title: Histone occupancy in vivo at the 601 nucleosome binding element is determined by transcriptional history.
abstract: We report in vivo analysis of histone and RNA polymerase II (pol II) occupancy at the 601 element, which functions as a strong in vitro nucleosome-positioning element and transcriptional pause site. Surprisingly, nucleosomes were not strongly positioned over the 601 element inserted either within a yeast chromosomal open reading frame (ORF) (GAL1-YLR454W) or in an intergenic region. In fact 601 within GAL1-YLR454W was actually depleted of histones relative to flanking sequences and did not cause pol II pausing. Upstream of an inserted 601 element within GAL1-YLR454W, a positioned nucleosome was formed whose location depended on transcriptional history; it shifted after a round of activation and repression. Transcriptional activation caused histone eviction throughout the GAL1-YLR454W ORF, except at 601, where there was no loss and some net histone deposition. In contrast, a second round of activation after glucose shutoff caused histone eviction both at 601 and elsewhere in the ORF. We conclude that the intrinsic high-affinity histone-DNA interactions at 601 do not necessarily play a dominant role in establishing nucleosomes or pol II pause sites within a coding region in vivo and that transcriptional history can have an important influence on histone occupancy flanking this sequence.
authors.affiliation: Program in Molecular Biology and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
authors.forename: Roberto
authors.initials: R
authors.lastname: Perales
authors.forename: Lian
authors.initials: L
authors.lastname: Zhang
authors.forename: David
authors.initials: D
authors.lastname: Bentley
mesh_terms: D042002:Chromatin Assembly and Disassembly; D005656:Fungal Proteins; D006657:Histones / Q000378:metabolism*; D009707:Nucleosomes / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism*; D014158:Transcription, Genetic; D015003:Yeasts / Q000235:genetics*
chemical_list: D005656:Fungal Proteins; D006657:Histones; D009707:Nucleosomes; D012319:RNA Polymerase II