title: Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.
abstract: We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over Escherichia coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro show strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor have fewer nucleosome-free regions, reduced rotational positioning and less translational positioning than obtained by intrinsic histone-DNA interactions. Notably, nucleosomes assembled in vitro have only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Zarmik
authors.initials: Z
authors.lastname: Moqtaderi
authors.forename: Barbara P
authors.initials: BP
authors.lastname: Rattner
authors.forename: Ghia
authors.initials: G
authors.lastname: Euskirchen
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: James T
authors.initials: JT
authors.lastname: Kadonaga
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
authors.forename: Kevin
authors.initials: K
authors.lastname: Struhl
mesh_terms: D002843:Chromatin / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004706:Endodeoxyribonucleases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D009707:Nucleosomes / Q000378:metabolism*; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D004269:DNA, Bacterial; D004271:DNA, Fungal; D029968:Escherichia coli Proteins; D006657:Histones; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D004706:Endodeoxyribonucleases