The direct association between messenger RNA (mRNA) 3'-end processing and the termination of transcription was established for the CYC1 gene of Saccharomyces cerevisiae. The mutation of factors involved in the initial cleavage of the primary transcript at the poly(A) site (RNA14, RNA15, and PCF11) disrupted transcription termination at the 3' end of the CYC1 gene. In contrast, the mutation of factors involved in the subsequent polyadenylation step (PAP1, FIP1, and YTH1) had little effect. Thus, cleavage factors link transcription termination of RNA polymerase II with pre-mRNA 3'-end processing.

Reconstruction of a gene with its introns removed results in reduced levels of cytoplasmic mRNA. This is partly explained by introns promoting the export of mRNA through coupling splicing to nuclear export processes. However, we show here that splicing signals can have a direct role in enhancing gene transcription. Removal of promoter proximal splice signals from a mammalian gene or the excision of introns from two different yeast genes results in a marked reduction in levels of nascent transcription, based on both nuclear run-on and direct image analysis. This further establishes that mRNA processing and transcription are tightly coupled mechanisms.

The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II plays an important role in transcription and processing of the nascent transcript by interacting with both transcription and RNA processing factors. We show here that the cleavage͞ polyadenylation factor IA of Saccharomyces cerevisiae directly contacts CTD. First by affinity chromatography experiments with yeast extracts we demonstrate that the Rna15p, Rna14p, and Pcf11p subunits of this complex are associated with phosphorylated CTD. This interaction is confirmed for Rna15p by yeast two-hybrid analysis. Second, Pcf11p, but not Rna15p, is shown to directly contact phosphorylated CTD based on in vitro binding studies with recombinant proteins. These findings establish a direct interaction of cleavage͞polyadenylation factor IA with the CTD. Furthermore, a quantitative analysis of transcription run-on performed on temperature-sensitive mutant strains reveals that the lack of either functional Rna14p or Pcf11p affects transcription termination more severely than the absence of a functional Rna15p. Moreover, these data reinforce the concept that CTD phosphorylation acts as a regulatory mechanism in the maturation of the primary transcript. In Saccharomyces cerevisiae the largest subunit of RNA polymerase II (pol II) contains a carboxyl-terminal domain (CTD) consisting of 26 tandem repeats of a heptapeptide module with the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser (1, 2). Two serines per heptad repeat may undergo reversible phosphorylation during each transcription cycle (3). The phosphorylation status of the CTD is correlated with different stages of the transcription cycle. Thus hypophosphorylated polymerase (IIA) is competent for initiation, whereas hyperphosphorylated polymerase (II0) is associated with transcription elongation. Increasing evidence has been provided in the last few years showing that the CTD acts as a direct physical link between transcription and nascent RNA processing: in mammals, the cleavage-polyadenylation specificity factor (CPSF) and the cleavage stimulation factor (CstF), as well as splicing factors and 5Ј capping enzyme, all bind to the CTD (4-9). Furthermore, CPSF and CstF copurify with pol II (4). The concept of a factor recruiting͞docking platform has emerged as one likely function of this peculiar polypeptide. Evidence for a more direct role of the CTD in polyadenylation has also been indicated (10).In S. cerevisiae, the proteins so far known to bind to the CTD are the Mediator complex (11, 12), the Elongator complex (13), proteins involved in 5Ј end capping of nascent RNA (8,14), and the Ess1 peptidylprolyl isomerase (15, 16). To date the interaction of cleavage͞polyadenylation factors with the CTD remains largely uncharacterized. In yeast 3Ј-end processing of pre-mRNA requires cleavage factor IA (CF IA), cleavage factor IB (CF IB), cleavage factor II (CF II), polyadenylation factor I (PFI), poly(A) polymerase, and the poly(A)-binding protein 1 (17-22). CF IA, which is involved in both cleavage and po...

an additional T-rich element located upstream of the Sir William Dunn School of Pathology, Chemical Pathology Unit, protein-binding site is also required to pause and release University of Oxford, Oxford OX1 3RE, UK the polymerase (Lang and Reeder, 1993; 1 Corresponding author Jeong et al., 1995) the T-rich element, followed by release of the enzyme appears to act by pausing the elongating polymerase.from the template (Matsuzaki et al., 1994). TRO analysis indicates that elevated levels of transcrib-A bipartite signal has been proposed to direct RNA ing polymerases accumulate over the DSE and that polymerase II (pol II) termination in higher eukaryotes. removal of this signal leads to transcription proceedingA functional polyadenylation element acts as the upstream beyond the normal termination region. Furthermore, signal, with mutation of this highly conserved processing when inserted between two competing polyadenylation signal leading to reduced termination efficiency downsignals, this DSE increases the utilization of upstream