Co-regulation of alternative splicing with transcription initiation and termination

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.