title: Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase.
abstract: Nucleosomes are barriers to transcription in vitro; however, their effects on RNA polymerase in vivo are unknown. Here we describe a simple and general strategy to comprehensively map the positions of elongating and arrested RNA polymerase II (RNAPII) at nucleotide resolution. We find that the entry site of the first (+1) nucleosome is a barrier to RNAPII for essentially all genes, including those undergoing regulated pausing farther upstream. In contrast to the +1 nucleosome, gene body nucleosomes are low barriers and cause RNAPII stalling both at the entry site and near the dyad axis. The extent of the +1 nucleosome barrier correlates with nucleosome occupancy but anticorrelates with enrichment of histone variant H2A.Z. Importantly, depletion of H2A.Z from a nucleosome position results in a higher barrier to RNAPII. Our results suggest that nucleosomes present significant, context-specific barriers to RNAPII in vivo that can be tuned by the incorporation of H2A.Z.
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Weber
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Srinivas
authors.initials: S
authors.lastname: Ramachandran
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address: steveh@fhcrc.org.
authors.forename: Steven
authors.initials: S
authors.lastname: Henikoff
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry; D003593:Cytoplasm / Q000737:chemistry; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D004330:Drosophila; D006657:Histones / Q000737:chemistry*; D009707:Nucleosomes / Q000737:chemistry*; D010766:Phosphorylation; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry; D034622:RNA Interference; D012319:RNA Polymerase II / Q000737:chemistry; D015203:Reproducibility of Results; D014158:Transcription, Genetic; D019076:Transgenes
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes; D012313:RNA; D012319:RNA Polymerase II; D012321:DNA-Directed RNA Polymerases