Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo

Yuichi Ichikawa, Nobuyuki Morohashi, Nobuyuki Tomita, Aaron P. Mitchell, Hitoshi Kurumizaka, Mitsuhiro Shimizu

    Research output: Contribution to journalArticle

    1 Citation (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)57-62
    Number of pages6
    JournalBiochemical and Biophysical Research Communications
    Volume476
    Issue number2
    DOIs
    Publication statusPublished - 2016 Jul 22

    Fingerprint

    Nucleosomes
    Transcription
    Yeast
    Yeasts
    Gene expression
    TATA Box
    DNA sequences
    Reporter Genes
    Gene Expression
    Genetic Promoter Regions
    Transcriptional Activation
    Genes
    Chemical activation
    Lac Operon
    Chromatin Assembly and Disassembly
    Chromatin

    Keywords

    • Chromatin
    • DNA structure
    • Nucleosome depleted-region
    • Nucleosome positioning
    • Transcription
    • Yeast

    ASJC Scopus subject areas

    • Biochemistry
    • Biophysics
    • Cell Biology
    • Molecular Biology

    Cite this

    Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo. / Ichikawa, Yuichi; Morohashi, Nobuyuki; Tomita, Nobuyuki; Mitchell, Aaron P.; Kurumizaka, Hitoshi; Shimizu, Mitsuhiro.

    In: Biochemical and Biophysical Research Communications, Vol. 476, No. 2, 22.07.2016, p. 57-62.

    Research output: Contribution to journalArticle

    Ichikawa, Yuichi ; Morohashi, Nobuyuki ; Tomita, Nobuyuki ; Mitchell, Aaron P. ; Kurumizaka, Hitoshi ; Shimizu, Mitsuhiro. / Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo. In: Biochemical and Biophysical Research Communications. 2016 ; Vol. 476, No. 2. pp. 57-62.
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