Eukaryotic genomes undergo pervasive genome-wide transcription, generating an enormous and diverse repertoire of RNA molecules. In plants, these RNAs are anything but silent players—they actively govern growth, development, and how crops respond to heat, drought, and other environmental stresses. The activities of these RNAs are determined not only by their nucleotide sequences but are also shaped by multiple regulatory layers—including processing, turnover, chemical modifications, and three-dimensional folding—each contributing critically to how the plant ultimately looks and performs. Over the past decade, the rapid advancement of cutting-edge technologies such as high-throughput sequencing, single-molecule sequencing, and precise genome editing has greatly propelled the progress of plant RNA biology research and substantially deepened our understanding of RNA regulatory mechanisms and functional networks. Meanwhile, the research paradigm of plant RNA biology has gradually broken through traditional limitations, expanding from foundational studies centered on the model plant Arabidopsis thaliana to a wide range of vital crops including rice, maize, and wheat. In-depth dissection of the sophisticated and intricate RNA regulatory networks in plants not only improves the fundamental theoretical framework of plant molecular biology but also provides critical theoretical basis and genetic resources for crop genetic improvement, including stress-resistant breeding, quality enhancement, and yield promotion, possessing great value for both basic research and agricultural application.
Against this backdrop, a landmark comprehensive review was recently published online in SCIENCE CHINA Life Sciences . This review is jointly authored by 16 leading experts in the field, including Professor Yijun Qi from Tsinghua University, Professor Yueqin Chen from Sun Yat-sen University, Professor Hongwei Guo and Professor Jixian Zhai from Southern University of Science and Technology, Researcher Huishan Guo from Institute of Microbiology, Chinese Academy of Sciences (CAS), Researcher Runlai Hang from Inner Mongolia University, Professor Guifang Jia and Researcher Danmeng Zhu from Peking University, Professor Beixin Mo from Shenzhen University, Professor Zhen Wang from Qingdao Agricultural University, Professor Liang Wu from Zhejiang University, Professor Yiji Xia from The Chinese University of Hong Kong, Shenzhen, Researcher Xiaofei Yang from CAS Center for Excellence in Molecular Plant Sciences, Professor Binglian Zheng from Fudan University, and Professor Xiaofeng Cao from Institute of Genetics and Developmental Biology, CAS. This review systematically delineates the biological functions and regulatory mechanisms of diverse plant RNAs, along with their structural features and chemical modification patterns, and further discusses their translational potential for the improvement of crop agronomic traits. It highlights the latest research breakthroughs in hot research areas such as non-coding RNAs, RNA epigenetic regulation, and RNA chemical modifications, and provides a forward-looking perspective on the future research directions and development trends of plant RNA biology.
Systematically covering the core research fields of plant RNA biology, this review is structured into eight progressive modules that elaborately illustrate the regulatory mechanisms and agricultural application potential of plant RNAs in a stepwise manner. The first section traces the life cycle of mRNA—from its birth through splicing and 3′ end formation to its eventual degradation. The authors highlight alternative splicing, particularly intron retention, and 3′ end processing as key mechanisms that shape transcriptome diversity in plants. They also discuss the 5′→3′ and 3′→5′ decay pathways that precisely regulate transcript stability, and detail the sophisticated quality control systems—including nonsense-mediated decay (NMD), no-go decay (NGD), and nonstop decay (NSD)—that eliminate aberrant transcripts and safeguard protein synthesis. The second section redefines the biological functions of classical housekeeping non-coding RNAs including rRNAs, tRNAs, snoRNAs and snRNAs. Breaking the traditional view that these RNAs merely participate in translation and splicing, the review confirms that they can respond to environmental signals, generate functional small RNAs, and participate in plant developmental regulation, stress adaptation, chromatin remodeling and gene silencing. The third section focuses on plant small RNAs (sRNAs), elucidating the biogenesis pathways and action modes of miRNAs and various siRNAs. It reveals that these sRNAs regulate plant growth, development and stress responses via target cleavage, translational repression, DNA methylation modification and other mechanisms, and identifies the non-cell-autonomous movement and cross-kingdom transport of sRNAs as core links connecting plant developmental regulation and stress adaptation. The fourth section summarizes the multifaceted regulatory mechanisms of long non-coding RNAs (lncRNAs), overturning the early perception of lncRNAs as transcriptional noise. It concludes that lncRNAs participate in plant flowering, reproduction, root development and stress responses through multiple regulatory strategies, including recruiting chromatin modification complexes, sequestering miRNAs, modulating protein activity, and encoding functional small peptides, establishing their pivotal status in plant regulatory networks. The fifth section centers on RNA higher-order structures. It introduces cutting-edge in vivo RNA structural profiling technologies, uncovers the biological functions of RNA secondary structures in RNA splicing, translational regulation and temperature sensing, and illustrates the vital value of TPP riboswitches and sequence variation-mediated RNA structural remodeling (ribosnitches) in the regulation of crop agronomic traits. The sixth section focuses on the emerging field of RNA modifications. It systematically summarizes non-canonical cap structures (e.g., m⁷G, NAD) and internal RNA modifications (e.g., m⁶A, m⁵C, ac⁴C), elaborating the writer, eraser and reader protein systems that mediate the installation, removal and recognition of these modifications. It further reveals that RNA modifications serve as a crucial post-transcriptional regulatory layer that extensively modulates plant development, immunity and stress responses. The seventh section focuses on agricultural application scenarios and summarizes the translational value of RNA regulation in crop genetic improvement. Artificial modification of miRNAs and lncRNAs can effectively enhance crop yield, stress tolerance and nutrient use efficiency. Furthermore, RNA interference (RNAi) technologies, including spray-induced gene silencing (SIGS), microbe-induced gene silencing (MIGS) and cross-kingdom RNAi mechanisms, provide innovative and eco-friendly strategies for green prevention and control of crop diseases and pests, overcoming the limitations of traditional chemical control methods. The eighth section prospects the future research directions and core challenges of plant RNA biology. It proposes the necessity of in-depth dissection of the synergistic mechanisms among diverse RNA regulatory pathways and advancement of single-cell-level research on RNA dynamics. It also points out that ncRNA editing, RNA synthetic biology, novel RNAi technologies and multi-tool combined gene editing systems will provide brand-new technical support for precision plant breeding and the development of green and sustainable agriculture.
Overall, this review comprehensively and systematically elucidates the regulatory mechanisms of plant life activities mediated by multiple types of RNAs, bridging the gap between fundamental theoretical research on plant RNAs and practical agricultural applications. It provides important theoretical references and frontier directions for further deciphering plant RNA regulatory networks, addressing food security issues, and promoting the high-quality development of sustainable agriculture. In-depth exploration of the sophisticated and intricate RNA regulatory networks in plants not only improves the theoretical system of plant molecular biology but also supplies vital theoretical basis and genetic resources for crop genetic improvement, including stress resistance breeding, quality optimization and yield enhancement, thereby possessing profound scientific significance for fundamental research and broad application prospects in modern agriculture.
Science China Life Sciences
Systematic review