biostudies-literatureSusanto TTNICHD NIH HHSNHLBI NIH HHSNIMH NIH HHSNCI NIH HHSNIH3545-3563.e25https://www.ebi.ac.uk/biostudies/studies/S-EPMC11460945biostudies-literatureUnknown84(18)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 characteriMolecular cellRAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages.PMC11460945R35 CA242986R01 HD105731K38 HL165490R01 HD086634R21 MH130323R38 HL143581Susanto TTFromm LFujii KYoo YBarna MKerr CHOses-Prieto JALevine AGBurlingame ALZhang ZLantz TCWernig MChen YHung VRuggero DfalseRAPIDASH: 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 characteri2024-01-01T00:00:00Z2024 Sep2026-06-02T09:39:01.946Z2026-05-26T03:06:40.511ZS-EPMC114609453926036710.1016/j.molcel.2024.08.023