Rice Genomics and Genetics 2025, Vol.16, No.4, 211-218 http://cropscipublisher.com/index.php/rgg 214 indicates that lncRNA can act as an upstream regulatory factor of key transcription factors during flowering transition (Gao et al., 2020; Shin et al., 2022). 4.2 Interaction with mRNAs and miRNAs to form regulatory networks lncRNA can also participate in regulatory networks by interacting with mRNA and miRNA. Some lncrnas act as endogenous targeting mimics (ETMs), binding mirnas to prevent them from inhibiting target mrnas. For instance, in rice, some lncrnas act as ETMs of osa-miR156 and osa-miR396, regulating the expression of SPL and GRF genes, which are crucial in terms of developmental timing and fertility. In addition, there are some lncrnas that may be precursors of mirnas, so they can also participate in post-transcriptional regulation (Wang et al., 2021; Li et al., 2024). 4.3 Participation in chromatin modification and epigenetic regulation lncRNA can also affect the flowering time through epigenetic mechanisms. For instance, RIFLA can bind to the histone methyltransferase OsiEZ1 (a homolog of Arabidopsis H3K27-specific methyltransferase) to form a complex. This will cause epigenetic suppression of OsMADS56, indicating that lncrnas can direct chromatin modification proteins to specific gene loci. Similarly, lncRNA LAIR binds to histone modification proteins OsMOF and OsWDR5, promoting the increase of two active chromatin markers, H3K4me3 and H4K16ac, in the LRK1 gene region, which is related to the improvement of gene expression and yield (Wang et al., 2018; Gao et al., 2020). 5 Case Studies of Representative lncRNAs 5.1 Key lncRNAs involved in photoperiod pathway regulation There is a flower-related gene called RIFLA in rice, which is an lncRNA transcribed from the intron of the OsMADS56 gene. It can inhibit the flowering inhibitory factor OsMADS56, thereby increasing the expression of flowering inducible factors Hd3a and RFT1. Overexpression of RIFLA can cause rice to flower earlier, which indicates its significance in the photoperiodic pathway. Mechanically, RIFLA binds to histone methyltransferase OsiEZ1 and participates in the epigenetic regulation of OsMADS56, adjusting the flowering time according to the length of daylight (Figure 2 ) (Shin et al., 2022). Figure 2 Heading date and phenotypes of RIFLA-overexpressing plants (Adopted from Shin et al., 2022) Image caption: (A) Expression of RIFLAin RIFLA-overexpressing plants. Total RNA was isolated from the second leaf blade (from the top) of WT and RIFLA-overexpressing plants grown under NLD photoperiod. Transcript levels of RIFLA were examined by real-time quantitative PCR (RT-qPCR) using gene-specific primers. (B) Heading date of WT and RIFLA-overexpressing plants under NLD conditions. Error bars indicate standard deviation. Asterisks ( *** ) indicate statistically significant differences in heading date (P < 0.001; Student’s t-test) between WT andRIFLA-overexpressing plants. DAG, days after germination. (C) Phenotypes of WT and RIFLA-overexpressing plants after heading under NLD conditions. Red arrows indicate panicles (Adopted from Shin et al., 2022) 5.2 lncRNAs affecting hormone signaling pathways Whole-genome analysis revealed that some lncrnas can serve as endogenous targeted mimics (ETMs) of mirnas such as osa-miR156 and osa-miR396. These mirnas regulate the SPL and GRF genes, which are related to
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