Long Noncoding RNAs in Plants
The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lnc
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Long Noncoding RNAs in Plants Hsiao-Lin V. Wang and Julia A. Chekanova
Abstract The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lncRNAs can function in both nuclear and cytoplasmic compartments. Emerging work has found that many lncRNAs regulate gene expression and can affect genome stability and nuclear domain organization both in plant and in the animal kingdom. Here, we describe the major plant lncRNAs and how they act, with a focus on research in Arabidopsis thaliana and our emerging understanding of lncRNA functions in serving as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA- directed DNA methylation, and in epigenetic regulation of flowering time. Keywords Plant lncRNAs • Noncoding RNAs • Epigenetics • Exosome • FLC • Transcriptional regulation
5.1 Introduction In eukaryotes, transcriptome studies showed that >90% of the genome is transcribed and a myriad of transcripts corresponds to noncoding RNAs (ncRNAs) [1, 2], including long ncRNAs (lncRNAs), which are classically >200 nt long and have no discernable coding potential [3–5]. Plant genomes produce tens of thousands of lncRNAs from intergenic, intronic, or coding regions. RNA Pol II transcribes most lncRNAs (from the sense or antisense strands); plants also have Pol IV and Pol V, the two plant-specific RNA polymerases that can produce lncRNAs [6, 7]. Majority of described up-to-date plant lncRNAs are polyadenylated, while in yeast and mammals, there are many non-polyadenylated lncRNAs as well [8]. However, there are
H.-L.V. Wang • J.A. Chekanova (*) School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA e-mail: [email protected] © Springer Nature Singapore Pte Ltd. 2017 M.R.S. Rao (ed.), Long Non Coding RNA Biology, Advances in Experimental Medicine and Biology 1008, DOI 10.1007/978-981-10-5203-3_5
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several well-studied important functional non-polyadenylated lncRNAs [9–11]; and the recent work in Arabidopsis found that abiotic stress induced the production of hundreds of non-polyadenylated lncRNAs [12–14]. Most lncRNAs can be broadly classified based on their relationships to protein- coding genes: (1) long intergenic ncRNAs (lincRNAs) (Fig. 5.1A); (2) lncRNAs produced from introns (incRNAs), which can be transcribed in any orientation relative to coding genes (Fig. 5.1B); and (3) antisense RNAs and natural antisense transcripts (NATs), which are transcribed from the antisense strand of genes (Fig. 5.1C and D) [15]. Various types of lncRNAs are also transcribed near transcription start sites (TSSs) and transcription termination sites (TTSs) or from enhancer regions (eRNAs) (Fig. 5.1G) and splice sites. For example, yeast produces cryptic unstable transcripts (CUTs) and stable unannotated transcripts
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