title: Nature of the nucleosomal barrier to RNA polymerase II.
abstract: In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged into nucleosomes, but in vitro encounters with the nucleosomes induce catalytic inactivation (arrest) of the pol II core enzyme. To determine potential mechanisms making nucleosomes transparent to transcription in vivo, we analyzed the nature of the nucleosome-induced arrest. We found that the arrests have been detected mostly at positions of strong intrinsic pause sites of DNA. The transient pausing makes pol II vulnerable to arrest, which involves backtracking of the elongation complex for a considerable distance on DNA. The histone-DNA contacts reestablished in front of pol II stabilize backtracked conformation of the polymerase. In agreement with this mechanism, blocking of backtracking prevents nucleosome-induced arrest. Transcript cleavage factor TFIIS reactivates the backtracked complexes and promotes pol II transcription through the nucleosome. Our findings establish the crucial role of elongation factors that suppress pol II pausing and backtracking for transcription in the context of chromatin.
authors.affiliation: NCI Center for Cancer Research, Frederick, Maryland 21702, USA.
authors.forename: Maria L
authors.initials: ML
authors.lastname: Kireeva
authors.forename: Brynne
authors.initials: B
authors.lastname: Hancock
authors.forename: Gina H
authors.initials: GH
authors.lastname: Cremona
authors.forename: Wendy
authors.initials: W
authors.lastname: Walter
authors.forename: Vasily M
authors.initials: VM
authors.lastname: Studitsky
authors.forename: Mikhail
authors.initials: M
authors.lastname: Kashlev
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics; D006657:Histones / Q000378:metabolism; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism*; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000378:metabolism
chemical_list: D006657:Histones; D009707:Nucleosomes; D035602:Transcriptional Elongation Factors; C018648:transcription factor S-II; D004247:DNA; D012319:RNA Polymerase II