title: Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.
abstract: Nucleosome-depleted regions (NDRs) (also called nucleosome-free regions or NFRs) are often found in the promoter regions of many yeast genes, and are formed by multiple mechanisms, including the binding of activators and enhancers, the actions of chromatin remodeling complexes, and the specific DNA sequences themselves. However, it remains unclear whether NDR formation per se is essential for transcriptional activation. Here, we examined the relationship between nucleosome organization and gene expression using a defined yeast reporter system, consisting of the CYC1 minimal core promoter and the lacZ gene. We introduced simple repeated sequences that should be either incorporated in nucleosomes or excluded from nucleosomes in the site upstream of the TATA boxes. The (CTG)12, (GAA)12 and (TGTAGG)6 inserts were incorporated into a positioned nucleosome in the core promoter region, and did not affect the reporter gene expression. In contrast, the insertion of (CGG)12, (TTAGGG)6, (A)34 or (CG)8 induced lacZ expression by 10-20 fold. Nucleosome mapping analyses revealed that the inserts that induced the reporter gene expression prevented nucleosome formation, and created an NDR upstream of the TATA boxes. Thus, our results demonstrated that NDR formation dictated by DNA sequences is sufficient for transcriptional activation from the core promoter in vivo.
authors.affiliation: Graduate School of Advanced Science and Engineering/RISE, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8640, Japan; Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Ichikawa
authors.affiliation: Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan.
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Morohashi
authors.affiliation: Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan.
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Tomita
authors.affiliation: Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Mitchell
authors.affiliation: Graduate School of Advanced Science and Engineering/RISE, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8640, Japan.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Kurumizaka
authors.affiliation: Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan. Electronic address: shimizum@chem.meisei-u.ac.jp.
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Shimizu
mesh_terms: D001483:Base Sequence; D015825:Chromosomes, Fungal / Q000737:chemistry / Q000235:genetics; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D007763:Lac Operon; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics*; D016385:TATA Box; D015533:Transcriptional Activation
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes
keywords: Chromatin; DNA structure; Nucleosome depleted-region; Nucleosome positioning; Transcription; Yeast