{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T14:06:21Z","timestamp":1789653981688,"version":"4.0.0"},"posted":{"date-parts":[[2026,9,13]]},"group-title":"Molecular Biology","reference-count":77,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,13]],"date-time":"2026-09-13T00:00:00Z","timestamp":1789257600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Pre-mRNA secondary structure can modulate the regulatory function of intronic sequences by masking or exposing splice-site signals and altering the accessibility of other features. Yet experimentally supported structural models for human pre-mRNAs have been largely restricted to splice-site-proximal sequences, leaving the deep intronic regions where \u223c70% of intronic disease-causing variants reside almost entirely unmapped. We developed RADIS (Reactivity Analysis of Deep and Intergenic RNA Structure), a strategy that yields strand-resolved chemical probing reactivity profiles across entire intron-rich loci by creating tiled arrays of RNAs that comprehensively span long genomic distances. This approach removes the abundance and locus-specificity constraints that otherwise limit pre-mRNA probing approaches. RADIS recovers known\n                  <jats:italic>E. coli<\/jats:italic>\n                  ribosomal RNA architectures and yields high-correlation with in-cell dimethyl sulfate (DMS)-MaP reactivities at representative splice sites (\n                  <jats:italic>r<\/jats:italic>\n                  = 0.87\u20130.90). RADIS-constrained folding of 109 5\u2032 and 88 3\u2032 splice sites uncovers an inverse relationship between base-pairing within the spliceosome footprint and splice-site strength, and partitions 81 branchpoints into three structural classes. Across 233 full-length Alu elements, sense Alu RNAs are more structured than antisense elements, and both partition into strand- and lineage-dependent structural classes. RADIS enables experimentally grounded structure analysis at disease-associated intronic and intergenic loci, complementing sequence-based variant-effect predictors.\n                <\/jats:p>","DOI":"10.64898\/2026.09.08.750205","type":"posted-content","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T04:35:12Z","timestamp":1789360512000},"source":"Crossref","is-referenced-by-count":0,"title":["Large-scale structural analysis of pre-mRNA structure using RADIS"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6971-6360","authenticated-orcid":false,"given":"Claire","family":"Fleurisson","sequence":"first","affiliation":[{"name":"Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA"},{"name":"Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, 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