Sequence and position requirements for uridylate-rich downstream elements of polyadenylation signals

We have defined the positional and sequence requirements of U-rich downstream elements using a simian virus 40 late polyadenylation signal containing a substituted downstream region. A UUUUU element will significantly increase the efficiency of 3' end processing when placed between 6 and 25 bases downstream from the cleavage site. Positions in this interval closer than 15 bases from the cleavage site, however, were noticeably less efficient. Placement of the UUUUU element between +20 and +25 caused a partial shift in cleavage site usage to a CA motif at +4. Mutational analysis indicated that the sequence requirements at individual positions of the UUUUU element were somewhat flexible. Changing more than one base of the UUUUU sequence, however, severely diminished the ability of the element to mediate efficient 3' end processing. Finally, although hnRNP C proteins specifically interact with U-rich sequences, this protein--RNA interaction is not required for efficient in vitro polyadenylation.