1
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Nucleosome assembly and disassembly pathways in vitro. PLoS One 2022; 17:e0267382. [PMID: 35830437 PMCID: PMC9278766 DOI: 10.1371/journal.pone.0267382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Structural fluctuations of nucleosomes modulate the access to internal DNA in eukaryotic cells; clearly characterisation of this fundamental process is crucial to understanding gene regulation. Here we apply PhAST (Photochemical Analysis of Structural Transitions) to monitor at a base pair level, structural alterations induced all along the DNA upon histone binding or release. By offering the first reliable, detailed comparison of nucleosome assembly and disassembly in vitro, we reveal similarities and differences between the two processes. We identify multiple, sequential intermediate states characterised by specific PhAST signals whose localisation and amplitude reflect asymmetries of DNA/histone interactions with respect to the nucleosome pseudo dyad. These asymmetries involve not only the DNA extremities but also regions close to the pseudo dyad. Localisations of asymmetries develop in a consistent manner during both assembly and disassembly processes; they primarily reflect the DNA sequence effect on the efficiency of DNA-histone binding. More unexpectedly, the amplitude component of PhAST signals not only evolves as a function of intermediate states but does so differently between assembly and disassembly pathways. Our observation of differences between assembly and disassembly opens up new avenues to define the role of the DNA sequence in processes underlying the regulation of gene expression. Overall, we provide new insights into how the intrinsic properties of DNA are integrated into a holistic mechanism that controls chromatin structure.
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2
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Chirico G, Gansen A, Leuba SH, Olins AL, Olins DE, Smith JC, Tóth K. Jörg Langowski: his scientific legacy and the future it promises. BMC BIOPHYSICS 2018; 11:5. [PMID: 30026939 PMCID: PMC6048899 DOI: 10.1186/s13628-018-0045-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/27/2018] [Indexed: 11/10/2022]
Abstract
Background With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for open access publishing and for the creation of effective scientific research networks. Methods Here, after reviewing some of Jörg's key research contributions and ideas, we offer through the personal remembrance of his closest collaborators, a deep analysis of the major results of his research and the future directions they have engendered. Conclusions The legacy of Jörg Langowski has been to propel a way of viewing biological function that considers living systems as dynamic and in three dimensions. This physical view of biology that he pioneered is now, finally, becoming established also because of his great effort.
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Affiliation(s)
- Giuseppe Chirico
- 1Dipartimento di Fisica, Università di Milano-Bicocca, Milan, Italy
| | - Alexander Gansen
- 2Biophysics of Macromolecules (B040), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sanford H Leuba
- 3Departments of Cell Biology and Bioengineering, 2.26a UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Ada L Olins
- 4Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME USA
| | - Donald E Olins
- 4Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME USA
| | - Jeremy C Smith
- 5Oak Ridge National Laboratory, P.O. Box 2008 MS6309, Oak Ridge, TN 37831-6309 USA.,6Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
| | - Katalin Tóth
- 2Biophysics of Macromolecules (B040), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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3
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Hazan NP, Tomov TE, Tsukanov R, Liber M, Berger Y, Masoud R, Toth K, Langowski J, Nir E. Nucleosome Core Particle Disassembly and Assembly Kinetics Studied Using Single-Molecule Fluorescence. Biophys J 2016; 109:1676-85. [PMID: 26488658 DOI: 10.1016/j.bpj.2015.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/16/2015] [Accepted: 07/02/2015] [Indexed: 10/22/2022] Open
Abstract
The stability of the nucleosome core particle (NCP) is believed to play a major role in regulation of gene expression. To understand the mechanisms that influence NCP stability, we studied stability and dissociation and association kinetics under different histone protein (NCP) and NaCl concentrations using single-pair Förster resonance energy transfer and alternating laser excitation techniques. The method enables distinction between folded, unfolded, and intermediate NCP states and enables measurements at picomolar to nanomolar NCP concentrations where dissociation and association reactions can be directly observed. We reproduced the previously observed nonmonotonic dependence of NCP stability on NaCl concentration, and we suggest that this rather unexpected behavior is a result of interplay between repulsive and attractive forces within positively charged histones and between the histones and the negatively charged DNA. Higher NaCl concentrations decrease the attractive force between the histone proteins and the DNA but also stabilize H2A/H2B histone dimers, and possibly (H3/H4)2 tetramers. An intermediate state in which one DNA arm is unwrapped, previously observed at high NaCl concentrations, is also explained by this salt-induced stabilization. The strong dependence of NCP stability on ion and histone concentrations, and possibly on other charged macromolecules, may play a role in chromosomal morphology.
