Engreitz, J.M. et al. Cell 159, 188–199 (2014).

RNA has evolved to play many roles in the cell, and RNA antisense purification (RAP) has been used to probe its interactions with DNA. Engreitz et al. now perform a combination of in vivo cross-linking, pulldown with biotinylated antisense oligonucleotides and RNA sequencing to map intermolecular RNA interactions in a method they call RAP-RNA. The method uses a psoralen cross-linker to capture only direct RNA-RNA interactions, formaldehyde to capture indirect RNA-RNA interactions via protein intermediates, or a combination of formaldehyde and the strong protein cross-linker disuccinimidyl glutarate to capture very indirect interactions. High-resolution maps of interactions at cross-link sites indicated that U1 small nuclear RNA, a spliceosome factor, binds new transcripts at 5′ splice-site motifs and that the RNA Malat1, found in nuclear speckles, binds to mRNA via RNA-binding proteins.