR1320, which targets the ERF TF OsERF096. Under cold stress, the expression of miR1320 decreases, leading to an increase in OsERF096 levels. Overexpression of miR1320 enhances cold tolerance, while its knockdown reduces it. OsERF096 negatively regulates cold stress tolerance by modifying hormone content and signaling pathways, particularly the JA-mediated signaling pathway (Figure 1) (Sun et al., 2022). Another study identified 18 cold-responsive miRNAs in rice, with most being down-regulated under cold stress. These miRNAs, including members of the miR-167 and miR-319 families, regulate stress responses by cleaving mRNAs and are involved in hormone signaling pathways (Lv et al., 2010). 6.2 Network motifs and modules in cold stress response Network motifs and modules are essential for understanding the complex regulatory networks in cold stress response. In rice, miRNAs and TFs form composite feedback loops, which are network motifs that provide high information flow for coordinated regulation. For instance, a study on Caenorhabditis elegans revealed that miRNA-TF feedback loops occur more frequently than expected by chance, suggesting their importance in regulatory networks (Martinez et al., 2008). In rice, similar motifs likely exist, where miRNAs and TFs interact to regulate stress responses. Additionally, the integration of miRNA and lncRNA interactions forms complex regulatory networks. For example, in wheat, lncRNAs and miRNAs interact to form ceRNA networks, which play significant roles in cold stress response by regulating antioxidant systems and hormone pathways (Lu et al., 2020). Figure 1 Expression of miR1320 under cold stress and in different transgenic lines (Adopted from Sun et al., 2022) Image caption: A and B, Expression profiles of miR1320-5p (A) and miR1320-3p (B) under cold stress. C and D, miR1320 expression detection in miR1320-OE (C) and miR1320-KD (D) lines. Three biological replicates and three technical repeats were performed. Data are means ± SE (n = 3). *P < 0.05; **P < 0.01 by Student’s t test (Adopted from Sun et al., 2022) 6.3 Comparative analysis of regulatory networks in different rice varieties Comparative analysis of regulatory networks in different rice varieties reveals distinct responses to cold stress. For instance, the expression of Osa-miR820 varies between salt-susceptible and salt-tolerant rice varieties under stress conditions. This miRNA is up-regulated in leaf tissues but down-regulated in root tissues under salt stress, indicating a common regulatory scheme with variations in miRNAs and target transcript levels (Sharma et al., 2015). Another study on tropical Asian rice cultivars identified Environmental Gene Regulatory Influence Networks (EGRINs) that coordinate gene expression in response to environmental signals, including cold stress. These networks involve multiple layers of regulation and distinct regulatory roles for TFs, such as heat shock factors, which connect abiotic stress responses to the circadian clock (Wilkins et al., 2016).
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