1. Structure of an RNA polymerase II–RNA inhibitor complex elucidates transcription regulation by noncoding RNAs
- Author
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Alexander Eisenführ, Florian Brueckner, Patrick Cramer, Michael Famulok, Hubert Kettenberger, and Mirko Theis
- Subjects
Models, Molecular ,RNA, Untranslated ,Transcription, Genetic ,Molecular Sequence Data ,RNA-dependent RNA polymerase ,RNA polymerase II ,Saccharomyces cerevisiae ,Biology ,Crystallography, X-Ray ,Structural Biology ,Transcription (biology) ,Gene Expression Regulation, Fungal ,RNA polymerase I ,RNA, Messenger ,Molecular Biology ,Base Sequence ,RNA ,Non-coding RNA ,Molecular biology ,Protein Structure, Tertiary ,RNA silencing ,biology.protein ,Nucleic Acid Conformation ,RNA Polymerase II ,Small nuclear RNA ,Protein Binding - 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.
- Published
- 2005
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