Abstract
Small non-coding RNAs have been extensively studied in plants over the last decade. In contrast, genome-wide identification of plant long non-coding RNAs (lncRNAs) has recently gained momentum. LncRNAs are now being recognized as important players in gene regulation, and their potent regulatory roles are being studied comprehensively in eukaryotes. LncRNAs were first reported in humans in 1992. Since then, research in animals, particularly in humans, has rapidly progressed, and a vast amount of data has been generated, collected, and organized using computational approaches. Additionally, numerous studies have been conducted to understand the roles of these long RNA species in several diseases. However, the status of lncRNA investigation in plants lags behind that in animals (especially humans). Efforts are being made in this direction using computational tools and high-throughput sequencing technologies, such as the lncRNA microarray technique, RNA-sequencing (RNA-seq), RNA capture sequencing, (RNA CaptureSeq), etc. Given the current scenario, significant amounts of data have been produced regarding plant lncRNAs, and this amount is likely to increase in the subsequent years. In this review we have documented brief information about lncRNAs and their status of research in plants, along with the plant-specific resources/databases for information retrieval on lncRNAs.
Highlights
Studies in the recent past have highlighted the pervasive nature of eukaryotic transcription and, have strongly emphasized on the complexity involved in the expression of eukaryotic genomes [1]
Abbreviations used in Table 1: EST, expressed sequence tag; lncRNA, long non-coding RNA; lincRNA, long intergenic non-coding RNA; lncNAT, long non-coding natural antisense transcript; ncRNA, non-coding RNA; RNA-seq, RNA sequencing; SBS, sequencing by synthesis
Abbreviations used in Table 2: AFGC, Arabidopsis Functional Genomics Consortium; JGI, Joint Genome Institue; lncRNA, long non-coding RNA; NAT, natural antisense transcript; ncRNA, non-coding RNA; RBP, RNA binding protein
Summary
Studies in the recent past have highlighted the pervasive nature of eukaryotic transcription and, have strongly emphasized on the complexity involved in the expression of eukaryotic genomes [1]. Like protein-coding messenger RNAs (mRNAs), the majority of lncRNAs in eukaryotes are transcribed by RNA polymerase II. These are regarded as stable “typical” or classic lncRNAs [12]. Unlike the mRNAs, lncRNAs are primarily located within the nucleus [18] These are generally found in very low quantity and in specific patterns in various tissue types [19]. Based on the reference annotation from the ENCODE (ENCyclopedia Of DNA Elements) project, GENCODE v7 (a project that has generated reference gene annotation and experimental confirmation for human and mouse genomes) introduced 12 biotypes of lncRNAs, which have been compiled in different databases for human lncRNAs and are mainly used to filter human lncRNA transcripts [22,23]
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