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  • 1.
    Levendosky, Robert F.
    et al.
    Johns Hopkins Univ, TC Jenkins Dept Biophys, Baltimore, MD 21218 USA..
    Sabantsev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Deindl, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bowman, Gregory D.
    Johns Hopkins Univ, TC Jenkins Dept Biophys, Baltimore, MD 21218 USA..
    The Chd1 chromatin remodeler shifts hexasomes unidirectionally2016In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e21356Article in journal (Refereed)
    Abstract [en]

    Despite their canonical two-fold symmetry, nucleosomes in biological contexts are often asymmetric: functionalized with post-translational modifications (PTMs), substituted with histone variants, and even lacking H2A/H2B dimers. Here we show that the Widom 601 nucleosome positioning sequence can produce hexasomes in a specific orientation on DNA, providing a useful tool for interrogating chromatin enzymes and allowing for the generation of nucleosomes with precisely defined asymmetry. Using this methodology, we demonstrate that the Chd1 chromatin remodeler from Saccharomyces cerevisiae requires H2A/H2B on the entry side for sliding, and thus, unlike the back-and-forth sliding observed for nucleosomes, Chd1 shifts hexasomes unidirectionally. Chd1 takes part in chromatin reorganization surrounding transcribing RNA polymerase II (Pol II), and using asymmetric nucleosomes we show that ubiquitin-conjugated H2B on the entry side stimulates nucleosome sliding by Chd1. We speculate that biased nucleosome and hexasome sliding due to asymmetry contributes to the packing of arrays observed in vivo.

  • 2.
    Sabantsev, Anton
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Levendosky, Robert F.
    Johns Hopkins Univ, TC Jenkins Dept Biophys, Baltimore, MD 21218 USA.
    Zhuang, Xiaowei
    Harvard Univ, Howard Hughes Med Inst, Cambridge, MA 02138 USA;Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA;Harvard Univ, Dept Phys, Cambridge, MA 02138 USA.
    Bowman, Gregory D.
    Johns Hopkins Univ, TC Jenkins Dept Biophys, Baltimore, MD 21218 USA.
    Deindl, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1720Article in journal (Refereed)
    Abstract [en]

    ATP-dependent chromatin remodelling enzymes (remodellers) regulate DNA accessibility in eukaryotic genomes. Many remodellers reposition (slide) nucleosomes, however, how DNA is propagated around the histone octamer during this process is unclear. Here we examine the real-time coordination of remodeller-induced DNA movements on both sides of the nucleosome using three-colour single-molecule FRET. During sliding by Chd1 and SNF2h remodellers, DNA is shifted discontinuously, with movement of entry-side DNA preceding that of exit-side DNA. The temporal delay between these movements implies a single ratelimiting step dependent on ATP binding and transient absorption or buffering of at least one base pair. High-resolution cross-linking experiments show that sliding can be achieved by buffering as few as 3 bp between entry and exit sides of the nucleosome. We propose that DNA buffering ensures nucleosome stability during ATP-dependent remodelling, and provides a means for communication between remodellers acting on opposite sides of the nucleosome.

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