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The exonuclease torpedo Xrn2 loads onto nascent RNA 5′-PO4ends and chases down pol II to promote termination downstream from polyA sites. We report that Xrn2 is recruited to preinitiation complexes and “travels” to 3′ ends of genes. Mapping of 5′-PO4ends in nascent RNA identified Xrn2 loading sites stabilized by an active site mutant, Xrn2(D235A). Xrn2 loading sites are approximately two to 20 bases downstream from where CPSF73 cleaves at polyA sites and histone 3′ ends. We propose that processing of all mRNA 3′ ends comprises cleavage and limited 5′–3′ trimming by CPSF73, followed by handoff to Xrn2. A similar handoff occurs at tRNA 3′ ends, where cotranscriptional RNase Z cleavage generates novel Xrn2 substrates. Exonuclease-dead Xrn2 increased transcription in 3′ flanking regions by inhibiting polyA site-dependent termination. Surprisingly, the mutant Xrn2 also rescued transcription in promoter-proximal regions to the same extent as in 3′ flanking regions. eNET-seq revealed Xrn2-mediated degradation of sense and antisense nascent RNA within a few bases of the TSS, where 5′-PO4ends may be generated by decapping or endonucleolytic cleavage. These results suggest that a major fraction of pol II complexes terminates prematurely close to the start site under normal conditions by an Xrn2-mediated torpedo mechanism.

Alternative polyadenylation yields many mRNA isoforms whose 3’ termini occur disproportionately in clusters within 3’ untranslated regions. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et al., 2020). Pol II derivatives with slow elongation rates confer an upstream-shifted poly(A) profile, whereas fast Pol II strains confer a downstream-shifted poly(A) profile. Within yeast isoform clusters, these shifts occur steadily from one isoform to the next across nucleotide distances. In contrast, the shift between clusters – from the last isoform of one cluster to the first isoform of the next – is much less pronounced, even over large distances. GC content in a region 13–30 nt downstream from isoform clusters correlates with their sensitivity to Pol II elongation rate. In human cells, the upstream shift caused by a slow Pol II mutant also occurs continuously at single nucleotide resolution within clusters but not between them. Pol II occupancy increases just downstream of poly(A) sites, suggesting a linkage between reduced elongation rate and cluster formation. These observations suggest that (1) Pol II elongation speed affects the nucleotide-level dwell time allowing polyadenylation to occur, (2) poly(A) site clusters are linked to the local elongation rate, and hence do not arise simply by intrinsically imprecise cleavage and polyadenylation of the RNA substrate, (3) DNA sequence elements can affect Pol II elongation and poly(A) profiles, and (4) the cleavage/polyadenylation and Pol II elongation complexes are spatially, and perhaps physically, coupled so that polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex.

Alternative polyadenylation yields many mRNA isoforms whose 3’ termini occur disproportionately in clusters within 3’ UTRs. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et., 2020). Pol II derivatives with slow elongation rates confer an upstream-shifted poly(A) profile, whereas fast Pol II strains confer a downstream-shifted poly(A) profile. In yeast, upstream and downstream shifts within isoform clusters occur steadily at the nucleotide level. In contrast, changes from one isoform to the next are much smaller between clusters, even when the distances between them are relatively large. GC content in a region 13-30 nt downstream from isoform clusters is linked to Pol II elongation rate. In human cells, the upstream shift caused by a slow Pol II mutant also occurs continuously at the nucleotide level within clusters, but not between them. Pol II occupancy increases just downstream of the most speed-sensitive poly(A) sites, suggesting a linkage between reduced elongation rate and cluster formation. These observations suggest that 1) Pol II elongation speed affects the nucleotide-level dwell time allowing polyadenylation to occur, 2) poly(A) site clusters are linked to the local elongation rate and hence do not arise simply by intrinsically imprecise cleavage and polyadenylation of the RNA substrate, 3) DNA sequence elements can affect Pol II elongation and poly(A) profiles, and 4) the cleavage/polyadenylation and Pol II elongation complexes are spatially, and perhaps physically, coupled so that polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex.

