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      Single and double box HMGB proteins differentially destabilize nucleosomes

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          Abstract

          Nucleosome disruption plays a key role in many nuclear processes including transcription, DNA repair and recombination. Here we combine atomic force microscopy (AFM) and optical tweezers (OT) experiments to show that high mobility group B (HMGB) proteins strongly disrupt nucleosomes, revealing a new mechanism for regulation of chromatin accessibility. We find that both the double box yeast Hmo1 and the single box yeast Nhp6A display strong binding preferences for nucleosomes over linker DNA, and both HMGB proteins destabilize and unwind DNA from the H2A–H2B dimers. However, unlike Nhp6A, Hmo1 also releases half of the DNA held by the (H3–H4) 2 tetramer. This difference in nucleosome destabilization may explain why Nhp6A and Hmo1 function at different genomic sites. Hmo1 is enriched at highly transcribed ribosomal genes, known to be depleted of histones. In contrast, Nhp6A is found across euchromatin, pointing to a significant difference in cellular function.

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          Probing the relation between force--lifetime--and chemistry in single molecular bonds.

          E. Evans (2001)
          On laboratory time scales, the energy landscape of a weak bond along a dissociation pathway is fully explored through Brownian-thermal excitations, and energy barriers become encoded in a dissociation time that varies with applied force. Probed with ramps of force over an enormous range of rates (force/time), this kinetic profile is transformed into a dynamic spectrum of bond rupture force as a function of loading rate. On a logarithmic scale in loading rate, the force spectrum provides an easy-to-read map of the prominent energy barriers traversed along the force-driven pathway and exposes the differences in energy between barriers. In this way, the method of dynamic force spectroscopy (DFS) is being used to probe the complex relation between force-lifetime-and chemistry in single molecular bonds. Most important, DFS probes the inner world of molecular interactions to reveal barriers that are difficult or impossible to detect in assays of near equilibrium dissociation but that determine bond lifetime and strength under rapid detachment. To use an ultrasensitive force probe as a spectroscopic tool, we need to understand the physics of bond dissociation under force, the impact of experimental technique on the measurement of detachment force (bond strength), the consequences of complex interactions in macromolecular bonds, and effects of multiply-bonded attachments.
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            Rapid spontaneous accessibility of nucleosomal DNA.

            Gu Li, Marcia Levitus, Carlos Daniel Bustamante … (2005)
            DNA wrapped in nucleosomes is sterically occluded, creating obstacles for proteins that must bind it. How proteins gain access to DNA buried inside nucleosomes is not known. Here we report measurements of the rates of spontaneous nucleosome conformational changes in which a stretch of DNA transiently unwraps off the histone surface, starting from one end of the nucleosome, and then rewraps. The rates are rapid. Nucleosomal DNA remains fully wrapped for only approximately 250 ms before spontaneously unwrapping; unwrapped DNA rewraps within approximately 10-50 ms. Spontaneous unwrapping of nucleosomal DNA allows any protein rapid access even to buried stretches of the DNA. Our results explain how remodeling factors can be recruited to particular nucleosomes on a biologically relevant timescale, and they imply that the major impediment to entry of RNA polymerase into a nucleosome is rewrapping of nucleosomal DNA, not unwrapping.
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              Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones.

              Roger Deal, Jorja Henikoff, Steven Henikoff (2010)
              Nucleosome disruption and replacement are crucial activities that maintain epigenomes, but these highly dynamic processes have been difficult to study. Here, we describe a direct method for measuring nucleosome turnover dynamics genome-wide. We found that nucleosome turnover is most rapid over active gene bodies, epigenetic regulatory elements, and replication origins in Drosophila cells. Nucleosomes turn over faster at sites for trithorax-group than polycomb-group protein binding, suggesting that nucleosome turnover differences underlie their opposing activities and challenging models for epigenetic inheritance that rely on stability of histone marks. Our results establish a general strategy for studying nucleosome dynamics and uncover nucleosome turnover differences across the genome that are likely to have functional importance for epigenome maintenance, gene regulation, and control of DNA replication.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 25 January 2019
                Publication date (Electronic): 16 November 2018
                Publication date PMC-release: 16 November 2018
                Volume: 47
                Issue: 2
                Pages: 666-678
                Affiliations
                [1 ]Department of Physics, Northeastern University, Boston, MA, USA
                [2 ]Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
                [3 ]Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
                [4 ]Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
                [5 ]Howard Hughes Medical Institute, Chevy Chase, MD, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 617 373 5705; Fax: +1 617 373 2943; Email: mark@ 123456neu.edu

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

                Author information
                http://orcid.org/0000-0001-5136-5331
                http://orcid.org/0000-0003-3219-376X
                Article
                Publisher ID: gky1119
                DOI: 10.1093/nar/gky1119
                PMC ID: 6344895
                PubMed ID: 30445475
                SO-VID: 9542935b-fd4b-46ce-abc0-09f659ca0ab8
                Copyright © © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                Date accepted : 23 October 2018
                Date revision received : 19 October 2018
                Date received : 07 September 2018
                Page count
                Pages: 13
                Funding
                Funded by: National Institutes of Health 10.13039/100000002
                Award ID: GM072462
                Funded by: National Sleep Foundation 10.13039/100003187
                Award ID: MCB-1817712
                Funded by: National Institutes of Health 10.13039/100000002
                Award ID: GM75965
                Award ID: GM067777
                Categories
                Subject: Gene regulation, Chromatin and Epigenetics

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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