Protein binding sites are conserved in U1 small nuclear RNA from insects and mammals.

To gain insight into the ribonucleoprotein (RNP) structure of small nuclear RNAs, HeLa cell poly(A)+ mRNA was translated in a reticulocyte lysate, and the in vitro binding of 35S-labeled proteins to individual small nuclear RNA species was examined by using human autoimmune antibodies. A Mr 32,000 protein binds to U1 RNA but not to U2, U4, U5, or U6. The resulting U1 RNP complex is recognized both by Sm and RNP antibodies. U2 RNA also forms a complex with protein, which is recognized by Sm antibody. Thus, the lack of binding of the Mr 32,000 protein to U2 RNA is not due to a failure of U2 to bind specific proteins in the in vitro system. Similar translation-assembly experiments with Drosophila poly(A)+ mRNA reveal that a Mr 26,000 protein identified previously in Drosophila U1 RNP [Wieben, E. D. & Pederson, T. (1982) Mol. Cell. Biol. 2, 914-920] also binds to U1 RNA in vitro. When the translation products of HeLa or Drosophila mRNA are presented with U1 RNA of the other species, the Mrs 32,000 and 26,000 proteins recognize binding sites on the heterologous U1 and, in both cases, form complexes recognized by RNP antibody. These results establish that a Mr 32,000 protein is unique to U1 RNA in human cells and that the U1 RNA binding sites for this and a Mr 26,000 homologue have been highly conserved in evolution. These sites may be the identical 13 nucleotides at the 5' ends of human and Drosophila U1 RNA or a highly conserved aspect of U1 secondary structure.