101
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Skulte KA, Phan L, Clark SJ, Taberlay PC. Chromatin remodeler mutations in human cancers: epigenetic implications. Epigenomics 2015; 6:397-414. [PMID: 25333849 DOI: 10.2217/epi.14.37] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Chromatin remodeler complexes exhibit the ability to alter nucleosome composition and positions, with seemingly divergent roles in the regulation of chromatin architecture and gene expression. The outcome is directed by subunit variation and interactions with accessory factors. Recent studies have revealed that subunits of chromatin remodelers display an unexpectedly high mutation rate and/or are inactivated in a number of cancers. Consequently, a repertoire of epigenetic processes are likely to be affected, including interactions with histone modifying factors, as well as the ability to precisely modulate nucleosome positions, DNA methylation patterns and potentially, higher-order genome structure. However, the true significance of chromatin remodeler genetic aberrations in promoting a cascade of epigenetic changes, particularly during initiation and progression of cancer, remains largely unknown.
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Affiliation(s)
- Katherine A Skulte
- Chromatin Dynamics Group, Cancer Division, Garvan Institute of Medical Research, 394 Victoria Rd, Darlinghurst 2010, New South Wales, Australia
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102
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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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103
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Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. Dynamic regulation of transcription factors by nucleosome remodeling. eLife 2015; 4. [PMID: 26047462 PMCID: PMC4456607 DOI: 10.7554/elife.06249] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/11/2015] [Indexed: 12/27/2022] Open
Abstract
The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes. DOI:http://dx.doi.org/10.7554/eLife.06249.001 Cells contain thousands of genes that are encoded by molecules of DNA. In yeast and other eukaryotic organisms, this DNA is wrapped around proteins called histones to make structures called nucleosomes. This compacts the DNA and allows it to fit inside the tiny nucleus within the cell. The positioning of the nucleosomes influences how tightly packed the DNA is, which in turn influences the activity of genes. Less active genes tend to be found within regions of DNA that are tightly packed, while more active genes are found in less tightly packed regions. To activate a gene, proteins called transcription factors bind to a section of DNA within the gene called the promoter. Enzymes known as ‘chromatin remodelers’ can alter the locations of nucleosomes on DNA to allow the transcription factors access to the promoters of particular genes. In yeast, the SWI/SNF family of chromatin remodelers can disassemble nucleosomes to promote gene activity, while the ISW1 family organises nucleosomes into closely spaced groups to repress gene activity. However, it is not clear if, or how, chromatin remodelers can influence transcription factors that are already bound to DNA. Here, Li et al. studied the interactions between a transcription factor and the chromatin remodelers in yeast. The experiment used a piece of DNA that contained a bound transcription factor and a single nucleosome. Li et al. used a technique called ‘single molecule DNA unzipping’, which enabled them to precisely locate the position of the nucleosome and transcription factor before and after the nucleosome was remodeled. The experiments found that a chromatin remodeler called ISW1a moved the nucleosome away from the transcription factor, while a SWI/SNF chromatin remodeler moved the nucleosome towards it. Significantly, Li et al. also found that a transcription factor is a major barrier to ISW1a's remodeling activity, suggesting that ISW1a may use transcription factors as reference points to position nucleosomes. In contrast, SWI/SNF was able to slide a nucleosome past the transcription factor, which led to the transcription factor falling off the DNA. Therefore, SWI/SNF is able to move transcription factors out of the way to deactivate genes. Li et al. propose a new model for how chromatin remodelers can move nucleosomes and regulate transcription factors to alter gene activity. A future challenge will be to observe these types of activities in living cells. DOI:http://dx.doi.org/10.7554/eLife.06249.002
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Affiliation(s)
- Ming Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Arjan Hada
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Payel Sen
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Lola Olufemi
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michael A Hall
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Benjamin Y Smith
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Scott Forth
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Jeffrey N McKnight
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Ashok Patel
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Blaine Bartholomew
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
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104
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Ngo TTM, Ha T. Nucleosomes undergo slow spontaneous gaping. Nucleic Acids Res 2015; 43:3964-71. [PMID: 25824950 PMCID: PMC4417179 DOI: 10.1093/nar/gkv276] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 01/08/2023] Open
Abstract
In eukaryotes, DNA is packaged into a basic unit, the nucleosome which consists of 147 bp of DNA wrapped around a histone octamer composed of two copies each of the histones H2A, H2B, H3 and H4. Nucleosome structures are diverse not only by histone variants, histone modifications, histone composition but also through accommodating different conformational states such as DNA breathing and dimer splitting. Variation in nucleosome structures allows it to perform a variety of cellular functions. Here, we identified a novel spontaneous conformational switching of nucleosomes under physiological conditions using single-molecule FRET. Using FRET probes placed at various positions on the nucleosomal DNA to monitor conformation of the nucleosome over a long period of time (30–60 min) at various ionic conditions, we identified conformational changes we refer to as nucleosome gaping. Gaping transitions are distinct from nucleosome breathing, sliding or tightening. Gaping modes switch along the direction normal to the DNA plane through about 5–10 angstroms and at minutes (1–10 min) time scale. This conformational transition, which has not been observed previously, may be potentially important for enzymatic reactions/transactions on nucleosomal substrate and the formation of multiple compression forms of chromatin fibers.
