title: Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs.
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.
authors.affiliation: Gene Center, University of Munich, Department of Chemistry and Biochemistry, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
authors.forename: Hubert
authors.initials: H
authors.lastname: Kettenberger
authors.forename: Alexander
authors.initials: A
authors.lastname: Eisenführ
authors.forename: Florian
authors.initials: F
authors.lastname: Brueckner
authors.forename: Mirko
authors.initials: M
authors.lastname: Theis
authors.forename: Michael
authors.initials: M
authors.lastname: Famulok
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D015966:Gene Expression Regulation, Fungal; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012319:RNA Polymerase II / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D012319:RNA Polymerase II