Transcriptome-wide DMS-MaPseq reveals structured elements and pervasive RNA structural rearrangements under cellular stress

RNA structure is central to post-transcriptional gene regulation, influencing RNA stability, translation, and interactions with RNA-binding proteins (RBPs). However, capturing RNA structure at scale remains technically challenging. Here we introduce DMS-TRAM-seq (dimethyl sulfate transcriptome-wide RNA accessibility mutational profiling by sequencing), a transcriptome-wide chemical probing method enabling RNA secondary structure prediction across over 9000 transcripts, made available through a free online database. . This high coverage also enabled the development of several novel analysis tools, including the identification of over 700 structured elements throughout the human transcriptome. Additionally, we identified specific RNA regions undergoing conformational changes in response to a cellular perturbation, using oxidative stress as an example, including changes resulting from translation inhibition and stress granule incorporation. Integrating these data with RBP binding sites further allowed the identification of perturbed RBP-RNA interactions at scale, without the need for additional experiments. DMS-TRAM-seq provides unprecedented insights into RNA conformations, opening new avenues for investigating post-transcriptional regulatory mechanisms in cellular adaptation and disease.