CDK7 associates with the 10-subunit TFIIH complex and regulates transcription by phosphorylating the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Few additional CDK7 substrates are known. Here, using the covalent inhibitor SY-351 and quantitative phosphoproteomics, we identified CDK7 kinase substrates in human cells. Among hundreds of high-confidence targets, the vast majority are unique to CDK7 (i.e., distinct from other transcription-associated kinases), with a subset that suggest novel cellular functions. Transcription-associated factors were predominant CDK7 substrates, including SF3B1, U2AF2, and other splicing components. Accordingly, widespread and diverse splicing defects, such as alternative exon inclusion and intron retention, were characterized in CDK7-inhibited cells. Combined with biochemical assays, we establish that CDK7 directly activates other transcription-associated kinases CDK9, CDK12, and CDK13, invoking a “master regulator” role in transcription. We further demonstrate that TFIIH restricts CDK7 kinase function to the RNAPII CTD, whereas other substrates (e.g., SPT5 and SF3B1) are phosphorylated by the three-subunit CDK-activating kinase (CAK; CCNH, MAT1, and CDK7). These results suggest new models for CDK7 function in transcription and implicate CAK dissociation from TFIIH as essential for kinase activation. This straightforward regulatory strategy ensures CDK7 activation is spatially and temporally linked to transcription, and may apply toward other transcription-associated kinases.

Paused RNA polymerase II (Pol II) that piles up near most human promoters is the target of mechanisms that control entry into productive elongation. Whether paused Pol II is a stable or dynamic target remains unresolved. We report that most 5′ paused Pol II throughout the genome is turned over within 2 min. This process is revealed under hypertonic conditions that prevent Pol II recruitment to promoters. This turnover requires cell viability but is not prevented by inhibiting transcription elongation, suggesting that it is mediated at the level of termination. When initiation was prevented by triptolide during recovery from high salt, a novel preinitiated state of Pol II lacking the pausing factor Spt5 accumulated at transcription start sites. We propose that Pol II occupancy near 5′ ends is governed by a cycle of ongoing assembly of preinitiated complexes that transition to pause sites followed by eviction from the DNA template. This model suggests that mechanisms regulating the transition to productive elongation at pause sites operate on a dynamic population of Pol II that is turning over at rates far higher than previously suspected. We suggest that a plausible alternative to elongation control via escape from a stable pause is by escape from premature termination.

Control of transcription speed, which influences many co-transcriptional processes, is poorly understood. We report that PNUTS-PP1 phosphatase is a negative regulator of RNA polymerase II (Pol II) elongation rate. The PNUTS W401A mutation, which disrupts PP1 binding, causes genome-wide acceleration of transcription associated with hyper-phosphorylation of the Spt5 elongation factor. Immediately downstream of poly(A) sites, Pol II decelerates from2 kb/min to 1 kb/min, which correlates with Spt5 dephosphorylation. Pol II deceleration and Spt5 dephosphorylation require poly(A) site recognition and the PNUTS-PP1 complex, which is in turn necessary for transcription termination. These results lead to a model for termination, the "sitting duck torpedo" mechanism, where poly(A) site-dependent deceleration caused by PNUTS-PP1 and Spt5 dephosphorylation is required to convert Pol II into a viable target for the Xrn2 terminator exonuclease. Spt5 and its bacterial homolog NusG therefore have related functions controlling kinetic competition between RNA polymerases and the termination factors that pursue them.

Most RNA processing occurs co-transcriptionally. We interrogated nascent pol II transcripts by chemical and enzymatic probing and determined how the "nascent RNA structureome" relates to splicing, A-I editing and transcription speed. RNA folding within introns and steep structural transitions at splice sites are associated with efficient co-transcriptional splicing. A slow pol II mutant elicits extensive remodeling into more folded conformations with increased A-I editing. Introns that become more structured at their 3' splice sites get co-transcriptionally excised more efficiently. Slow pol II altered folding of intronic Alu elements where cryptic splicing and intron retention are stimulated, an outcome mimicked by UV, which decelerates transcription. Slow transcription also remodeled RNA folding around alternative exons in distinct ways that predict whether skipping or inclusion is favored, even though it occurs post-transcriptionally. Hence, co-transcriptional RNA folding modulates post-transcriptional alternative splicing. In summary, the plasticity of nascent transcripts has widespread effects on RNA processing.

CDK7 phosphorylates the RNA polymerase II (pol II) CTD and activates the P-TEFb-associated kinase, CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoterproximal pausing, and defective termination at gene 3'-ends upon CDK7 inhibition. Surprisingly, we also noted CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5'-ends and H3K36me3 was displaced toward gene 3'-ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated vs. P-TEFb-phosphorylated CTD (vs. unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7 dependent "CTD code" that regulates epigenetic marks in addition to RNA processing and pol II pausing.

