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Published online 26 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 6 1904-1916
© 2004 Oxford University Press

Characterization of a novel RNA polymerase II arrest site which lacks a weak 3' RNA–DNA hybrid

Peter J. Hawryluk1,2, Andrea Újvári1 and Donal S. Luse*,1,2

1 Department of Molecular Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA and 2 Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA

*To whom correspondence should be addressed at Department of Molecular Biology, Mail Location NC20, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA. Tel: +1 216 445 7688; Fax: +1 216 444 0512; Email: lused{at}ccf.org

Received as resubmission February 12, 2004; Accepted March 4, 2004

Transcript elongation by RNA polymerase II is blocked at DNA sequences called arrest sites. An exceptionally weak RNA–DNA hybrid is often thought to be necessary at the point of arrest. We have identified an arrest site from the tyrosine hydroxylase (TH) gene which does not fit this pattern. Transcription of many sequence variants of this site shows that the RNA–DNA hybrid over the three bases immediately preceding the major arrest point may be strong (i.e. C:G) without interfering with arrest. However, arrest at the TH site requires the presence of a pyrimidine at the 3' end and arrest increases when the 3'-most segment is pyrimidine rich. We also demonstrated that arrest at the TH site is completely dependent on the presence of a purine-rich element immediately upstream of the RNA–DNA hybrid. Thus, the RNA polymerase II arrest element from the TH gene has several unanticipated characteristics: arrest is independent of a weak RNA–DNA hybrid at the 3' end of the transcript, but it requires both a pyrimidine at the 3' end and a polypurine element upstream of the RNA–DNA hybrid.


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