Editorial: Epigenetics, transcriptomics and epitranscriptomic – deal with old friends or new direction of regulation?

Abstract

Gene regulation in plants is orchestrated through a multilayered network of molecular mechanisms encompassing chromatin organization, transcriptional control, RNA processing, RNA modification, and other processes. Epigenetics and transcriptomics have long provided foundational frameworks for understanding how gene expression is established and maintained. In recent years, however, increasing attention has been directed toward epitranscriptomic regulation, revealing an additional layer of control that substantially expand the regulatory landscape. This Research Topic, Epigenetics, Transcriptomics, and Epitranscriptomic-Deal With Old Friends or New Direction of Regulation, was conceived to explore how these regulatory dimensions operate independently and in concert, and to assess whether emerging RNA-centered mechanisms represent extensions of established paradigms or mark a genuine shift in our understanding of plant gene regulation. The six articles brought together in this Topic span diverse biological contexts, including development, stress adaptation, disease resistance, and RNA metabolism, and encompass a range of experimental and analytical approaches. Collectively, they underscore a central theme: gene regulation in plants is inherently integrative, with epigenetic, transcriptional, and epitranscriptional processes forming interconnected regulatory networks rather than functioning as isolated layers. Several contributions highlight the power of transcriptome-wide analyses in resolving complex regulatory processes. Genome-wide identification and expression profiling of the CesA/Csl gene family in Eucalyptus grandis provide a comprehensive view of transcriptional regulation underlying cell wall biosynthesis and secondary wall formation in a woody species. By integrating phylogenetic relationships, promoter cis-element analysis, and tissue-specific expression patterns, this study illustrates how transcriptional networks coordinate structural growth and stress-associated functions in long-lived plants ([An et al.]()).