The torpedo model of transcription termination asserts that the exonuclease Xrn2 attacks the 5'PO4-end exposed by nascent RNA cleavage and chases down the RNA polymerase. We tested this mechanism using a dominant-negative human Xrn2 mutant and found that it delayed termination genome-wide. Xrn2 nuclease inactivation caused strong termination defects downstream of most poly(A) sites and modest delays at some histone and U snRNA genes, suggesting that the torpedo mechanism is not limited to poly(A) site-dependent termination. A central untested feature of the torpedo model is that there is kinetic competition between the exonuclease and the pol II elongation complex. Using pol II rate mutants, we found that slow transcription robustly shifts termination upstream, and fast elongation extends the zone of termination further downstream. These results suggest that kinetic competition between elongating pol II and the Xrn2 exonuclease is integral to termination of transcription on most human genes.

Summary: CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3′ ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5′ ends and H3K36me3 was displaced toward gene 3′ ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated versus P-TEFb-phosphorylated CTD (versus unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD, and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent “CTD code” that regulates chromatin marks in addition to RNA processing and pol II pausing. : Ebmeier et al. use targeted proteomics to identify distinct interactomes for full-length mammalian pol II CTD phosphorylated by TFIIH or P-TEFb. In vitro and cell-based assays uncover expanded roles for the TFIIH-associated kinase CDK7, including regulation of SETD1A/B methyltransferase activity and regulation of transcription-associated histone modifications (i.e., H3K4me3 and H3K36me3). Keywords: RNA-seq, proteomics, Mediator, THZ1, chromatin, epigenetic, TFIIH, P-TEFb, H3K4me3, H3K36me3

The Saccharomyces cerevisiae mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A that links export to 3' end formation. We found that an unexpected consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit Clp1 for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit; instead, Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice, particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A 3' processing factor.

A chromatin code appears to mark introns and exons with distinct patterns of nucleosome enrichment and histone methylation. We investigated whether a causal relationship exists between splicing and chromatin modification by asking whether splice-site mutations affect the methylation of histone H3K36. Deletions of the 3′ splice site in intron 2 or in both introns 1 and 2 of an integrated β-globin reporter gene caused a shift in relative distribution of H3K36 trimethylation away from 5′ ends and toward 3′ ends. The effects of splice-site mutations correlated with enhanced retention of a U5 snRNP subunit on transcription complexes downstream of the gene. In contrast, a poly(A) site mutation did not affect H3K36 methylation. Similarly, global inhibition of splicing by spliceostatin A caused a rapid repositioning of H3K36me3 away from 5′ ends in favor of 3′ ends. These results suggest that the cotranscriptional splicing apparatus influences establishment of normal patterns of histone modification.

Phosphorylation of the RNA polymerase (Pol) II C-terminal domain (CTD) repeats (1-YSPTSPS-7) is coupled to transcription and may act as a 'code' that controls mRNA synthesis and processing. To examine the code in budding yeast, we mapped genome-wide CTD Ser2, Ser5 and Ser7 phosphorylations and the CTD-associated termination factors Nrd1 and Pcf11. Phospho-CTD dynamics are not scaled to gene length and are gene-specific, with highest Ser5 and Ser7 phosphorylation at the 5' ends of well-expressed genes with nucleosome-occupied promoters. The CTD kinases Kin28 and Ctk1 markedly affect Pol II distribution in a gene-specific way. The code is therefore written differently on different genes, probably under the control of promoters. Ser7 phosphorylation is enriched on introns and at sites of Nrd1 accumulation, suggesting links to splicing and Nrd1 recruitment. Nrd1 and Pcf11 frequently colocalize, suggesting functional overlap. Unexpectedly, Pcf11 is enriched at centromeres and Pol III-transcribed genes.

