GoldCLIP-seq analysis of RPL22HaloTag and RPL22L1HaloTag RNA-binding

Ribosome biosynthesis is essential for cancer growth and proliferation. This dependency is therapeutically exploitable by blocking the rate-limiting step, RNA polymerase I (Pol I) transcription. Here we investigated the ability of RPL22 and RPL22L1 to interact with cellular RNAs. We discovered that Pol I inhibition prominently altered splicing of hundreds of mRNAs. RPL22 and RPL22L1 resided at splice junctions and interacted with hundreds of coding and non-coding RNAs in addition to the 28S rRNA. Further, their genetic manipulation prominently altered the splicing of a multitude of mRNAs. We generated RPL22-HaloTag and RPL22L1-HaloTag HCT116 cells. We conducted RNA-pulldowns using GoldCLIP-RNA sequencing.