RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure

RAD-seq, using TadA8.20-mediated adenosine deamination, maps transcriptome-wide RNA accessibility in vivo and yields high-resolution RBP footprints plus structural signatures.

• Why it matters: RNA regulation depends on RNA folding and RBP occupancy, but existing assays separately measure structure or binding and struggle to capture their combined, dynamic effects.
• What they did: RAD-seq reports local adenosine exposure by integrating base pairing, RNA folding, and RBP occupancy in one experiment, then combines it with RNA Bind-n-Seq motifs and an unsupervised model with motif priors.
• The result: RAD-seq recapitulates known structural signatures, detects RBP footprints, tracks remodeling during oxidative and heat-shock stress, and links EIF4A3 knockdown to local enrichment of TRA2A near m6A-related motifs.

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