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Molecular and Cellular Biology, November 2001, p. 7495-7508, Vol. 21, No. 21
0270-7306/01/$04.00+0   DOI: 10.1128/MCB.21.21.7495-7508.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Mechanism of Poly(A) Signal Transduction to RNA Polymerase II In Vitro

Dong P. Tran, Steven J. Kim, Noh Jin Park, Tiffany M. Jew, and Harold G. Martinson*

Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095-1569

Received 29 March 2001/Returned for modification 25 May 2001/Accepted 26 July 2001

Termination of transcription by RNA polymerase II usually requires the presence of a functional poly(A) site. How the poly(A) site signals its presence to the polymerase is unknown. All models assume that the signal is generated after the poly(A) site has been extruded from the polymerase, but this has never been tested experimentally. It is also widely accepted that a "pause" element in the DNA stops the polymerase and that cleavage at the poly(A) site then signals termination. These ideas also have never been tested. The lack of any direct tests of the poly(A) signaling mechanism reflects a lack of success in reproducing the poly(A) signaling phenomenon in vitro. Here we describe a cell-free transcription elongation assay that faithfully recapitulates poly(A) signaling in a crude nuclear extract. The assay requires the use of citrate, an inhibitor of RNA polymerase II carboxyl-terminal domain phosphorylation. Using this assay we show the following. (i) Wild-type but not mutant poly(A) signals instruct the polymerase to stop transcription on downstream DNA in a manner that parallels true transcription termination in vivo. (ii) Transcription stops without the need of downstream elements in the DNA. (iii) cis-antisense inhibition blocks signal transduction, indicating that the signal to stop transcription is generated following extrusion of the poly(A) site from the polymerase. (iv) Signaling can be uncoupled from processing, demonstrating that signaling does not require cleavage at the poly(A) site.

* Corresponding author. Mailing address: Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569. Phone: (310) 825-3767. Fax: (310) 206-4038. E-mail: hgm{at}chem.ucla.edu.

Molecular and Cellular Biology, November 2001, p. 7495-7508, Vol. 21, No. 21
0270-7306/01/$04.00+0   DOI: 10.1128/MCB.21.21.7495-7508.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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