{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE346nnn/GSE346485/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Homo sapiens"],"gds_type":[" Other","Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE346485"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Co-regulation of alternative splicing with transcription initiation and termination","description":"Nascent RNA processing requires coordination between transcription and splicing, yet the mechanisms underlying this coupling remain unclear. Here, we develop longPASS, a framework to identify and quantify transcription start site (TSS) and polyadenylation site (PAS) usage in long-read RNA sequencing data. In human cells, longPASS reveals thousands of TSS/PAS-associated alternative splicing events (TASEs) and reproducible links between TSS/PAS choice and exon inclusion across genetic perturbations, human tissues and individuals. Co-occurring pairs of TASE-exons and TASE-TSS/PASs tend to be proximal and show enriched RNA-RNA spatial interactions. Large-scale screening shows that RBMX specifically binds PAS-TASE pairs; RBMX depletion disrupts coordinated splicing and PAS usage, whereas canonical splicing-factor depletion has no significant effect. Manipulating RNA polymerase II elongation affects PAS-TASE coupling, with slower elongation increasing co-occurrence. Together, these findings establish genome-wide coupling between alternative splicing and TSS/PAS usage, implicate RBMX and polymerase II elongation in its regulation, and link this process to ageing.","dates":{"publication":"2026/09/09"},"accession":"GSE346485","cross_references":{"GSM":["GSM10034855","GSM10034844","GSM10034843","GSM10034854","GSM10034853","GSM10034842","GSM10034852","GSM10034841","GSM10034840","GSM10034851","GSM10034850","GSM10034839","GSM10034849","GSM10034838","GSM10034848","GSM10034837","GSM10034836","GSM10034847","GSM10034846","GSM10034857","GSM10034835","GSM10034845","GSM10034834","GSM10034856"],"GPL":["26167","24106"],"GSE":["346485"],"taxon":["Homo sapiens"]}}