RNA polymerase II elongation complex

Wang, Z. and Rana, T.M. (1997) DNA damage-dependent transcriptional arrest and termination of RNA polymerase II elongation complexes in DNA template containing HIV-1 promoter. Proc. Natl. Acad. Sci. USA,... 

Kireeva, M. L., Komissarova, N., Waugh, D. S., and Kashlev, M. (2000). The 8-nucleo-tide-long RNA DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. / Biol. Chem. 275(9), 6530-6536. 

Yamaguchi Y, Takagi T, Wada T, Yano K, Euruya A, Sugimoto S, Hasegawa J, Handa H (1999) NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97 41-51... 

Fiedler, U., and Timmers, H. T. (2001). Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation. Nucleic Acids Res. 29(13), 2706-2714. 

Izban, M. G., and Luse, D. S. (1993a). The increment of SII facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes. J. Biol. Chem. 268, 12874-12885. 

Samkurashvili, I., and Luse, D. S. (1998). Structural changes in the RNA polymerase II transcription complex during transition from initiation to elongation. Mol. Cell. Biol. 18(9), 5343-5354. 

This consists of DNA-dependent RNA polymerase II and basal transcription factors (TFIIX, X = A - H). First, the basal factor TFIID binds to the promoter. TFIID, a large complex of numerous proteins, contains TATA boxbinding protein (TBP) and so-called TAFs (TBP-associated factors). The polymerase is attached to this core with the help of TFIIB. Before transcription starts, additional TFs have to bind, including TFIIH, which has heli-case activity and separates the two strands of DNA during elongation. In all, some 35 differ-... 

The large subimit of RNA polymerase II plays an important role at the beginning of the transcription process. The large subimit of the mammalian enzyme contains 52 copies of the heptamer sequence YSPTSPS in the C-terminal domain (CTD) at which phosphorylation occurs. Phosphorylation occurs extensively on the Ser-residues of the CTD, to a lesser degree at the Thr-residues, and, very rarely, at the Tyr-residues. Two forms of RNA polymerase II can be isolated from cellular extracts a underphosphory-lated form and a hyper-phosphorylated form. The isoforms fulfill different functions RNA polymerase found in the initiation complex tends to display little or no phosphorylation at the C-terminus of the large subunit, while RNA polymerase II active in elongation is hyperphosphorylated in this region of the protein. 

Fig. 1.32. Phosphorylation of the C-terminal domain of RNA polymerase II and the beginning of transcription. The transition from the initiation complex to actual begin of transcription is regulated via phosphorylation of the C-terminal domain (CTD) of RNA polymerase II. In the above model it is assumed that initially a complex is formed between TFIID and a holoenzyme of RNA polymerase consisting of RNA polymerase II and associated factors (mediators, SRB proteins) and the basal transcription factors. Phosphorylation of the C-terminal domain effects the dissociation of the RNA polymerase from the initation complex and the transition to the elongation phase. A protein kinase, which is part of TFIIH, is responsible for the phosphorylation. The nature of the signal that induces phosphorylation of RNA polymerase II remains unknown. SRB suppressor of RNA polymerase B. After Koleske and Young (1995).

Studies have shown that quercetin, kaempferol, and fisetin inhibited transcription with RNA polymerase II in permeabilized normal human fibroblasts (WI-38 cells) flavone and chrysin exhibited weak activity. Addition of quercetin to an ongoing transcription reaction arrested it promptly, suggesting that quercetin was inhibiting the elongation step. The effects of several flavonoids (quercetin, quercetagetin, myricetin, and baicalein) exhibited complex interactions with DNA and RNA polymerases, depending on the particular flavonoid and the enzyme species. 

Cyclin T-CDK9 (review Simone and Girodano, 2001) functions as a positive transcription factor during transcription elongation of RNA polymerase II by phosphor-ylating the CTD. The HIV regulatory protein Tat binds to and specifically activates the cyclin T-CDK9 complex. 

TFIID (which contains the TATA-box binding protein, TBP) binds to the TATA box. TFIIA and TFIIB then bind, followed by recruitment of RNA polymerase II and TFIIF. TFIIH and TFIIE then bind to form the preinitiation complex (PIC). Kinases phosphorylate the C-terminal domain of Pol II, leading to the open complex in which the DNA strands are separated. RNA is produced during elongation as Pol II and TFIIF leave the promoter and the other general transcription factors behind. Pol II dissociates during the termination phase, and the CTD is dephosphorylated. Pol II/TFIIF is then recycled to bind to another promoter. 

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