Keeping UTRs in Their Place: Clarifying Transcript-Genomic Boundaries

Untranslated regions (UTRs) are defining features of mature messenger RNAs (mRNAs), yet a brief, non-exhaustive survey of recent literature reveals numerous instances of conceptually significant conflation between transcript-defined UTRs and genomic DNA segments. Because UTRs arise only after transcription initiation, RNA processing, and transcript maturation, applying UTR terminology directly to promoter-proximal or downstream flanking regions of a protein-coding gene obscures the fundamental distinction between genomic coordinates and the RNA molecules they encode. In this Viewpoint, we highlight this recurring conceptual drift and use the well-characterized Arabidopsis thaliana PHOSPHATE2 (PHO2) locus to illustrate how transcript, cDNA, and genomic representations differ and why they must not be interchanged. Representative examples from plant biology and related fields suggest that this misapplication has spread across otherwise credible studies and is now appearing in the secondary literature. Although such errors rarely alter empirical conclusions, they undermine terminological clarity, complicate genome annotation and figure labeling, and hinder the training of early-career researchers. Reinforcing the transcript-specific definition of UTRs is therefore essential for maintaining precision and coherence in scientific communication.