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.

Identification and characterization of long non-coding RNAs in porcine granulosa cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin

“…Previously, ncRNAs were considered as evolutionary junk or transcriptional noise, but recently they were reported to play a crucial role in the regulation of gene expression [ 1 , 2 ]. The class of ncRNAs includes short ncRNAs (e.g., microRNA, piwiRNA), housekeeping ncRNAs (e.g., ribosomal RNA, transfer RNA) as well as long non-coding RNAs (lncRNAs), which constitute the largest group of ncRNAs [ 3 , 4 ]. In broad terms, lncRNAs are defined as non-coding transcripts longer than 200 nucleotides (nt).…”

realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)

“…Gene families, especially transcription factor families, control various physiological processes and are breeding targets ( 17–27 ). miRNAs have been extensively studied in land plants and green algae ( 12 , 28 , 29 ). However, little is known about its function and evolutionary trajectory in red algae.…”

“…To meet the ever-rapid increasing amounts of genomic and transcriptome data and their tremendous potential in understanding developmental process ( 12 ) and to assist molecular breeding, we build an online, searchable platform for integrating the ome data with the use of multiple omics tools. The Information gained will be a valuable to boost the understanding red algae genomes and the evolution of plant genomes.…”

LncRNAs: genetic and epigenetic effects in plants

“…In plants, lncRNAs are involved in diverse biological processes such as phosphate homeostasis, flowering, photomorphogenesis, stress response [20] and fertility [21]. As previously reviewed in greater detail [20], they also play important roles to: (1) process into shorter ncRNAs [22], (2) act as decoys for the target mimics of miRNAs [23,24], (3) repress histone modifying activities and direct epigenetic silencing through interaction with specific chromatin domains [25][26][27][28], (4) function as molecular cargo for protein re-localization [29,30] and (5) regulate of post-translational processes via protein modifications and protein-protein interactions [31].…”