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J. Biol. Chem., Vol. 278, Issue 50, 50101-50111, December 12, 2003

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Combinatorial Control of Human RNA Polymerase II (RNAP II) Pausing and Transcript Cleavage by Transcription Factor IIF, Hepatitis Antigen, and Stimulatory Factor II^*

Chunfen Zhang, Honggao Yan, and Zachary F. Burton

From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319

When RNA polymerase II (RNAP II) is forced to stall, elongation complexes (ECs) are observed to leave the active pathway and enter a paused state. Initially, ECs equilibrate between active and paused conformations, but with stalls of a long duration, ECs backtrack and become sensitive to transcript cleavage, which is stimulated by the EC rescue factor stimulatory factor II (TFIIS/SII). In this work, the rates for equilibration between the active and pausing pathways were estimated in the absence of an elongation factor, in the presence of hepatitis antigen (HDAg), and in the presence of transcription factor IIF (TFIIF), with or without addition of SII. Rates of equilibration between the active and paused states are not very different in the presence or absence of elongation factors HDAg and TFIIF. SII facilitates escape from stalled ECs by stimulating RNAP II backtracking and transcript cleavage and by increasing rates into and out of the paused EC. TFIIF and SII cooperate to merge the pausing and active pathways, a combinatorial effect not observed with HDAg and SII. In the presence of HDAg and SII, pausing is observed without stimulation of transcript cleavage, indicating that the EC can pause without backtracking beyond the pre-translocated state.

Received for publication, July 15, 2003 , and in revised form, September 2, 2003.

^* This work was supported in part by National Institutes of Health Grant GM57461 (to Z. F. B.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Recipient of support from the Michigan State University Agricultural Experiment Station. To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Biology; Michigan State University, E. Lansing, MI 48824-1319. Tel.: 517-353-0859; Fax: 517-353-9334; E-mail: burton{at}msu.edu.

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