The transcription initiation and elongation steps of protein-coding genes usually rely on unrelated protein complexes. However, the TFIIS elongation factor is implicated in both processes. We found that, in the absence of the Med31 Mediator subunit, yeast cells required the TFIIS polymerase II (Pol II)-binding domain but not its RNA cleavage stimulatory activity that is associated with its elongation function. We also found that the TFIIS Pol II-interacting domain was needed for the full recruitment of Pol II to several promoters in the absence of Med31. This work demonstrated that, in addition to its thoroughly characterized role in transcription elongation, TFIIS is implicated through its Pol II-binding domain in the formation or stabilization of the transcription initiation complex in vivo.RNA polymerase II ͉ Saccharomyces cerevisiae ͉ transcription regulation ͉ Med31 ͉ Mediator subunit T he transcription of protein-coding eukaryotic genes by RNA polymerase II (Pol II) requires three successive steps: initiation, elongation, and termination. Transcription initiation of class II genes involves the binding of activators to regulatory sequences; the recruitment of RNA Pol II to the core promoter via interactions with activators, coactivators, and general transcription factors; and the initiation reaction per se with DNA strand opening and abortive initiation (1). A major coactivator target of transcriptional activators is the Mediator (2, 3). One of its activities is the recruitment and/or stabilization of Pol II at core promoters (4). After transcription initiation, Pol II enters elongation, during which it can be arrested because of the presence of specific DNA sequences that promote pausing, or because of obstacles such as DNA damage or bound proteins. To avoid or escape arrest, Pol II requires different elongation factors, including TFIIS (5). Evidence suggests that TFIIS could be implicated in both initiation and elongation.In vitro, TFIIS can reactivate arrested elongation complexes by stimulating endonucleolytic cleavage by Pol II of the nascent RNA (5). TFIIS is composed of three domains that fold independently, as demonstrated by NMR analysis of its structure (6, 7). Cleavage-stimulating activity minimally requires the Cterminal two-thirds of the protein, that is, its domain II and III separated by a 15-aa linker (7,8). Domain II forms a three-helix bundle followed by three short helices, with a basic patch on the third helix (␣-3) that is essential for TFIIS binding to Pol II (7). Crystallographic analysis of a TFIIS-Pol II complex confirmed that this basic patch lies at the TFIIS-Pol II interface (7,8). TFIIS binding to Pol II is required for domain III to reach the Pol II active site. Domain III forms a zinc ribbon that contains a conserved RSADE motif, responsible for the stimulation of RNA cleavage (7,8).TFIIS is also implicated in transcription initiation. First, the deletion of the DST1 gene, encoding TFIIS in yeast, is colethal with the deletion of the gene encoding the Med31 subunit of the Medi...