U1snRNP activates downstream promoters by inhibiting premature polyadenylation

The intricate interplay between transcription and splicing is underscored by emerging evidence, with splicing factors, such as U1 small nuclear ribonucleoprotein particle (U1snRNP), acting as crucial mediators of this connection. U1snRNP, known for its role as the initial component of the spliceosome, was investigated for its impact on alternative promoter utilization. Using antisense morpholinos (AMOs) to inhibit U1snRNP, we observed a substantial reduction in downstream promoter activity, particularly in genes featuring premature polyadenylation sites located between two promoters. Overexpressing wild-type or gene-specific U1snRNP restored downstream promoter activity, while introducing a premature polyadenylation site had the opposite effect. The molecular mechanisms revealed diminished serine 5 phosphorylation of RNA polymerase II and reduced chromatin accessibility at downstream promoters following U1snRNP inhibition. In-depth analyses, including RNA-seq, TT-seq, CUT&RUN-seq, and ATAC-seq with control AMO or U1 AMO, provided a comprehensive view of U1snRNP's influence on alternative promoter usage.