Dynamic modification of the RNA polymerase II (Pol II) C-terminal domain (CTD) by phosphorylation and dephosphorylation plays important roles in controlling both transcription and cotranscriptional RNA processing (9, 31). There are 52 heptad repeats with the consensus sequence Y1S2P3T4S5P6S7 in the human CTD that can be phosphorylated cotranscriptionally on serines 2, 5, and 7 (S2, S5, and S7, respectively) (6, 31). S5 phosphorylation normally occurs early in the transcription cycle coincident with initiation, whereas S2 phosphorylation predominates later, during elongation and termination (13, 20). The complex pattern of heptad repeat phosphorylation serves in part to control binding of partner proteins, including elongation factors, RNA processing factors (31), and chromatin modifiers (25, 39). Ser5 phosphorylation enhances cotranscriptional mRNA capping (17), and Ser2 facilitates 3′-end formation by cleavage/polyadenylation (1, 4, 29). Ser7 phosphorylation has been specifically implicated in formation of U snRNA 3′ ends but is also found on mRNA coding genes (10) (6). Exactly how S2, S5, and S7 phosphorylation affect initiation, elongation, and termination remains poorly understood. It is generally thought that the positive transcription elongation factor PTEFb (Cdk9/cyclin T [CycT]) is the principal S2 kinase and that Cdk7 associated with TFIIH is the principal S5 kinase (31, 32, 38). How Cdk7 affects CTD phosphorylation on metazoan genes in vivo is still an unresolved question, and the S7 kinase is yet to be identified. In the only previous investigation of Cdk7 effects on CTD phosphorylation at the site of transcription in a multicellular organism, phospho-S5 and total Pol II levels were reduced equivalently at the Drosophila melanogaster Hsp70 gene in a Cdk7 temperature-sensitive (TS) mutant, and it was suggested that multiple S5 kinases may operate in vivo (36). Indeed, there is evidence that Cdk9 can phosphorylate CTD S5 from RNA interference knockdown of this kinase in Drosophila (11) and from the fact that the Cdk9 inhibitor 5,6-5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) reduced S5 phosphorylation on the human p21 gene (14). Promoter-proximal pausing is an obligate step in the RNA Pol II transcription cycle for thousands of human genes and constitutes a rate-limiting step in mRNA synthesis with particular importance for inducible genes and in stem cells (8, 16, 21). Paused Pol II complexes have recently been shown to regulate enhancer function by acting as insulators (7). The mechanisms responsible for establishment of the pause are not fully understood; however, two key regulators have been identified: negative elongation factor NELF and DRB sensitivity-inducing factor DSIF (Spt4/5) (30, 33, 41). Knockdown of NELF inhibits transcription of some genes, suggesting that the promoter-proximal pause can facilitate gene activation (12). Pausing is antagonized by the positive transcription elongation factor PTEFb (Cdk9/CycT), which can phosphorylate DSIF, NELF, and the Pol II CTD and is sensitive to the inhibitor, DRB (27, 30, 33, 41-43). Exactly how the TFIIH-associated Cdk7 activity affects Pol II transcription remains unclear. The kinase is dispensable for initiation in vitro in many cases (26, 37, 40) but has been implicated in early elongation of dihydrofolate reductase transcripts (3). Interestingly, in Drosophila, inactivation of TS Cdk7 reduced the amount of Pol II accumulated at the 5′ end prior to gene activation, suggesting that TFIIH helps establish promoter-proximal pausing (36). However, it is difficult to distinguish in this case whether reduced amounts of paused Pol II are specifically caused by loss of Cdk7 activity or by a secondary effect on initiation due to destabilization of TFIIH, which requires Cdk7 for its integrity (40). Pol II encounters a second prominent pause site on many human genes in the 3′-flanking region several hundred base pairs past the poly(A) site (13, 15), and following this pause, termination occurs. S2 phosphorylation is maximal at the 3′ pause, and DRB inhibition of the S2 kinase Cdk9 inhibits 3′ pausing (13). Whether TFIIH-associated Cdk7 might also function in 3′ pausing and termination is unknown. In this report we investigated the roles of Cdk7 in CTD phosphorylation and polymerase pausing on human genes using mutant HCT116 cells in which both copies of the Cdk7 gene driven by its endogenous promoter were replaced by homologous recombination with an analogue-sensitive (as) mutant of the ATP-binding site (23). This strategy permits specific inhibition of kinases with cell-permeable ATP analogues and has been used to target budding yeast Cdk7 (18), human Cdk7 (23), and many other kinases in vivo (19). This strategy is preferable to TS or deletion mutations or RNA interference-mediated knockdown because it permits one to distinguish between the catalytic and structural functions of kinases (19). We combined targeted inhibition of Cdk7(as) with high-resolution chromatin immunoprecipitation (ChIP) analysis of Pol II and associated elongation factors to show that this kinase can phosphorylate S7 and S5 in vivo and affects both the 5′ and 3′ pausing events that are characteristic features of transcription on many human genes. While this work was in progress, it was independently reported that budding yeast TFIIH phosphorylates CTD Ser7 residues (2).

The toll-like receptors (TLRs) are a class of transmembrane molecules that have important functions in both innate and acquired immunity. As part of the body's normal immune defense against microbial pathogens, stimulation of these receptors will trigger the inflammatory response cascade and the release of cytokines. Activation of these receptors also plays a role in a variety of systemic inflammatory diseases such as asthma, sepsis, atherosclerosis, acute coronary artery disease, and left ventricular remodeling. Pharmacologic approaches to modify the actions of TLRs are now under consideration as potential treatments for inflammatory systemic diseases that include atherosclerosis. At the same time, it is essential to characterize the benefits and risks of modifying such an important part of the body's innate immune system.