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Affiliation(s)
- Noa Plavner Hazan
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Toma E Tomov
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Roman Tsukanov
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Miran Liber
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yaron Berger
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Rula Masoud
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Katalin Toth
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Joerg Langowski
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Eyal Nir
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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4
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Gansen A, Tóth K, Schwarz N, Langowski J. Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure––a FRET study. Nucleic Acids Res 2015; 43:1433-43. [PMID: 25589544 PMCID: PMC4330349 DOI: 10.1093/nar/gku1354] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Using FRET in bulk and on single molecules, we assessed the structural role of histone acetylation in nucleosomes reconstituted on the 170 bp long Widom 601 sequence. We followed salt-induced nucleosome disassembly, using donor–acceptor pairs on the ends or in the internal part of the nucleosomal DNA, and on H2B histone for measuring H2A/H2B dimer exchange. This allowed us to distinguish the influence of acetylation on salt-induced DNA unwrapping at the entry–exit site from its effect on nucleosome core dissociation. The effect of lysine acetylation is not simply cumulative, but showed distinct histone-specificity. Both H3- and H4-acetylation enhance DNA unwrapping above physiological ionic strength; however, while H3-acetylation renders the nucleosome core more sensitive to salt-induced dissociation and to dimer exchange, H4-acetylation counteracts these effects. Thus, our data suggest, that H3- and H4-acetylation have partially opposing roles in regulating nucleosome architecture and that distinct aspects of nucleosome dynamics might be independently controlled by individual histones.
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Affiliation(s)
- Alexander Gansen
- To whom correspondence should be addressed. Tel: +49 6221 423396; Fax: +49 6221 423391;
| | | | | | - Jörg Langowski
- Correspondence may also be addressed to Jörg Langowski. Tel: +49 6221 423390; Fax: +49 6221 423391;
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Mendonca A, Chang EH, Liu W, Yuan C. Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1323-9. [DOI: 10.1016/j.bbagrm.2014.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 09/04/2014] [Accepted: 09/08/2014] [Indexed: 12/18/2022]
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6
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Andresen K, Jimenez-Useche I, Howell SC, Yuan C, Qiu X. Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal. PLoS One 2013; 8:e78587. [PMID: 24265699 PMCID: PMC3827064 DOI: 10.1371/journal.pone.0078587] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.
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Affiliation(s)
- Kurt Andresen
- Department of Physics, Gettysburg College, Gettysburg, Pennsylvania, United States of America
- * E-mail:
| | - Isabel Jimenez-Useche
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Steven C. Howell
- Department of Physics, George Washington University, Washington, District of Columbia, United States of America
| | - Chongli Yuan
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Xiangyun Qiu
- Department of Physics, George Washington University, Washington, District of Columbia, United States of America
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7
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Jimenez-Useche I, Yuan C. The effect of DNA CpG methylation on the dynamic conformation of a nucleosome. Biophys J 2012; 103:2502-12. [PMID: 23260052 DOI: 10.1016/j.bpj.2012.11.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 10/19/2012] [Accepted: 11/13/2012] [Indexed: 10/27/2022] Open
Abstract
DNA methylation is an important epigenetic mark that is known to induce chromatin condensation and gene silencing. We used a time-domain fluorescence lifetime measurement to quantify the effects of DNA hypermethylation on the conformation and dynamics of a nucleosome. Nucleosomes reconstituted on an unmethylated and a methylated DNA both exhibit dynamic conformations under physiological conditions. The DNA end breathing motion and the H2A-H2B dimer destabilization dominate the dynamic behavior of nucleosomes at low to medium ionic strength. Extensive DNA CpG methylation, surprisingly, does not help to restrain the DNA breathing motion, but facilitates the formation of a more open nucleosome conformation. The presence of the divalent cation, Mg(2+), essential for chromatin compaction, and the methyl donor molecule SAM, required for DNA methyltransferase reaction, facilitate the compaction of both types of nucleosomes. The difference between the unmethylated and the methylated nucleosome persists within a broad range of salt concentrations, but vanishes under high magnesium concentrations. Reduced DNA backbone rigidity due to the presence of methyl groups is believed to contribute to the observed structural and dynamic differences. The observation of this study suggests that DNA methylation alone does not compact chromatin at the nucleosomal level and provides molecular details to understand the regulatory role of DNA methylation in gene expression.
