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      Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling

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          Abstract

          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 rate-limiting 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.

          Abstract

          Chromatin remodelling enzymes (remodellers) regulate DNA accessibility of eukaryotic genomes, which rely in large part on an ability to reposition nucleosomes. Here the authors use three-colour single-molecule FRET to simultaneously monitor remodeller-induced DNA movements on both sides of the nucleosome in real-time.

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          Computer control of microscopes using µManager.

          With the advent of digital cameras and motorization of mechanical components, computer control of microscopes has become increasingly important. Software for microscope image acquisition should not only be easy to use, but also enable and encourage novel approaches. The open-source software package µManager aims to fulfill those goals. This unit provides step-by-step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software. © 2010 by John Wiley & Sons, Inc.
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            Structure and mechanism of helicases and nucleic acid translocases.

            Helicases and translocases are a ubiquitous, highly diverse group of proteins that perform an extraordinary variety of functions in cells. Consequently, this review sets out to define a nomenclature for these enzymes based on current knowledge of sequence, structure, and mechanism. Using previous definitions of helicase families as a basis, we delineate six superfamilies of enzymes, with examples of crystal structures where available, and discuss these structures in the context of biochemical data to outline our present understanding of helicase and translocase activity. As a result, each superfamily is subdivided, where appropriate, on the basis of mechanistic understanding, which we hope will provide a framework for classification of new superfamily members as they are discovered and characterized.
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              Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome.

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                Author and article information

                Contributors
                gdbowman@jhu.edu
                sebastian.deindl@icm.uu.se
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                12 April 2019
                12 April 2019
                2019
                : 10
                : 1720
                Affiliations
                [1 ]ISNI 0000 0004 1936 9457, GRID grid.8993.b, Department of Cell and Molecular Biology, Science for Life Laboratory, , Uppsala University, ; 75237 Uppsala, Sweden
                [2 ]ISNI 0000 0001 2171 9311, GRID grid.21107.35, T.C. Jenkins Department of Biophysics, , Johns Hopkins University, ; Baltimore, MD 21218 USA
                [3 ]ISNI 000000041936754X, GRID grid.38142.3c, Howard Hughes Medical Institute, , Harvard University, ; Cambridge, MA 02138 USA
                [4 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Chemistry and Chemical Biology, , Harvard University, ; Cambridge, MA 02138 USA
                [5 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Physics, , Harvard University, ; Cambridge, MA 02138 USA
                Author information
                http://orcid.org/0000-0002-6034-7853
                Article
                9657
                10.1038/s41467-019-09657-1
                6461674
                30979890
                69d25a42-2480-43ce-be6c-81f9b3e97704
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 5 December 2018
                : 20 March 2019
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