Abstract
Non-coding RNAs (ncRNAs) that were once considered “dark matter” or “transcriptional noise” in genomes are research hotspots in the field of epigenetics. The most well-known microRNAs (miRNAs) are a class of short non-coding, small molecular weight RNAs with lengths of 20–24 nucleotides that are highly conserved throughout evolution. Through complementary pairing with the bases of target sites, target gene transcripts are cleaved and degraded, or translation is inhibited, thus regulating the growth and development of organisms. Unlike miRNAs, which have been studied thoroughly, long non-coding RNAs (lncRNAs) are a group of poorly conserved RNA molecules with a sequence length of more than 200 nucleotides and no protein encoding capability; they interact with large molecules, such as DNA, RNA, and proteins, and regulate protein modification, chromatin remodeling, protein functional activity, and RNA metabolism in vivo through cis- or trans-activation at the transcriptional, post-transcriptional, and epigenetic levels. Research on plant lncRNAs is just beginning and has gradually emerged in the field of plant molecular biology. Currently, some studies have revealed that lncRNAs are extensively involved in plant growth and development and stress response processes by mediating the transmission and expression of genetic information. This paper systematically introduces lncRNA and its regulatory mechanisms, reviews the current status and progress of lncRNA research in plants, summarizes the main techniques and strategies of lncRNA research in recent years, and discusses existing problems and prospects, in order to provide ideas for further exploration and verification of the specific evolution of plant lncRNAs and their biological functions.
Highlights
Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
Polymerase II; some long non-coding RNAs (lncRNAs) are transcribed by RNA polymerase III, and a small number of lncRNAs in plants are produced by plant-specific RNA polymerases IV and V
According to the position of lncRNAs relative to adjacent protein-coding genes in the genome, lncRNAs can be divided into five types: sense lncRNA, antisense lncRNA, bidirectional lncRNA, intronic lncRNA, and large intergenic lncRNA
Summary
For lncRNAs in higher plants, the earliest literature reports that lncRNA Enod in M. truncatula can produce biological functions through the production of short peptides during the process of root nodule formation [32], and that ASCO-lncRNA generated by the transcription of ENOD40 homologs in A. thaliana can compete with messenger RNA (mRNA) to bind nuclear speckle RNA-binding protein (NSR), AS regulators, affecting AS patterns and expression levels of downstream auxin response genes and further regulating root development in A. thaliana [33]. Studies targeting herbaceous model plants have revealed the biological functions and mechanisms of a small number of lncRNAs. It has been gradually recognized that lncRNAs widely mediate the transmission and expression of genetic information, thereby regulating plant growth and development, secondary metabolism and stress adaptation.
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