After transcription initiation, RNA polymerase (Pol) II escapes from the promoter and recruits elongation factors. The molecular basis for the initiation-elongation factor exchange during this transition remains poorly understood. Here, we used chromatin immunoprecipitation (ChIP) to elucidate the initiation-elongation transition of Pol II in the budding yeast Saccharomyces cerevisiae. We show that the early Pol II elongation factor Spt5 contributes to stable recruitment of the mRNA capping enzymes Cet1, Ceg1, and Abd1. Genome-wide occupancy for Cet1 and Ceg1 is restricted to the transcription start site (TSS), whereas occupancy for Abd1 peaks at ϳ110 nucleotides downstream, and occupancy for the cap-binding complex (CBC) rises subsequently. Abd1 and CBC are important for recruitment of the kinases Ctk1 and Bur1, which promote elongation and capping enzyme release. These results suggest that cap completion stimulates productive Pol II elongation.T ranscription of protein-coding genes by RNA polymerase (Pol) II begins with assembly of an initiation complex at the promoter. As the RNA grows, initiation factors dissociate from Pol II, and elongation factors are recruited (1-3). The initiationelongation transition begins when the nascent RNA grows to about 12 nucleotides (nt), which releases initiation factor TFIIB (4, 5). Release of initiation factors frees the Pol II clamp domain, which binds the conserved elongation factor Spt5 (6, 7). Here, we refer to the exchange of initiation by elongation factors as the initiation-elongation transition. The transition starts with the dissociation of initiation factors and ends with completed recruitment of elongation factors.During initiation, the C-terminal repeat domain (CTD) of Pol II gets phosphorylated at the serine 5 (S5) and S7 residues (8-10). CTD S5 phosphorylation is important for recruitment of RNA 5= capping enzymes (11-13). Capping starts with removal of the terminal ␥-phosphate from the 5= triphosphate end of the nascent RNA, which is catalyzed by the RNA triphosphatase (14-16). The truncated RNA 5= end is then linked to an inverted guanylyl group by the guanylyltransferase. Finally, the cap methyltransferase methylates position N7 of the newly added terminal guanine. In Saccharomyces cerevisiae the three catalytic activities are encoded by Cet1, Ceg1, and Abd1, respectively. In metazoans the first two steps of the capping reaction are catalyzed by a single capping enzyme consisting of an N-terminal triphosphatase and a C-terminal guanylyltransferase domain. The resulting 7-methylguanosine (m7G) cap protects the transcript from degradation and promotes translation initiation of the mRNA (17, 18). The complete cap associates with the cap-binding complex (CBC) that functions in pre-mRNA splicing and mRNA export (19,20).We have previously obtained high-resolution genome-wide occupancy profiles for Pol II initiation and elongation factors by chromatin immunoprecipitation (ChIP) in S. cerevisiae. These studies showed that initiation factor occupancy peaked around 50...