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Review
. 2017 Jul 5:4:17031.
doi: 10.1038/hortres.2017.31. eCollection 2017.

New technologies accelerate the exploration of non-coding RNAs in horticultural plants

Degao Liu  1 , Ritesh Mewalal  1 , Rongbin Hu  1 , Gerald A Tuskan  1 , Xiaohan Yang  1
Affiliations
Review

New technologies accelerate the exploration of non-coding RNAs in horticultural plants

Degao Liu et al. Hortic Res. .

Abstract

Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Classification of plant non-coding RNAs (ncRNAs). circRNAs, circular ncRNAs; UTR, untranslated region; rRNAs, ribosomal RNAs; tRNAs, transfer RNAs; snoRNAs, small nucleolar RNAs; sRNAs, small RNAs; lncRNAs, long ncRNAs; miRNAs, microRNAs; siRNAs, small interfering RNAs; hc-siRNAs, heterochromatic siRNAs; NAT-siRNAs, natural antisense transcript siRNAs.
Figure 2
Figure 2
A pipeline for discovery of non-coding RNAs (ncRNAs) in plants. rRNAs, ribosomal RNAs; NGS, next-generation sequencing; CIRI, circular RNA identifier; circRNAs, circular ncRNAs; CPC, coding potential calculator; HMM, hidden markov models.
Figure 3
Figure 3
A pipeline for functional characterization of ncRNAs in plants. SHAPE, RNA-selective 2′-hydroxyl acylation and primer extension; PARS, parallel analysis of RNA structure; DMS-seq, dimethyl sulfate-modified RNA for sequencing; CHIRP, chromatin isolation by RNA purification; CHART, capture hybridization analysis of RNA targets, CLASH, crosslinking, ligation, sequencing of hybrids; CLIP, crosslinking immunoprecipitation.
See this image and copyright information in PMC

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