Noncanonical caps, m⁶A, and Ψ RNA modifications in plant and animal development

RNA modifications constitute a dynamic layer of gene regulation during development. Among them, noncanonical caps, N⁶-methyladenosine (m⁶A), and pseudouridine (Ψ) represent three major classes of chemical marks. Noncanonical caps diversify the 5' end of RNA, whereas m⁶A and Ψ act as internal modifications that modulate RNA structure and RNA-protein interactions. Through these molecular effects, noncanonical caps, m⁶A, and Ψ influence RNA processing, localization, and function, thereby governing RNA fate in response to developmental and environmental cues. Advances in detection, quantification, and transcriptome-wide profiling have greatly expanded our understanding of these modifications, while revealing important technical challenges. In this review, we discuss how these three major RNA modifications regulate developmental programs in plants and animals, with emphasis on their molecular mechanisms and biological functions. We further highlight their potential relevance for therapeutic strategies in human diseases and agricultural approaches for crop improvement under climate change.