Two structurally different RNA molecules are bound by the spliceosomal protein U1A using the same recognition strategy

Abstract

Background: Human U1A protein binds to hairpin II of U1 small nuclear RNA (snRNA) and, together with other proteins, forms the U1 snRNP essential in pre-mRNA splicing. U1A protein also binds to the 3′ untranslated region (3′UTR) of its own pre-mRNA, inhibiting polyadenylation of the 3′ end and thereby downregulating its own expression. The 3′UTR folds into an evolutionarily conserved secondary structure with two internal loops; one loop contains the sequence AUUGCAC and the other its variant AUUG UAC. The sequence AUUGCAC is also found in hairpin II of U1 snRNA; hence, U1A protein recognizes the same heptanucleotide sequence in two different structural contexts. In order to better understand the control mechanism of the polyadenylation process, we have built a model of the U1A protein–3′UTR complex based on the crystal structure of the U1A protein–hairpin II RNA complex which we determined previously. Results In the crystal structure of the U1A protein–hairpin II RNA complex the AUUGCAC sequence fits tightly into a groove on the surface of U1A protein. The conservation of the heptanucleotide in the 3′UTR strongly suggests that U1A protein forms identical sequence-specific contacts with the heptanucleotide sequence when complexed with the 3′UTR. The crystal structure of the hairpin II complex and the twofold symmetry in the 3′UTR RNA provide sufficient information to restrict the conformation of the 3′UTR RNA and have enabled us to build a model of the 3′UTR complex. Conclusion In the U1A–3′UTR complex, sequence-specific interactions are made entirely by the conserved heptanucleotide and the last base pair (C:G) of the stem. The structure is stabilized by protein–protein contacts and by electrostatic interactions between basic amino acids of the protein and the phosphate backbone of the RNA stem regions. The formation of a protein dimer necessary for the inhibition of poly(A) polymerase requires a conformational change of the C termini of the proteins upon RNA binding. This mechanism could prevent the inhibition of poly(A) polymerase by free U1A protein. The model is consistent with biochemical data, and the protein–protein interactions within the 3′UTR complex account for the cooperativity of U1A protein binding to the 3′UTR. The model also serves as an important structural guide for designing further experiments to understand the interaction between the U1A–3′UTR complex and poly(A) polymerase.