Integrating transcriptomics, epitranscriptomics, and spatial transcriptomics to decode plant regulatory complexity

Plant molecular biology is entering a new era of transcriptomic precision. Over the past decade, the progression from bulk RNA sequencing to single-cell and spatial transcriptomics has profoundly changed how researchers map gene activity and regulation. Beyond traditional measures of transcript abundance, the discovery of epitranscriptomic mechanisms, chemical modifications such as m⁶A, m⁵C, and pseudouridylation, has revealed new layers of post-transcriptional control that modulate RNA stability, translation, and splicing. Together, these techniques offer multidimensional insights into how individual cell types and tissues orchestrate complex physiological and developmental programs. While transcriptomics has long illuminated what genes are expressed, the integration of epitranscriptomic and spatial data now enables investigations into how and where transcripts function, providing fine-scale views of regulatory logic in plant adaptation, growth, and stress response.This Research Topic aims to bring together researchers advancing the study of plant gene expression through RNA chemistry and spatial biology. The goal is to unify transcriptome-wide and spatially defined analyses to understand how RNA modifications, localization, and molecular interactions translate into physiological outcomes. It invites contributions that examine the interplay between RNA modification dynamics, tissue architecture, and regulatory networks driving responses to environmental change, development, and evolution. By combining molecular and computational approaches, the collection seeks to reveal how chemical and spatial modulation of RNA integrates into the broader systems biology of plants.• To gather further insights into RNA regulation and spatial organization in plant biology, we welcome articles addressing, but not limited to, the following themes:• RNA modification dynamics (m⁶A, m⁵C, A-to-I editing) and their functional roles in plant development and stress response• Spatially resolved transcriptome profiling in plant tissues and organs• Integration of single-cell, epitranscriptomic, and spatial multi‑omics data in crops and model species• Computational pipelines, machine learning, and visualization tools for plant RNA modification and spatial mapping• Regulatory networks connecting RNA‑level modifications to downstream physiology and developmental outcomes• Comparative and evolutionary perspectives on transcriptomic and epitranscriptomic regulation across plant lineagesWe welcome Original Research, Review, Mini Review, Methods, and Perspective articles. Studies encompassing both model species (e.g., Arabidopsis thaliana) and agronomically relevant crops are particularly encouraged. Topic editors: APOORV TIWARI, Bin Zhang, Marcos Fernando Basso, Matteo Buti Source: https://www.frontiersin.org/research-topics/83520/integrating-transcriptomics-epitranscriptomics-and-spatial-transcriptomics-to-decode-plant-regulatory-complexity