U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation [CUT&RUN]

Transcription and splicing are inherently intertwined. Accumulating evidence support a role of splicing factors in mediating this coupling. U1 small nuclear ribonucleoprotein particle (U1 snRNP), a key splicing factor, acts as the initial building block of the spliceosome, interacting with nascent pre-mRNA at 5' splice sites. In addition to its role in splicing, U1 snRNP is crucial for preventing premature cleavage and polyadenylation, enabling long-distance transcription elongation. Here, we show that U1snRNP can regulate the usage of alternative promoters through its role in inhibiting premature polyadenylation. Using antisense oligonucleotides to inhibit U1 snRNP, we first observed a markedly decrease in downstream promoter activity at the newly synthesized RNA level. Interestingly, U1 snRNP inhibition selectively impacts downstream promoters of genes featuring premature polyadenylation sites located between two promoters. Overexpressing a wild-type U1 snRNP or a gene-specific U1 snRNP designed to inhibit premature polyadenylation sites restores downstream promoter activity. Conversely, introducing a premature polyadenylation site between two promoters reduces downstream promoter activity. Exploring the underlying molecular mechanisms, we identified a substantial decrease in serine 5 phosphorylation levels in newly recruited RNA polymerase II at downstream promoters following U1 snRNP inhibition, and reduced chromatin accessibility in the vicinity of downstream promoters. Overall, our model is consistent with productive transcription from upstream promoters triggering downstream promoter activation in the presence of U1 snRNP by destabilizing nucleosomes and promoting promoter escape at downstream promoters.