GEOGenomicsHomo sapiensNon-coding RNA profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288266GEOGSEfalseQuantitative profiling of RNA modifications enriched in non-membrane bound cellular structures using APEX-RNA-MSThe dynamic behavior of RNA underlies fundamental biological processes. RNA function is controlled by post-transcriptional modifications that are spatiotemporally regulated, but characterizing the distribution of modified RNA transcripts with subcellular resolution is a major challenge. Here we present APEX-RNA-MS, which combines APEX2 proximity labeling with LC-MS quantification of modified ribonucleotides. We use APEX-RNA-MS to characterize RNA modifications proximal to RNA-binding proteins enriched in non-membrane bound cellular structures. We measure changes in protein-proximal RNA modification levels upon induction of DNA damage foci and stress granules, consistent with previous studies using antibody-based imaging and biochemical fractionation. Further, we show that tRNA-specific modifications are proximal to G3BP1 and use RNA sequencing and RNA FISH to demonstrate the accumulation of multiple tRNAs in stress granules. Taken together, our work provides a general approach for characterizing the subcellular distribution of RNA modifications and reveals new insights into the composition and function of cellular condensates.2026/05/12GSE288266GSM8762529GSM8762530GSM8762531GSM8762532GSM8762533GSM8762534GSM8762535GSM876253624676288266Homo sapiens