Transcription termination downstream of the Saccharomyces cerevisiae FPB1 poly(A) site does not depend on efficient 3′ end processing

Abstract

Efficient transcription termination downstream of poly(A) sites has been shown to correlate with the strength of an upstream polyadenylation signal and the presence of a polymerase pause site. To further investigate the mechanism linking termination with 3′-end processing, we analyzed the cis-acting elements that contribute to these events in the Saccharomyces cerevisiae FBP1 gene. FBP1 has a complex polyadenylation signal, and at least three efficiency elements must be present for efficient processing. However, not all combinations of these elements are equally effective. This gene also shows a novel organization of sequence elements. A strong positioning element is located upstream, rather than downstream, of the efficiency elements, and functions to select the cleavage site in vitro and in vivo. Transcription run-on analysis indicated that termination occurs within 61 nt past the poly(A) site. Deletion of two UAUAUA-type efficiency elements greatly reduces polyadenylation in vivo and in vitro, but transcription termination is still efficient, implying that FBP1 termination signals may be distinct from those for polyadenylation. Alternatively, assembly of a partial, but nonfunctional, polyadenylation complex on the nascent transcript may be sufficient to cause termination.