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8
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Miyagi A, Ando T, Lyubchenko YL. Dynamics of nucleosomes assessed with time-lapse high-speed atomic force microscopy. Biochemistry 2011; 50:7901-8. [PMID: 21846149 DOI: 10.1021/bi200946z] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fundamental challenge of gene regulation is the accessibility of DNA within nucleosomes. Recent studies performed by various techniques, including single-molecule approaches, led to the realization that nucleosomes are quite dynamic rather than static systems, as they were once considered. Direct data are needed to characterize the dynamics of nucleosomes. Specifically, if nucleosomes are dynamic, the following questions need to be answered. What is the range of nucleosome dynamics? Is a non-ATP-dependent unwrapping of nucleosomes possible? What are the factors facilitating the large-scale opening and unwrapping of nucleosomes? In previous studies using time-lapse atomic force microscopy (AFM) imaging, we were able, for the first time, to observe spontaneous, ATP-independent unwrapping of nucleosomes. However, low temporal resolution did not allow visualization of various pathways of nucleosome dynamics. In the studies described here, we applied high-speed time-lapse AFM (HS-AFM) capable of visualizing molecular dynamics on the millisecond time scale to study the nucleosome dynamics. The mononucleosomes were assembled on a 353 bp DNA substrate containing nucleosome-specific 601 sequence. With HS-AFM, we were able to observe the dynamics of nucleosome on a subsecond time scale and visualize various pathways of nucleosome dynamics, such as sliding and unwrapping to various extents, including complete dissociation. These studies highlight an important role of electrostatic interactions in chromatin dynamics. Overall, our findings shed new light on nucleosome dynamics and provide a novel hypothesis for the mechanisms controlling the spontaneous dynamics of chromatin.
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Affiliation(s)
- Atsushi Miyagi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA
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9
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Menshikova I, Menshikov E, Filenko N, Lyubchenko YL. Nucleosomes structure and dynamics: effect of CHAPS. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 2:129-137. [PMID: 21969098 PMCID: PMC3180101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 03/06/2011] [Indexed: 05/31/2023]
Abstract
Dynamics of nucleosomes and spontaneous unwrapping of DNA are fundamental property of the chromatin enabling access to nucleosomal DNA for regulatory proteins. Probing of such dynamics of nucleosomes performed by single molecule techniques revealed a large scale dynamics of nucleosomes including their spontaneous unwrapping. Dissociation of nucleosomes at low concentrations is a complicating issue for studies with single molecule techniques. In this paper, we tested the ability of 3-[(3-Cholamidopropyl)dimethylammonio]-l-propanesulfonate (CHAPS) to prevent dissociation of nucleosomes. The study was performed with mononucleosome system assembled with human histones H2A, H2B, H3 and H4 on the DNA substrate containing sequence 601 that provides the sequencespecific assembly of nucleosomes. We used Atomic Force Microscopy (AFM) to directly identify nucleosomes and analyze their structure at the nanometer level. These studies showed that in the presence of CHAPS at millimolar concentrations, nucleosomes, even at sub-nanomolar concentrations, remain intact over days compared to a complete dissociation of the same nucleosome sample over 10 min in the absence of CHAPS. Importantly, CHAPS does not change the conformation of nucleosomes as confirmed by the AFM analysis. Moreover, 16 µM CHAPS stabilizes nucleosomes in over one hour incubation in the solution containing as low as 0.4 nM in nucleosomes. The stability of nucleosomes is slightly reduced at physiological conditions (150 mM NaCl), although the nucleosomes dissociate rapidly at 300 mM NaCl. The sequence specificity of the nucleosome in the presence of CHAPS decreased suggesting that the histone core translocates along the DNA substrate utilizing sliding mechanism.
