Sequences 5' to the polyadenylation signal mediate differential poly(A) site use in hepatitis B viruses

Most genetic elements that employ reverse transcription generate a terminally redundant genomic RNA that serves as the template for this reaction. Because the identical polyadenylation signal is present in each terminally redundant segment, synthesis of this RNA requires that this signal be ignored on the first pass of the transcription machinery, then recognized and used on the second pass. We have studied the mechanism of this differential poly(A) site use in one family of retroid elements, the hepatitis B viruses (hepadnaviruses). Our results indicate that two features are involved: the presence of a variant poly(A) signal (TATAAA) and the participation of multiple sequences 5' to this signal that act to increase the efficiency of its use. Deletion of these upstream elements abolishes proper poly(A) site use, despite the presence of the poly(A) signal and downstream GT- and T-rich motifs known to be required for polyadenylation. Sequences from the corresponding regions of retroviral genomes can restore proper processing to these hepadnaviral deletion mutants. Thus, functionally analogous upstream elements exist in other classes of retroid elements, including those employing the canonical AATAAA hexanucleotide signal.