Characterization of yeast U1 snRNP A protein: Identification of the N-terminal RNA binding domain (RBD) binding site and evidence that the C-terminal RBD functions in splicing

The yeast U1A protein is a U1 snRNP-specific protein. Like its human counterpart (hU1A), it has two conserved RNA binding domains (RBDs). The N-terminal RED is quite different from the human protein, and a binding site on yeast U1 snRNA is not readily apparent. The C-terminal RED is of unknown function. Using in vivo dimethyl sulfate (DMS) protection of mutant strains, we defined a region in yeast U1 snRNA as the likely U1A N-terminal RED binding site. This was confirmed by direct in vitro binding assays. The site is very different from its vertebrate counterpart, but its location within yeast U1 snRNA suggests a conserved structural relationship to other U1 snRNP components. Genetic studies and sensitive in vivo splicing measurements indicate that the yeast U1A C-terminal RED also functions in pre-mRNA splicing. We propose that the N-terminal RED serves to tether the splicing-relevant C-terminal RED to the snRNP.