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Affiliation(s)
| | | | | | - Yuri L. Lyubchenko
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025USA
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10
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Böhm V, Hieb AR, Andrews AJ, Gansen A, Rocker A, Tóth K, Luger K, Langowski J. Nucleosome accessibility governed by the dimer/tetramer interface. Nucleic Acids Res 2010; 39:3093-102. [PMID: 21177647 PMCID: PMC3082900 DOI: 10.1093/nar/gkq1279] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nucleosomes are multi-component macromolecular assemblies which present a formidable obstacle to enzymatic activities that require access to the DNA, e.g. DNA and RNA polymerases. The mechanism and pathway(s) by which nucleosomes disassemble to allow DNA access are not well understood. Here we present evidence from single molecule FRET experiments for a previously uncharacterized intermediate structural state before H2A–H2B dimer release, which is characterized by an increased distance between H2B and the nucleosomal dyad. This suggests that the first step in nucleosome disassembly is the opening of the (H3–H4)2 tetramer/(H2A–H2B) dimer interface, followed by H2A–H2B dimer release from the DNA and, lastly, (H3–H4)2 tetramer removal. We estimate that the open intermediate state is populated at 0.2–3% under physiological conditions. This finding could have significant in vivo implications for factor-mediated histone removal and exchange, as well as for regulating DNA accessibility to the transcription and replication machinery.
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Affiliation(s)
- Vera Böhm
- Abteilung Biophysik der Makromoleküle, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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11
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Single-pair FRET experiments on nucleosome conformational dynamics. Biochimie 2010; 92:1729-40. [DOI: 10.1016/j.biochi.2010.08.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 08/09/2010] [Indexed: 01/11/2023]
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12
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Xu F, Colasanti AV, Li Y, Olson WK. Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures. Nucleic Acids Res 2010; 38:6872-82. [PMID: 20647418 PMCID: PMC2978337 DOI: 10.1093/nar/gkq506] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Revised: 05/15/2010] [Accepted: 05/18/2010] [Indexed: 12/23/2022] Open
Abstract
The packaging of DNA into nucleosomes impedes the binding and access of molecules involved in its processing. The SWI/SNF multi-protein assembly, found in yeast, is one of many regulatory factors that stimulate the remodeling of DNA required for its transcription. Amino-acid point mutations in histones H3 or H4 partially bypass the requirement of the SWI/SNF complex in this system. The mechanisms underlying the observed remodeling, however, are difficult to discern from the crystal structures of nucleosomes bearing these so-called SIN (SWI/SNF INdependent) mutations. Here, we report detailed analyses of the conformations and interactions of the histones and DNA in these assemblies. We find that the loss of direct protein-DNA contacts near point-mutation sites, reported previously, is coupled to unexpected additional long-range effects, i.e. loss of intermolecular contacts and accompanying DNA conformational changes at sequentially and spatially distant sites. The SIN mutations seemingly transmit information relevant to DNA binding across the nucleosome. The energetic cost of deforming the DNA to the states found in the SIN-mutant structures helps to distinguish the mutants that show phenotypes in yeast from those that do not. Models incorporating these deformed dimer steps suggest ways that nucleosomal DNA may be remodeled during its biological processing.
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Affiliation(s)
| | | | | | - Wilma K. Olson
- Rutgers, the State University of New Jersey, Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854, USA
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13
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Santoso Y, Kapanidis AN. Probing biomolecular structures and dynamics of single molecules using in-gel alternating-laser excitation. Anal Chem 2010; 81:9561-70. [PMID: 19863108 DOI: 10.1021/ac901423e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gel electrophoresis is a standard biochemical technique used for separating biomolecules on the basis of size and charge. Despite the use of gels in early single-molecule experiments, gel electrophoresis has not been widely adopted for single-molecule fluorescence spectroscopy. We present a novel method that combines gel electrophoresis and single-molecule fluorescence spectroscopy to simultaneously purify and analyze biomolecules in a gel matrix. Our method, in-gel alternating-laser excitation (ALEX), uses nondenaturing gels to purify biomolecular complexes of interest from free components, aggregates, and nonspecific complexes. The gel matrix also slows down translational diffusion of molecules, giving rise to long, high-resolution time traces without surface immobilization, which allow extended observations of conformational dynamics in a biologically friendly environment. We demonstrated the compatibility of this method with different types of single molecule spectroscopy techniques, including confocal detection and fluorescence-correlation spectroscopy. We demonstrated that in-gel ALEX can be used to study conformational dynamics at the millisecond time scale; by studying a DNA hairpin in gels, we directly observed fluorescence fluctuations due to conformational interconversion between folded and unfolded states. Our method is amenable to the addition of small molecules that can alter the equilibrium and dynamic properties of the system. In-gel ALEX will be a versatile tool for studying structures and dynamics of complex biomolecules and their assemblies.
