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Some evidence supports that condensates can modulate RNA folding, but measuring RNA structure within native condensates remains an unsolved challenge. Here we introduce RAID-MaP, a strategy that combines APEX proximity labeling with dimethyl sulfate (DMS) chemical probing to measure RNA structure within defined subcellular compartments. We applied RAID-MaP to resolve late stages of ribosomal RNA (rRNA) folding within the granular component (GC) of the nucleolus, revealing that both the 18S and 28S rRNAs feature widespread differences in structure compared to assembled ribosomes consistent with ongoing folding of both secondary and tertiary structure. We further combined RAID-MaP with transcription inhibition to resolve kinetics of rRNA maturation. The maturation kinetics of both subunits progressed on comparable timescales but with characteristic domain-level ordering, with late GC-resident intermediates often becoming more protected than mature ribosomes suggestive of stabilization by nucleolar accessory factors. Perturbing this 28S assembly pathway using antisense oligonucleotides produces distinct nucleolar phenotypes depending on whether early versus late folding domains are disrupted, demonstrating a direct link between rRNA folding and phase separation. We additionally applied RAID-MaP to discover that the 7SK small nuclear RNA undergoes spatially regulated structural switching consistent with localized release of the transcription factor P-TEFb at sites of active transcription. Together, our results establish subcellular spatial control of RNA structure as a new dimension of RNA regulation.<\/jats:p>","DOI":"10.64898\/2026.05.21.726738","type":"posted-content","created":{"date-parts":[[2026,5,23]],"date-time":"2026-05-23T05:25:17Z","timestamp":1779513917000},"source":"Crossref","is-referenced-by-count":1,"title":["Mapping RNA structure assembly and remodeling in biomolecular condensates"],"prefix":"10.64898","author":[{"given":"Ritwika","family":"Bose","sequence":"first","affiliation":[{"name":"Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX"},{"name":"Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik W.","family":"Bergstrom","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sovanny R.","family":"Taylor","sequence":"additional","affiliation":[{"name":"Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Boeynaems","sequence":"additional","affiliation":[{"name":"Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX"},{"name":"Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, TX, USA"},{"name":"Center for Alzheimer\u2019s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX, USA"},{"name":"Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua A.","family":"Riback","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Furqan M.","family":"Fazal","sequence":"additional","affiliation":[{"name":"Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX"},{"name":"Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9346-1559","authenticated-orcid":false,"given":"Anthony M.","family":"Mustoe","sequence":"additional","affiliation":[{"name":"Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX"},{"name":"Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026052609350746000_2026.05.21.726738v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2019.05.027"},{"key":"2026052609350746000_2026.05.21.726738v1.2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad249"},{"key":"2026052609350746000_2026.05.21.726738v1.3","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.chembiol.2023.12.010","article-title":"Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states","volume":"31","year":"2024","journal-title":"Cell Chem. 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