{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE341nnn/GSE341315/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Homo sapiens"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE341315"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Structural analysis of chemically probed pre-mRNA structure using RADIS","description":"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 grounded structural models for human pre-mRNAs have been largely restricted to experimentally grounded structural models for human pre-mRNAs have been largely restricted to splice-site-proximal regions, leaving the deep intronic regions, where ~70% 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 E. coli ribosomal RNA architectures and yields high-correlation in-cell dimethyl sulfate (DMS)-MaP reactivities at representative splice sites (r = 0.87–0.90). RADIS-constrained folding of 109 5′ and 88 3′ splice sites uncovers an inverse relationship between base-pairing across 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 provides a generalizable route to experimentally grounded interpretation at intron-rich disease-associated and intergenic loci, complementing sequence-based variant-effect predictors.","dates":{"publication":"2026/09/13"},"accession":"GSE341315","cross_references":{"GSM":["GSM9903630","GSM9903639","GSM9903635","GSM9903636","GSM9903637","GSM9903638","GSM9903631","GSM9903632","GSM9903633","GSM9903634","GSM9903640","GSM9903641","GSM9903606","GSM9903607","GSM9903608","GSM9903609","GSM9903646","GSM9903647","GSM9903604","GSM9903648","GSM9903649","GSM9903605","GSM9903642","GSM9903643","GSM9903644","GSM9903645","GSM9903650","GSM9903651","GSM9903652","GSM9903617","GSM9903618","GSM9903619","GSM9903613","GSM9903657","GSM9903658","GSM9903614","GSM9903615","GSM9903659","GSM9903616","GSM9903653","GSM9903610","GSM9903654","GSM9903655","GSM9903611","GSM9903612","GSM9903656","GSM9903660","GSM9903661","GSM9903662","GSM9903663","GSM9903628","GSM9903629","GSM9903624","GSM9903625","GSM9903626","GSM9903627","GSM9903620","GSM9903664","GSM9903621","GSM9903665","GSM9903666","GSM9903622","GSM9903623"],"GPL":["30882","15520"],"GSE":["341315"],"taxon":["Homo sapiens"]}}