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Affiliation(s)
- Yusdi Santoso
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford, OX1 3PU, United Kingdom.
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14
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Okuwaki M, Kato K, Nagata K. Functional characterization of human nucleosome assembly protein 1-like proteins as histone chaperones. Genes Cells 2010; 15:13-27. [DOI: 10.1111/j.1365-2443.2009.01361.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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15
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Koopmans WJA, Buning R, Schmidt T, van Noort J. spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes. Biophys J 2009; 97:195-204. [PMID: 19580757 DOI: 10.1016/j.bpj.2009.04.030] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 03/30/2009] [Accepted: 04/13/2009] [Indexed: 11/17/2022] Open
Abstract
Accessibility to DNA wrapped in nucleosomes is essential for nuclear processes such as DNA transcription. Large conformational changes in nucleosome structure are required to facilitate protein binding to target sites within nucleosomal DNA. Transient unwrapping of DNA from nucleosome ends can provide an intrinsic exposure of wrapped DNA, allowing proteins to bind DNA that would otherwise be occluded in the nucleosome. The molecular details underlying these mechanisms remain to be resolved. Here we show how DNA unwrapping occurs progressively from both nucleosome ends. We performed single-pair fluorescence resonance energy transfer (spFRET) spectroscopy with alternating laser excitation (ALEX) on nucleosomes either in free solution or confined in a gel after PAGE separation. We combined ALEX-spFRET with a correlation analysis on selected bursts of fluorescence, to resolve a variety of unwrapped nucleosome conformations. The experiments reveal that nucleosomes are unwrapped with an equilibrium constant of approximately 0.2-0.6 at nucleosome ends and approximately 0.1 at a location 27 basepairs inside the nucleosome, but still remain stably associated. Our findings, obtained using a powerful combination of single-molecule fluorescence techniques and gel electrophoresis, emphasize the delicate interplay between DNA accessibility and condensation in chromatin.
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Affiliation(s)
- W J A Koopmans
- Physics of Life Sciences, Leiden University, Leiden, The Netherlands
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16
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Shlyakhtenko LS, Lushnikov AY, Lyubchenko YL. Dynamics of nucleosomes revealed by time-lapse atomic force microscopy. Biochemistry 2009; 48:7842-8. [PMID: 19618963 DOI: 10.1021/bi900977t] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The dynamics of chromatin provides the access to DNA within nucleosomes, and therefore, this process is critically involved in the regulation of chromatin function. However, our knowledge of the large-range dynamics of nucleosomes is limited. Answers to the questions, such as the range of opening of the nucleosome and the mechanism via which the opening occurs and propagates, remain unknown. Here we applied single-molecule time-lapse atomic force microscopy (AFM) imaging to directly visualize the dynamics of nucleosomes and identify the mechanism of the large range DNA exposure. With this technique, we are able to observe the process of unwrapping of nucleosomes. The unwrapping of nucleosomes proceeds from the ends of the particles, allowing for the unwrapping of DNA regions as large as dozens of base pairs. This process may lead to a complete unfolding of nucleosomes and dissociation of the histone core from the complex. The unwrapping occurs in the absence of proteins involved in the chromatin remodeling that require ATP hydrolysis for their function, suggesting that the inherent dynamics of nucleosomes can contribute to the chromatin unwrapping process. These findings shed a new light on molecular mechanisms of nucleosome dynamics and provide novel hypotheses about the understanding of the action of remodeling proteins as well as other intracellular systems in chromatin dynamics.
