Termination of transcription by RNA polymerase II usually requires the presence of a functional poly(A) site. How the poly(A) site signals its presence to the polymerase is unknown. All models assume that the signal is generated after the poly(A) site has been extruded from the polymerase, but this has never been tested experimentally. It is also widely accepted that a "pause" element in the DNA stops the polymerase and that cleavage at the poly(A) site then signals termination. These ideas also have never been tested. The lack of any direct tests of the poly(A) signaling mechanism reflects a lack of success in reproducing the poly(A) signaling phenomenon in vitro. Here we describe a cell-free transcription elongation assay that faithfully recapitulates poly(A) signaling in a crude nuclear extract. The assay requires the use of citrate, an inhibitor of RNA polymerase II carboxyl-terminal domain phosphorylation. Using this assay we show the following. It has become clear in recent years that RNA polymerase II (RNAPII) not only transcribes the mRNA but shepherds it through the stages of processing as well (42, 67). An early indicator of this coupling between transcription and processing was the finding that the poly(A) signal for cleavage and polyadenylation of pre-mRNA directs not only 3Ј-end processing of the transcript but also termination of transcription by the polymerase (20,32,50,61,77,79). A major challenge has been to explain how the poly(A) signal communicates with the polymerase.The core poly(A) signal in vertebrates consists of two recognition elements flanking a cleavage-polyadenylation site (76,82). Typically, an almost invariant AAUAAA hexamer lies 20 to 50 nucleotides (nt) upstream of a more variable element rich in U or GU residues. Cleavage of the nascent transcript occurs between these two elements and is coupled to the addition of up to 250 adenosines to the 5Ј cleavage product. The cleavage is mediated in vitro by a large, multicomponent protein complex that can be separated into five distinguishable factors. Two of these factors are the cleavage and polyadenylation specificity factor (CPSF), which binds the AAUAAA motif, and the cleavage stimulation factor (CstF), which binds the downstream U-rich element. In vitro studies suggest that CPSF (26) and probably CstF as well (55, 71) are recruited to the polymerase at the promoter. Presumably they then ride with the polymerase during transcription, scanning the extruding transcript so as to snare the poly(A) site when it emerges. The situation in yeast may be similar (8,29). Strictly speaking, the term "poly(A) site" refers only to the point at which cleavage occurs and the poly(A) tail is appended, but we use the term here to refer to the poly(A) signal as a whole when this helps to distinguish between the poly(A) signal as an entity and poly(A) signal transduction [or "poly(A) signaling"] as a process.Models that attempt to explain transduction of the signal from the poly(A) site to the polymerase can be divided into two categories (50): (i) cl...