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

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.

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

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

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.