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Affiliation(s)
- Luda S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA
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17
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Nucleosome disassembly intermediates characterized by single-molecule FRET. Proc Natl Acad Sci U S A 2009; 106:15308-13. [PMID: 19706432 DOI: 10.1073/pnas.0903005106] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleosome has a central role in the compaction of genomic DNA and the control of DNA accessibility for transcription and replication. To help understanding the mechanism of nucleosome opening and closing in these processes, we studied the disassembly of mononucleosomes by quantitative single-molecule FRET with high spatial resolution, using the SELEX-generated "Widom 601" positioning sequence labeled with donor and acceptor fluorophores. Reversible dissociation was induced by increasing NaCl concentration. At least 3 species with different FRET were identified and assigned to structures: (i) the most stable high-FRET species corresponding to the intact nucleosome, (ii) a less stable mid-FRET species that we attribute to a first intermediate with a partially unwrapped DNA and less histones, and (iii) a low-FRET species characterized by a very broad FRET distribution, representing highly unwrapped structures and free DNA formed at the expense of the other 2 species. Selective FCS analysis indicates that even in the low-FRET state, some histones are still bound to the DNA. The interdye distance of 54.0 A measured for the high-FRET species corresponds to a compact conformation close to the known crystallographic structure. The coexistence and interconversion of these species is first demonstrated under non-invasive conditions. A geometric model of the DNA unwinding predicts the presence of the observed FRET species. The different structures of these species in the disassembly pathway map the energy landscape indicating major barriers for 10-bp and minor ones for 5-bp DNA unwinding steps.
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18
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Kelbauskas L, Yodh J, Woodbury N, Lohr D. Intrinsic promoter nucleosome stability/dynamics variations support a novel targeting mechanism. Biochemistry 2009; 48:4217-9. [PMID: 19374398 DOI: 10.1021/bi900476t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genomic processes like transcription initiation typically involve the alteration of nucleosome structure, to expose DNA elements for regulatory factor binding. Nucleosome altering/modifying complexes have been identified, but precisely how these complexes find their specific targets remains unclear. We have shown that nucleosomes can exhibit significant DNA sequence-dependent stability and dynamics variations and have suggested that these inherent variations could facilitate nucleosome recognition and thus aid in specific targeting. Here, we confirm an important prediction of the model, namely, that stability and DNA dynamics features can correlate with the transcriptional involvement of specific promoter nucleosomes. A transcriptionally inert Mouse Mammary Tumor Virus promoter-region nucleosome (MMTV-D) has greater inherent stability than and reduced dynamics compared to a nearby nucleosome (MMTV-B) that is the initial target of transcription activation-associated processes on this promoter. MMTV-D stability could help direct activation-associated events to the less stable and more dynamic target, MMTV-B.
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Kelbauskas L, Woodbury N, Lohr D. DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysisThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2009; 87:323-35. [DOI: 10.1139/o08-126] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Förster resonance energy transfer (FRET) techniques provide powerful and sensitive methods for the study of conformational features in biomolecules. Here, we review FRET-based studies of nucleosomes, focusing particularly on our work comparing the widely used nucleosome standard, 5S rDNA, and 2 promoter-derived regulatory element-containing nucleosomes, mouse mammary tumor virus (MMTV)-B and GAL10. Using several FRET approaches, we detected significant DNA sequence-dependent structure, stability, and dynamics differences among the three. In particular, 5S nucleosomes and 5S H2A/H2B-depleted nucleosomal particles have enhanced stability and diminished DNA dynamics, compared with MMTV-B and GAL10 nucleosomes and particles. H2A/H2B-depleted nucleosomes are of interest because they are produced by the activities of many transcription-associated complexes. Significant location-dependent (intranucleosomal) stability and dynamics variations were also observed. These also vary among nucleosome types. Nucleosomes restrict regulatory factor access to DNA, thereby impeding genetic processes. Eukaryotic cells possess mechanisms to alter nucleosome structure, to generate DNA access, but alterations often must be targeted to specific nucleosomes on critical regulatory DNA elements. By endowing specific nucleosomes with intrinsically higher DNA accessibility and (or) enhanced facility for conformational transitions, DNA sequence-dependent nucleosome dynamics and stability variations have the potential to facilitate nucleosome recognition and, thus, aid in the crucial targeting process. This and other nucleosome structure and function conclusions from FRET analyses are discussed.
