Abstract
Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.
Highlights
90% of the genome is pervasively transcribed into RNA
Mining more than 200 transcriptome datasets for Arabidopsis [32] revealed that 70% of Long non-coding RNAs (lncRNAs) (~40,000 candidate lncRNAs; >30,000 natural antisense transcripts (NATs); >6000 long intergenic non-coding RNAs (ncRNAs)) were transcribed from coding loci to be associated with antisense transcripts [33,34]
The development of high-throughput screening and other new techniques has helped to tailor the identification of lncRNAs and their biology
Summary
Only 1–2% of the transcribed genome encodes for putative protein-coding RNAs, whereas the remaining 98–99% RNAs remain uncharacterized or do not code for any functional protein and are regarded as “dark matter,” transcriptional “noise,” “junk DNA,” or an “experimental artifact” [1,2,3] Such RNAs are considered to be non-coding RNAs (ncRNAs) [1]. Plant lncRNAs are involved in diverse biological processes, including photomorphogenesis, flowering, phosphate homeostasis, stress tolerance, and fertility [9,12] They play a vital role as a molecular sink for the target mimics of miRNAs to process into shorter ncRNAs [13], in protein subcellular re-localization [14], as repressors of histone acetylation, in direct epigenetic silencing mediated by specific chromatin domains [15], and in regulating protein post-transcriptional regulation [13,16]. We aim to elucidate the lncRNA-mediated regulation of important plant developmental processes such as vernalization, fertility, lateral root development, photomorphogenesis, nodulation, and fiber development, and provide guidance for developing optimal plant breeding strategies in future crop breeding programs
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