The specific RNA-protein interactions responsible for the production of mature 3' ends of eukaryotic mRNAs are not well understood. Sequence elements at the 3' ends of yeast genes have been identified that specify the position of the poly(A) site and the efficiency of polyadenylation. To provide additional insights into the interaction between important sequences that direct 3'-end formation in vivo and nuclear proteins, we utilized gel mobility shift assays and UV-crosslinking studies. The data indicate that a protein, with an apparent molecular weight of 80 kDa, interacts specifically with pre-mRNA at the (UA)3 efficiency element. Although the interaction is specific, it can be competed by RNA sequences that do not contain the same type of efficiency element; that is, a sequence lacking a (UA)3 repeat. This result implies that the protein binding site is flexible. Using immunoprecipitation techniques, the protein has been identified as Hrp1, a heteronuclear RNA binding protein. The role of Hrp1p in 3'-end formation including RNA processing and transcription termination is addressed.
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