U1 snRNP regulates early spliceosome assembly by disrupting the interaction between SR proteins and the pre-mRNA

The pre-mRNA features that define the splice signals at or near exon-intron junctions for assembly of the early spliceosome are not well understood. Here we show that, similar to an adenovirus 2 transcript, human β-globin pre-mRNA also folds into a 3D scaffold to regulate recognition of the splice signals (SS) by the early spliceosomal components. We find that stabilization of U1 snRNP and U2AF65 requires multiple serine-arginine-rich (SR) proteins to cooperatively bind the pre-mRNA and remodel it. Paradoxically, this complex of pre-mRNA and SR proteins, particularly SRSF1, engages U1 snRNP and U2AF65 non-specifically. Excess U1 snRNP displaces some of the SR protein molecules leading to SS-specific recruitment of U1 snRNP and U2AF65. Our work thus reveals a novel splicing-regulatory function of U1 snRNP, which optimizes SS-specific recruitment of early spliceosomal components by displacing SR proteins from the pre-mRNA, potentially acting as a checkpoint signal. These findings also explain the need for excess U1 snRNP in vivo and how excess SR proteins inhibit splicing.