title: When transcription goes on Holliday: Double Holliday junctions block RNA polymerase II transcription in vitro.
abstract: Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJs), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact. Thus, the DHJ structure should strongly resist transient unwinding during transcription; consequently, it is predicted to cause significantly stronger blockage than single HJ structures. The patterns of transcription blockage obtained for RNA polymerase II transcription in HeLa cell nuclear extracts were in accordance with this prediction. However, we did not detect transcription blockage with purified T7 phage RNA polymerase; we discuss a possible explanation for this difference. In general, our findings implicate naturally occurring Holliday junctions in transcription arrest.
authors.affiliation: Department of Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Anne
authors.initials: A
authors.lastname: Pipathsouk
authors.affiliation: Department of Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Boris P
authors.initials: BP
authors.lastname: Belotserkovskii
authors.affiliation: Department of Biology, Stanford University, Stanford, CA 94305, USA. Electronic address: hanawalt@stanford.edu.
authors.forename: Philip C
authors.initials: PC
authors.lastname: Hanawalt
mesh_terms: D045744:Cell Line, Tumor; D004247:DNA / Q000235:genetics; D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D045566:DNA, Cruciform / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D042822:Genomic Instability / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D012319:RNA Polymerase II / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D045566:DNA, Cruciform; D014764:Viral Proteins; D004247:DNA; D012319:RNA Polymerase II; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases
keywords: Genomic instability; Holliday junctions; Repair; Transcription; Unusual DNA structures