Genome-Wide Mapping of RNA-Protein Associations via Sequencing

To identify RNA-binding proteins and their associated RNA-protein associations at transcriptomic scale by sequencing PRIM-seq starts with the SMART-display technology that labels tens of thousands of proteins with each protein’s own mRNA to generate a library of RNA-labeled proteins (Johnson et al. 2021). SMART-display extracts total human mRNAs from input cells, appends a linker to the 3’ ends of these mRNAs, and translates the mRNAs to yield proteins that are covalently linked with the mRNAs (mRNA-linker-protein). The second module, termed REILIS (Reverse transcription, Incubation, Ligation, and Sequencing), enables RNA-protein association by incubating the library of labeled proteins with an RNA library. The associated protein-RNA pairs are then recorded by co-sequencing the protein’s labels and the associated RNAs through paired-end sequencing.