Transcriptome-wide RNA accessibility mapping reveals structured RNA elements and pervasive conformational rearrangements under stress

Abstract

RNA structure plays a central role in post-transcriptional gene regulation, modulating RNA stability, translation, and interactions with RNA-binding proteins (RBPs). However, capturing RNA conformations at scale remains challenging. Here, we introduce DMS-TRAM-seq (Dimethyl Sulfate-Transcriptome-wide RNA Accessibility Mapping by sequencing), which probes RNA structure across nearly the entire transcriptome. Using DMS-TRAM-seq, we generated secondary structure predictions for over 9,000 human transcripts, including hundreds of non-coding RNAs, and identified more than 700 previously unannotated, high-confidence structured elements. Importantly, the enhanced coverage provided by DMS-TRAM-seq enabled comparative analyses, revealing RNAs that undergo structural rearrangements in response to cellular perturbations. Integration with RBP motifs and ribosome profiling uncovered altered RNA-RBP interactions during oxidative stress and showed that translation inhibition broadly drives RNAs toward their thermodynamically favored conformations. DMS-TRAM-seq enables interrogation of the RNA structurome and its plasticity at an unprecedented scale, opening new directions for elucidating the structural basis of RNA regulation.