ChemCLIP-seq method for transcriptome-wide mapping of small molecule RNA binding sites in cells

Herein, we discovered small molecules that bind cellular RNAs and precisely defined the binding site within most enriched targets in unbiased fashion. The interactions between cellular RNAs in MDA-MB-231 triple negative breast cancer cells and a panel of small molecules appended with a diazirine cross-linking moiety and an alkyne tag were probed transcriptome-wide. The alkyne tag allows for facile pull-down of cellular RNAs bound by each small molecule, and the enrichment of each RNA target defines the compound’s molecular footprint. Of the 34 chemically diverse small molecules studied, six bind and enrich cellular RNAs. Inter-estingly, modeling the structure of their RNA targets revealed that compounds bind to both highly structured regions as well as sites with no easily discernable structure. This is a supplemental dataset for our manuscript describing more in details about our method.