Terminating the transcript: breaking up is hard to do.

Transcription termination occurs when a transcribing RNA polymerase releases the DNA template and the nascent RNA. Termination is required for preventing the inappropriate transcription of downstream genes, and for recycling of the polymerase. Recent studies in yeast point to the existence of gene loops, in which a transcriptionally active gene’s termination region can be physically linked to its promoter site; in this situation, termination can additionally serve to facilitate transcriptional reinitiation (O’Sullivan et al. 2004; Ansari and Hampsey 2005). Termination by prokaryotic RNA polymerases, as well as eukaryotic RNA polymerase (Pol) I and Pol III, occurs at specific positions, requiring DNA or RNA cis elements that can directly or indirectly destabilize the elongating polymerase–DNA–RNA ternary complex (for reviews, see Henkin 2000; Paule and White 2000). However, for protein-encoding genes, transcribed exclusively by Pol II, transcription in most cases terminates stochastically, independently of simple cis signals, and frequently 500 or more base pairs (bp) downstream of the poly(A) signal. This unique and complex mode of termination by Pol II may have arisen to allow for transcription of very long genes without prematurely stopping at terminator-like sequences that occur by chance throughout the gene. Studies in the area of Pol II termination have sparked some debate, as two models, each supported by many studies, have emerged to explain what provokes Pol II to release the template (Fig. 1). A new study by Luo et al. (2006) presents evidence, however, that aspects of both models can be linked together and leads to new, integrated models of transcription termination. It has been known for some time that termination is functionally connected with cleavage and polyadenylation of the nascent transcript’s 3 end. In the two-step pre-mRNA 3 -processing reaction, transcription of the poly(A) signal triggers the endonucleolytic cleavage of the nascent transcript, generating an upstream cleavage product that is immediately polyadenylated (for reviews, see Colgan and Manley 1997; Zhao et al. 1999). The remaining downstream cleavage product, with an uncapped phosphate at its 5 end, is highly unstable and is rapidly degraded (e.g., Manley et al. 1982). In mammals, the majority of protein-encoding genes contain a well conserved hexanucleotide element (AAUAAA) positioned 10–30 nucleotides (nt) upstream of the cleavage site, and a less conserved Uor GU-rich sequence ∼10–30 nt downstream of the cleavage site. Multisubunit factors are responsible for recognizing these signals and catalyzing the cleavage and polyadenylation reactions. In mammals, these include the cleavage-polyadenylation specificity factor, CPSF; cleavage stimulatory factor, CstF; cleavage factors I and II, CFI and CFII; and poly(A) polymerase, PAP, which catalyzes the addition of adenosines in the poly(A) tail. Most of the components of these complexes have homologs in the yeast cleavage/ polyadenylation apparatus, which is comprised of the cleavage-polyadenylation factor, CPF, and cleavage factors, CFIA and CFIB. The idea of a connection between termination and cleavage/polyadenylation was first postulated in 1982 when Zaret and Sherman noticed that the aberrantly long transcripts generated from the yeast CYC1 gene lacking a 38-bp element at its 3 end, reflecting defects in termination, were polyadenylated as efficiently as wildtype transcripts (Zaret and Sherman 1982). Direct support for this connection came from studies demonstrating that cleavage/polyadenylation-directing signals are also the cis elements required for normal termination in mammalian and viral systems (Whitelaw and Proudfoot 1986; Logan et al. 1987; Connelly and Manley 1988), as well as in yeast (e.g., Russo 1995). Furthermore, several yeast cleavage/polyadenylation factors are also required for normal termination, including CFIA components Rna14, Rna15, and Pcf11 (e.g., Birse et al. 1998; Sadowski et al. 2003; Kim et al. 2004a), and CPF subunits Yhh1 (Dichtl et al. 2002) and Ssu72, the latter of which is required for termination of only some genes (Ganem et al. 2003). To address the mechanistic basis for the connection between termination and cleavage/polyadenylation, two models have emerged: the so-called “torpedo” and “allosteric” models (Fig. 1). The former model proposes that These authors contributed equally to this work. Corresponding author. E-MAIL jlm2@columbia.edu; FAX (212) 865-8246. Article and publication are at http://www.genesdev. org/cgi/doi/10.1101/ gad.1431606.