In transcriptional regulation, RNA polymerase II (pol II) interacts and forms complexes with a number of protein factors. To isolate and identify the pol II-associated proteins, we constructed a Schizosaccharomyces pombe strain carrying a FLAG tag sequence fused to the rpb3 gene encoding the pol II subunit Rpb3. By immunoaffinity purification with anti-FLAG antibody-resin, a pol II complex containing the Rpb1 subunit with a nonphosphorylated carboxyl-terminal domain (CTD) was isolated. In addition to the pol II subunits, the complex was found to contain three subunits of a transcription factor TFIIF (TFIIF␣, TFIIF, and Tfg3) and TFIIF-interacting CTD-phosphatase Fcp1. The same type of pol II complex could also be purified from an Fcp1-tagged strain. The isolated Fcp1 showed CTD-phosphatase activity in vitro. The fcp1 gene is essential for cell viability. Fcp1 and pol II interacted directly in vitro. Furthermore, by chemical cross-linking, glutathione S-transferase pulldown, and affinity chromatography, the Fcp1-interacting subunit of pol II was identified as Rpb4, which plays regulatory roles in transcription. We also constructed an S. pombe thiamine-dependent rpb4 shut-off system. On repression of rpb4 expression, the cell produced more of the nonphosphorylated form of Rpb1, but the pol II complex isolated with the anti-FLAG antibody contained less Fcp1 and more of the phosphorylated form of Rpb1 with a concomitant reduction in Rpb4. This result indicates the importance of Fcp1-Rpb4 interaction for formation of the Fcp1/TFIIF/pol II complex in vivo.RNA polymerase II (pol II), which is involved in the synthesis of all mRNAs, is a highly structured complex consisting of as many as 12 subunits, Rpb1 to Rpb12 (30,37,60,67,75), but for accurate transcription, pol II is controlled by a number of factors through protein-protein interactions (56). In preinitiation complex (PIC) formation, a general transcription factor (GTF), TFIIF, associates with pol II to recruit it to the complex on a promoter, which is formed of GTFs, including TFIIA, TFIIB, and TFIID (19). TFIIB (22,39,68) and one of the TATA binding protein (TBP)-associating factor (TAF) subunits of TFIID (7) interacts with pol II, and the TBP subunit of TFIID also binds to the nonphosphorylated carboxyterminal domain (CTD) of Rpb1 (69). TFIIE assembles into the complex through direct interaction with pol II (39, 46) and then promotes association of TFIIH, which phosphorylates the CTD (17, 43, 51). The kinase subunit of TFIIH binds to pol II (18).The alternative pathway of PIC formation is the prior assembly of pol II and factors to form pol II holoenzyme (38,50). This large complex consists of pol II, a subset of GTFs, and a mediator complex, and it is recruited to a promoter through the interaction of mediators with DNA-binding activators. In the holoenzyme, the mediator complex, which is composed of SRBs (for suppressor of RNA pol B), mediators, and other subunits, is attached to the CTD (49) and possibly other parts of pol II (3). Srb10 in the mediator comp...