TAS-seq: Subcellular RNA secondary structure profiling by signal peptide-assisted adenosine deamination
RNA structure critically facilitates RNA function and regulation across a range of biological processes. Recent developments have led to a diversity of structure profiling technologies.  Nonetheless, these methods are challenged to profile RNA structure at the resolution of the subcellular compartment. Here, we present TadA-8e-assisted subcellular RNA secondary structure sequencing (TAS-seq), a deaminase-assisted sequencing technology that probes adenosine in single-strand RNA, especially the loop of hairpin structure, and labels it with A-to-G base substitution. By anchoring TadA-8e to nuclear or cytoplasm with signal peptides, TAS-seq profiled the secondary RNA structure of transcriptome localized in these two subcellular compartments respectively. Together, our data revealed that while the majority of the RNA structures remain stable, certain RNAs are subject to conformational change as transit from the nucleus to the cytoplasm, revealing the structural regulation of RNA. Overall design: To profile subcellular RNA structure, we expressed adenosine deaminase TadA-8e in human cells. TadA-8e is anchored into two subcellular compartments, nuclear and cytoplasm, by signal peptide NLS and NES, separately. Then the poly(A) RNAs and total RNAs were extracted and sequenced, separately. Adenosines in specific RNA structure were modified by TadA-8E resulting into A-to-G substitution in high-throughput data.