Plant long non-coding RNAs: identification and analysis to unveil their physiological functions

Abstract

Eukaryotic genomes encode thousands of RNA molecules; however, only a minimal fraction is translated into proteins. Among the non-coding elements, long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. LncRNAs are associated mainly with the regulation of the expression of the genome; nonetheless, their study has just scratched the surface. This is somewhat due to the lack of widespread conservation at the sequence level, in addition to their relatively low and highly tissue-specific expression patterns, which makes their exploration challenging, especially in plant genomes where only a few of these molecules have been described completely. Recently published high-quality genomes of crop plants, along with new computational tools, are considered promising resources for studying these molecules in plants. This review briefly summarizes the characteristics of plant lncRNAs, their presence and conservation, the different protocols to find these elements, and the limitations of these protocols. Likewise, it describes their roles in different plant physiological phenomena. We believe that the study of lncRNAs can help to design strategies to reduce the negative effect of biotic and abiotic stresses on the yield of crop plants and, in the future, help create fruits and vegetables with improved nutritional content, higher amounts of compounds with positive effects on human health, better organoleptic characteristics, and fruits with a longer postharvest shelf life.

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

“…Regulatory ncRNAs, on the other hand, are divided into two classes based on their length: long-non-coding RNAs (lncRNAs) exceeding 200 nucleotides and small non-coding RNAs (sRNAs), including microRNAs (miRNAs) of 19-25 nucleotides, small interfering RNAs (siRNAs) of 20-24 nucleotides, and piwi-interacting RNAs (piRNAs) with a length of 24-32 nucleotides [10,11]. The ncRNAs are further categorized based on chromosomal location, sequence/structure, ways of splicing, and biological functions [12,13]. Recently, a unique group of endogenous ncRNAs called "circular" RNAs (circRNAs) with a closedloop structure has been identified [14,15].…”

Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long “Non-Coding” RNAs

“…These RNAs are mostly transcribed in the nucleus with RNA polymerase II in an mRNA-like way. The mechanisms by which plant lncRNAs function are numerous, and some of them are better understood in animals [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 ]. Recent studies have shown that the short open reading frames (sORFs) of some plant lncRNAs encode functional small peptides (micropeptides) with a size of around 5 to 100 amino acids [ 10 , 12 , 17 , 18 , 19 , 20 , 21 , 22 ].…”