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. 2006 Jan;13(1):44-8.
doi: 10.1038/nsmb1032. Epub 2005 Dec 11.

Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs

Hubert Kettenberger  1 , Alexander Eisenführ, Florian Brueckner, Mirko Theis, Michael Famulok, Patrick Cramer
Affiliations

Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs

Hubert Kettenberger et al. Nat Struct Mol Biol. 2006 Jan.

Abstract

The noncoding RNA B2 and the RNA aptamer FC bind RNA polymerase (Pol) II and inhibit messenger RNA transcription initiation, but not elongation. We report the crystal structure of FC(*), the central part of FC RNA, bound to Pol II. FC(*) RNA forms a double stem-loop structure in the Pol II active center cleft. B2 RNA may bind similarly, as it competes with FC(*) RNA for Pol II interaction. Both RNA inhibitors apparently prevent the downstream DNA duplex and the template single strand from entering the cleft after DNA melting and thus interfere with open-complex formation. Elongation is not inhibited, as nucleic acids prebound in the cleft would exclude the RNA inhibitors. The structure also indicates that A-form RNA could interact with Pol II similarly to a B-form DNA promoter, as suggested for the bacterial transcription inhibitor 6S RNA.

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