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Affiliation(s)
- L. Kelbauskas
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - N. Woodbury
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - D. Lohr
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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Koopmans WJA, Schmidt T, van Noort J. Nucleosome immobilization strategies for single-pair FRET microscopy. Chemphyschem 2009; 9:2002-9. [PMID: 18792054 DOI: 10.1002/cphc.200800370] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
All genomic transactions in eukaryotes take place in the context of the nucleosome, the basic unit of chromatin, which is responsible for DNA compaction. Overcoming the steric hindrance that nucleosomes present for DNA-processing enzymes requires significant conformational changes. The dynamics of these have been hard to resolve. Single-pair Fluorescence Resonance Energy Transfer (spFRET) microscopy is a powerful technique for observing conformational dynamics of the nucleosome. Nucleosome immobilization allows the extension of observation times to a limit set only by photobleaching, and thus opens the possibility of studying processes occurring on timescales ranging from milliseconds to minutes. It is crucial however, that immobilization itself does not introduce artifacts in the dynamics. Here we report on various nucleosome immobilization strategies, such as single-point attachment to polyethylene glycol (PEG) or surfaces coated with bovine serum albumin (BSA), and confinement in porous agarose or polyacrylamide gels. We compare the immobilization specificity and structural integrity of immobilized nucleosomes. A crosslinked star polyethylene glycol coating performs best with respect to tethering specificity and nucleosome integrity, and enables us to reproduce for the first time bulk nucleosome unwrapping kinetics in single nucleosomes without immobilization artifacts.
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Affiliation(s)
- Wiepke J A Koopmans
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
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Kelbauskas L, Sun J, Woodbury N, Lohr D. Nucleosomal Stability and Dynamics Vary Significantly When Viewed by Internal Versus Terminal Labels. Biochemistry 2008; 47:9627-35. [DOI: 10.1021/bi8000775] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laimonas Kelbauskas
- Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287
| | - Jenny Sun
- Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287
| | - Neal Woodbury
- Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287
| | - D. Lohr
- Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287
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Leuba SH, Anand SP, Harp JM, Khan SA. Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time. Chromosome Res 2008; 16:451-67. [PMID: 18461484 PMCID: PMC2413326 DOI: 10.1007/s10577-008-1235-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many questions in molecular and cellular biology can be reduced to questions about 'who talks to whom, when and how frequently'. Here, we review approaches we have used with single-pair fluorescence resonance energy transfer (spFRET) to follow the motions between two well-placed fluorescent probes to ask similar questions. We describe two systems. We have used a nucleosomal system in which the naked DNA molecule has the acceptor and donor dyes too far apart for FRET to occur whereas the dyes are close enough in the reconstituted nucleosome for FRET. As these individual nucleosomes were tethered on a surface, we could follow dynamics in the repositioning of these two dyes, inferring that nucleosomes stochastically and reversibly open and close. These results imply that most of the DNA on the nucleosome can be sporadically accessible to regulatory proteins and proteins that track the DNA double helix. In the case of following the binding of recombination protein RecA to double-stranded DNA (dsDNA) and the RecA filament displacement by DNA helicase motor PcrA, the dsDNA template is prepared with the two dyes close enough to each other to generate high FRET. Binding of the RecA molecules to form a filament lengthens the dsDNA molecule 1.5-fold and reduces the FRET accordingly. Once added, DNA motor protein helicase PcrA can displace the RecA filament with concomitant return of the DNA molecule to its original B-form and high FRET state. Thus, appropriately placed fluorescent dyes can be used to monitor conformational changes occurring in DNA and or proteins and provide increased sensitivity for investigating dynamic DNA-protein interactions in real time.
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Affiliation(s)
- Sanford H Leuba
- Department of Cell Biology, University of Pittsburgh School of Medicine and Swanson School of Engineering, Petersen Institute of NanoScience and Engineering and University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA.
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Gurunathan K, Levitus M. Applications of fluorescence correlation spectroscopy to the study of nucleic acid conformational dynamics. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2008; 82:33-69. [PMID: 18929138 DOI: 10.1016/s0079-6603(08)00002-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kaushik Gurunathan
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
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