Rice Genomics and Genetics 2025, Vol.16, No.4, 211-218 http://cropscipublisher.com/index.php/rgg 213 activity of key flowering genes, combining developmental signals with environmental signals to ensure that flowering occurs at the most appropriate time and under the most suitable conditions, thereby helping to increase yield and adaptability (Cho et al., 2017; Vicentini et al., 2023; Li, 2024). 3 Characteristics and Functional Classification of lncRNAs 3.1 Definition, structure, and main characteristics of lncRNAs Long non-coding RNA (lncRNA) is a type of RNA molecule that exceeds 200 nucleotides in length and has no obvious protein-coding function. They can be transcribed by RNA polymerase II or III, and some can be capped, spliced and polyadenylate added, but not all lncrnas have these characteristics (Quinn and Chang, 2015). The sequences and structures of lncrnas vary greatly and are usually expressed only at specific tissue or developmental stages. They are different from mRNA and function more through their own secondary or tertiary structures. They can bind to DNA, RNA and proteins and regulate gene expression at multiple levels (Wang et al., 2017). This regulation includes chromatin modification, transcription and post-transcriptional regulation, as well as influencing processes such as cell differentiation and development (Dahariya et al., 2019). 3.2 Classification by mode of action lncRNA can be classified into several types based on its genomic location, mechanism of action and function: Cis-acting lncrnas: Regulating genes near them by recruiting chromatin modification factors or altering the transcriptional activity of adjacent genes (Ma et al., 2013; Kopp and Mendell, 2018). Transacting lncrnas: They act on genes located far from themselves, including those on other chromosomes, often serving as molecular scaffolds or guide protein complexes. Competitive endogenous RNA (ceRNA) : Binding to microRNA like a sponge, preventing them from inhibiting target mRNA (Benchi et al., 2023; Chodurska and Kunej, 2025). Other functional types: Some act as "baits", isolating proteins or RNA; Some act as "scaffolds", bringing together multiple proteins. Some act as "guides", bringing regulatory complexes to specific gene locations (Dahariya et al., 2019). According to genomic distribution, lncrnas can also be classified into intergenic type, antisense type, intron type, overlapping type and divergent type, etc., which reflect their different origins and regulatory capabilities (St Laurent et al., 2015). 3.3 Technical approaches and advances in studying plant lncRNA functions The development of high-throughput RNA sequencing and bioinformatics enables scientists to identify and annotate tens of thousands of lncrnas in the genomes of animals and plants (Choi et al., 2019; Klapproth et al., 2021). Experimental methods for studying their functions include: conducting loss-of-function or loss-of-function experiments, analyzing their locations within cells, and mapping their interactions with other molecules (Delas and Hannon, 2017; Wu and Du, 2017). Nowadays, computational models and databases can also predict the functions and similarities of lncrnas on a large scale, accelerating the discovery of novel regulatory lncrnas (Chen et al., 2018). In addition, ribosome analysis and mass spectrometry techniques have revealed that some lncrnas can also encode short peptides, which enriches their functions (Choi et al., 2019; Tian et al., 2024 Zhang, 2024). However, distinguishing functional lncrnas from transcriptional noise and clarifying their mechanisms of action remains a challenge. 4 Mechanisms of lncRNAs in Regulating Rice Flowering Time 4.1 Regulation of flowering time through controlling transcription factor gene expression lncRNA can directly affect the expression of key transcription factors, thereby regulating the flowering time of rice. For instance, the intron lncRNA RICE FLOWERING ASSOCIATED (RIFLA) inhibits the flowering suppressor gene OsMADS56. Overexpression of RIFLA can lead to a decrease in OsMADS56 levels and an increase in the expression of flower-inducing factors Hd3a and RFT1, resulting in earlier flowering of rice. This
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