Ribo-Tweezer: Rapid removal of ribosomal proteins reveals additional layers of post-transcriptional gene regulation

The ribosome is a ribozyme, but it also acts as a dynamic regulator of gene expression. Although ribosomal protein (RP) composition varies, dissecting the functional contributions of individual RPs beyond their housekeeping roles is challenging because of the lack of tools for manipulation in situ . Here, we developed Ribo-Tweezer, a degron-based system directly tethered to mature ribosomes that enables rapid, reversible, and selective depletion of specific RPs. Using Ribo-Tweezer in mouse embryonic stem cells (mESC), we find a previously uncharacterized role for RACK1 in stem cell fate control via translational regulation of zinc-finger transcriptional networks and long interspersed nuclear element-1 (LINE1) expression. This translation-transcription coupling provides a mechanism by which translation control is further amplified in gene regulation. Distinct translational programs induced by RPLP0 and RPLP1 depletion further demonstrate RP-specific regulatory functions in translation. Together, these findings establish Ribo-Tweezer as a powerful platform that has illuminated selective functions for RPs in gene regulation, which gives biological meaning to ribosome heterogeneity.