The U1 snRNP protein U1C recognizes the 5′ splice site in the absence of base pairing

Abstract

Splicing of precursor messenger RNA takes place in the spliceosome, a large RNA/protein macromolecular machine¹. Spliceosome assembly occurs in an ordered pathway in vitro and is conserved between yeast and mammalian systems. The earliest step is commitment complex formation in yeast or E complex formation in mammals, which engages the pre-mRNA in the splicing pathway and involves interactions between U1 small nuclear ribonucleoprotein (snRNP) and the pre-mRNA 5′ splice site^2,3. Complex formation depends on highly conserved base pairing between the 5′ splice site and the 5′ end of U1 snRNA, both in vivo and in vitro^4,5,6,7. U1 snRNP proteins also contribute to U1 snRNP activity^8,9,10. Here we show that U1 snRNP lacking the 5′ end of its snRNA retains 5′-splice-site sequence specificity. We also show that recombinant yeast U1C protein, a U1 snRNP protein, selects a 5′-splice-site-like sequence in which the first four nucleotides, GUAU, are identical to the first four nucleotides of the yeast 5′-splice-site consensus sequence. We propose that a U1C 5′-splice-site interaction precedes pre-mRNA/U1 snRNA base pairing and is the earliest step in the splicing pathway.