Most mammalian genes produce transcripts whose 3' ends are processed at multiple alternative positions by cleavage/polyadenylation (CPA). Poly(A) site cleavage frequently occurs cotranscriptionally and is facilitated by CPA factor binding to the RNA polymerase II (Pol II) C-terminal domain (CTD) phosphorylated on Ser2 residues of its heptad repeats (YS2PTSPS). The function of cotranscriptional events in the selection of alternative poly(A) sites is poorly understood. We investigated Pol II pausing, CTD Ser2 phosphorylation, and processing factor CstF recruitment at wild-type and mutant IgM transgenes that use alternative poly(A) sites to produce mRNAs encoding the secreted and membrane-bound forms of the immunoglobulin (Ig) heavy chain. The results show that the sites of Pol II pausing and processing factor recruitment change depending on which poly(A) site is utilized. In contrast, the extent of Pol II CTD Ser2 phosphorylation does not closely correlate with poly(A) site selection. We conclude that changes in properties of the transcription elongation complex closely correlate with utilization of different poly(A) sites, suggesting that cotranscriptional events may influence the decision between alternative modes of pre-mRNA 3' end processing.

Objective : To bridge gaps identified during the 2009 H1N1 influenza pandemic by developing a system that provides public health departments improved capability to manage and track medical countermeasures at the state and local levels and to report their inventory levels to the Centers for Disease Control and Prevention (CDC). Materials and Methods : The CDC Countermeasure Tracking Systems (CTS) program designed and implemented the Inventory Management and Tracking System (IMATS) to manage, track, and report medical countermeasure inventories at the state and local levels. IMATS was designed by CDC in collaboration with state and local public health departments to ensure a “user-centered design approach.” A survey was completed to assess functionality and user satisfaction. Results : IMATS was deployed in September 2011 and is provided at no cost to public health departments. Many state and local public health departments nationwide have adopted IMATS and use it to track countermeasure inventories during public health emergencies and daily operations. Discussion: A successful response to public health emergencies requires efficient, accurate reporting of countermeasure inventory levels. IMATS is designed to support both emergency operations and everyday activities. Future improvements to the system include integrating barcoding technology and streamlining user access. To maintain system readiness, we continue to collect user feedback, improve technology, and enhance its functionality. Conclusion: IMATS satisfies the need for a system for monitoring and reporting health departments’ countermeasure quantities so that decision makers are better informed. The “user-centered design approach” was successful, as evident by the many public health departments that adopted IMATS.

Spt6 is a transcriptional elongation factor and histone chaperone that reassembles transcribed chromatin. Genome-wide H3 mapping showed that Spt6 preferentially maintains nucleosomes within the first 500 bases of genes and helps define nucleosome-depleted regions in 5′ and 3′ flanking sequences. In Spt6-depleted cells, H3 loss at 5′ ends correlates with reduced pol II density suggesting enhanced transcription elongation. Consistent with its ‘Suppressor of Ty' (Spt) phenotype, Spt6 inactivation caused localized H3 eviction over 1–2 nucleosomes at 5′ ends of Ty elements. H3 displacement differed between genes driven by promoters with ‘open'/DPN and ‘closed'/OPN chromatin conformations with similar pol II densities. More eviction occurred on genes with ‘closed' promoters, associated with ‘noisy' transcription. Moreover, swapping of ‘open' and ‘closed' promoters showed that they can specify distinct downstream patterns of histone eviction/deposition. These observations suggest a novel function for promoters in dictating histone dynamics within genes possibly through effects on transcriptional bursting or elongation rate.

Summary We report a function of human mRNA decapping factors in control of transcription by RNA polymerase II. Decapping proteins Edc3, Dcp1a, and Dcp2 and the termination factor TTF2 coimmunoprecipitate with Xrn2, the nuclear 5′–3′ exonuclease "torpedo" that facilitates transcription termination at the 3′ ends of genes. Dcp1a, Xrn2, and TTF2 localize near transcription start sites (TSSs) by ChIP-seq. At genes with 5′ peaks of paused pol II, knockdown of decapping or termination factors Xrn2 and TTF2 shifted polymerase away from the TSS toward upstream and downstream distal positions. This redistribution of pol II is similar in magnitude to that caused by depletion of the elongation factor Spt5. We propose that coupled decapping of nascent transcripts and premature termination by the "torpedo" mechanism is a widespread mechanism that limits bidirectional pol II elongation. Regulated cotranscriptional decapping near promoter-proximal pause sites followed by premature termination could control productive pol II elongation.