RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages

Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including Dhx30 and Llph, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed that RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts. [Display omitted] •Tag-free method to enrich ribosomes and associated proteins from any sample•Dhx30 and Elavl2 are embryonic forebrain ribosome-associated proteins (RAPs)•The RAP Llph may be important for neural development and translation of long mRNAs•Macrophages exhibit ribosome composition changes upon different stimuli Susanto et al. developed a tag-free method to characterize ribosome-associated proteins from any sample. They identified hundreds of candidate ribosome-associated proteins, some of which were dynamic across embryonic tissues or during responses to cell stimuli. These included proteins that may be important for neural development or during immune activation.