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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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http://dx.doi.org/10.1038/hortres.2017.31 | DOI Listing |
Plant Genome
September 2025
Donald Danforth Plant Science Center, Saint Louis, Missouri, USA.
PhasiRNAs (phased small interfering RNAs) are a major class of plant small RNAs (sRNA) known to be key regulators in male reproductive development of maize (Zea mays) and rice (Oryza sativa), among other plants. Earlier research focused primarily on premeiotic 21-nucleotide (nt) phasiRNAs and meiotic 24-nt phasiRNAs, while new studies uncovered a premeiotic class of 24-nt phasiRNAs. The biogenesis and function of these phasiRNAs remain unclear.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
September 2025
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China.
As global climate change exacerbates extreme heat events, the interplay between heat stress and blast disease resistance in rice remains poorly understood. In this study, through integrated transcriptome profiling and systematic phenotyping of mutants in several thermosensory pathways, we identified HsfA1 as a positive regulator of heat priming-enhanced blast resistance in rice. Systematic analysis of microRNA (miRNA) dynamics, bioinformatics prediction, and RNA pull-down experiments revealed that , a temperature-responsive miRNA, directly suppresses the expression of by targeting the second exon of messenger RNA (mRNA).
View Article and Find Full Text PDFJ Biosci
September 2025
Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, India.
Plants, being sessile organisms, are continually exposed to diverse combinations of biotic and abiotic stresses in their natural habitats. Combined stresses are considered significant threats to plants, particularly in the context of today's climate change. Despite the vast amount of data generated by OMICS experiments, information remains widely dispersed and inaccessible within the literature.
View Article and Find Full Text PDFPLoS Genet
September 2025
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
The plant life cycle progresses through distinct phases defined by the morphology of the organs formed on the shoot. In Arabidopsis, age-dependent reduction in the related microRNAs miR156 and miR157 controls transitions from juvenile to adult vegetative phase and from adult to reproductive phase. However, whether these miRNA isoforms have specific contributions remains unclear.
View Article and Find Full Text PDFAdv Exp Med Biol
August 2025
Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori Prefecture, Japan.
Circular RNAs (circRNAs) have been attracting attention as biomarkers of various diseases, including cancer, because, as non-coding RNA (ncRNA)/protein sponges, they regulate gene expression and can be detected in various body fluids. Several comprehensive databases have been published to allow easy identification of target circRNAs.In all, 43 circRNA-related databases have been established and are listed in Database Commons since the development of the first comprehensive database of circRNAs, Circ2Traits, in 2013.
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