title: Structural analysis of nucleosomal barrier to transcription.
abstract: Thousands of human and Drosophila genes are regulated at the level of transcript elongation and nucleosomes are likely targets for this regulation. However, the molecular mechanisms of formation of the nucleosomal barrier to transcribing RNA polymerase II (Pol II) and nucleosome survival during/after transcription remain unknown. Here we show that both DNA-histone interactions and Pol II backtracking contribute to formation of the barrier and that nucleosome survival during transcription likely occurs through allosterically stabilized histone-histone interactions. Structural analysis indicates that after Pol II encounters the barrier, the enzyme backtracks and nucleosomal DNA recoils on the octamer, locking Pol II in the arrested state. DNA is displaced from one of the H2A/H2B dimers that remains associated with the octamer. The data reveal the importance of intranucleosomal DNA-protein and protein-protein interactions during conformational changes in the nucleosome structure on transcription. Mechanisms of nucleosomal barrier formation and nucleosome survival during transcription are proposed.
authors.affiliation: Department of Pharmacology, Rutgers University School of Medicine, Piscataway, NJ 08854;
authors.forename: Daria A
authors.initials: DA
authors.lastname: Gaykalova
authors.affiliation: Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111;
authors.forename: Olga I
authors.initials: OI
authors.lastname: Kulaeva
authors.affiliation: Biology Faculty, Lomonosov Moscow State University, Moscow, Russia 119991.
authors.forename: Olesya
authors.initials: O
authors.lastname: Volokh
authors.affiliation: Biology Faculty, Lomonosov Moscow State University, Moscow, Russia 119991.
authors.forename: Alexey K
authors.initials: AK
authors.lastname: Shaytan
authors.affiliation: Department of Pharmacology, Rutgers University School of Medicine, Piscataway, NJ 08854;
authors.forename: Fu-Kai
authors.initials: FK
authors.lastname: Hsieh
authors.affiliation: Biology Faculty, Lomonosov Moscow State University, Moscow, Russia 119991.
authors.forename: Mikhail P
authors.initials: MP
authors.lastname: Kirpichnikov
authors.affiliation: Biology Faculty, Lomonosov Moscow State University, Moscow, Russia 119991.
authors.forename: Olga S
authors.initials: OS
authors.lastname: Sokolova
authors.affiliation: Department of Pharmacology, Rutgers University School of Medicine, Piscataway, NJ 08854; Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111; Biology Faculty, Lomonosov Moscow State University, Moscow, Russia 119991 vasily.studitsky@fccc.edu.
authors.forename: Vasily M
authors.initials: VM
authors.lastname: Studitsky
mesh_terms: D004247:DNA / Q000378:metabolism; D004257:DNA Polymerase II / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D006657:Histones; D009707:Nucleosomes; D004247:DNA; D004257:DNA Polymerase II
keywords: RNA polymerase II; backtracking; chromatin; elongation; transcription