Proteomics and RNA-seq of RIBOTAC treatment in MDA-MB-231 cells

C1-RIBOTAC is a small molecule RNA degrader developed in our lab that selectively binds to human pre-miR-155 in cells and recruits RnaseL to degrade the transcript. Some RNA-binding compounds were expected to elicit a biological response as they bind functional sites, but most binders would not be expected to affect biological function. In these latter cases, an alternative way to modulate RNA biology is by cleaving the target via a ribonuclease targeting chimera, where an RNA-binding molecule is appended to a heterocycle that binds and locally activates RNase L. Overlay of the substrate specificity for RNase L with the binding landscape of small molecules in this study revealed many favorable candidate binders that are inactive but could be potently bioactive when converted into a degrader. We provide proof-of-concept by design of a degrader of the precursor to disease-associated microRNA-155 (pre-miR-155) in multiple cell lines and disease settings. These studies illustrate that small molecule RNA-targeted degradation can be leveraged to convert avid, yet inactive, binding interactions into potent and specific modulators of RNA function. The uploaded datasets include global proteomics and total RNA-seq studies to evaluate the effect on C1-RIBOTAC on the proteome and transcriptome of MDA-MB-231 cells.