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Affiliation(s)
- Thuy T M Ngo
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA
| | - Taekjip Ha
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801-2902, USA
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105
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 314] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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106
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Ngo TTM, Zhang Q, Zhou R, Yodh JG, Ha T. Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. Cell 2015; 160:1135-44. [PMID: 25768909 PMCID: PMC4409768 DOI: 10.1016/j.cell.2015.02.001] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/07/2014] [Accepted: 01/17/2015] [Indexed: 02/06/2023]
Abstract
Dynamics of the nucleosome and exposure of nucleosomal DNA play key roles in many nuclear processes, but local dynamics of the nucleosome and its modulation by DNA sequence are poorly understood. Using single-molecule assays, we observed that the nucleosome can unwrap asymmetrically and directionally under force. The relative DNA flexibility of the inner quarters of nucleosomal DNA controls the unwrapping direction such that the nucleosome unwraps from the stiffer side. If the DNA flexibility is similar on two sides, it stochastically unwraps from either side. The two ends of the nucleosome are orchestrated such that the opening of one end helps to stabilize the other end, providing a mechanism to amplify even small differences in flexibility to a large asymmetry in nucleosome stability. Our discovery of DNA flexibility as a critical factor for nucleosome dynamics and mechanical stability suggests a novel mechanism of gene regulation by DNA sequence and modifications.
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Affiliation(s)
- Thuy T M Ngo
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA
| | - Qiucen Zhang
- Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA
| | - Ruobo Zhou
- Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA
| | - Jaya G Yodh
- Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA.
| | - Taekjip Ha
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Department of Physics, Center for Physics in Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2902, USA; Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801-2902, USA.
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107
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Brysbaert G, Lensink MF, Blossey R. Regulatory motifs on ISWI chromatin remodelers: molecular mechanisms and kinetic proofreading. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064108. [PMID: 25563573 DOI: 10.1088/0953-8984/27/6/064108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recently, kinetic proofreading scenarios have been proposed for the regulation of chromatin remodeling, first on purely theoretical grounds (Blossey and Schiessel 2008 HFSP J. 2 167-70) and deduced from experiments on the ISWI/ACF system (Narlikar 2010 Curr. Opin. Chem. Biol. 14 660). In the kinetic proofreading scenario of chromatin remodeling, the combination of the recognition of a histone tail state and ATP-hydrolysis in the remodeler motor act together to select (i.e. proofread) a nucleosomal substrate. ISWI remodelers have recently been shown to have an additional level of regulation as they contain auto-inhibitory motifs which need to be inactivated through an interaction with the nucleosome. In this paper we show that the auto-regulatory effect enhances substrate recognition in kinetic proofreading. We further report some suggestive additional insights into the molecular mechanism underlying ISWI-autoregulation.
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Affiliation(s)
- Guillaume Brysbaert
- Interdisciplinary Research Institute, Université des Sciences et des Technologies de Lille (USTL), CNRS USR3078, 50 Avenue Halley, 59568 Villeneuve d'Ascq, France
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108
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A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler. Mol Cell 2015; 57:850-859. [PMID: 25684208 DOI: 10.1016/j.molcel.2015.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 11/24/2014] [Accepted: 01/05/2015] [Indexed: 11/20/2022]
Abstract
The ATP-dependent chromatin assembly factor (ACF) spaces nucleosomes to promote formation of silent chromatin. Two copies of its ATPase subunit SNF2h bind opposite sides of a nucleosome, but how these protomers avoid competition is unknown. SNF2h senses the length of DNA flanking a nucleosome via its HAND-SANT-SLIDE (HSS) domain, yet it is unclear how this interaction enhances remodeling. Using covalently connected SNF2h dimers we show that dimerization accelerates remodeling and that the HSS contributes to communication between protomers. We further identify a nucleotide-dependent conformational change in SNF2h. In one conformation the HSS binds flanking DNA, and in another conformation the HSS engages the nucleosome core. Based on these results, we propose a model in which DNA length sensing and translocation are performed by two distinct conformational states of SNF2h. Such separation of function suggests that these activities could be independently regulated to affect remodeling outcomes.
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109
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Taguchi H, Horikoshi N, Arimura Y, Kurumizaka H. A method for evaluating nucleosome stability with a protein-binding fluorescent dye. Methods 2014; 70:119-26. [DOI: 10.1016/j.ymeth.2014.08.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 11/29/2022] Open
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110
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Ma L, Yang F, Zheng J. Application of fluorescence resonance energy transfer in protein studies. J Mol Struct 2014; 1077:87-100. [PMID: 25368432 DOI: 10.1016/j.molstruc.2013.12.071] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Since the physical process of fluorescence resonance energy transfer (FRET) was elucidated more than six decades ago, this peculiar fluorescence phenomenon has turned into a powerful tool for biomedical research due to its compatibility in scale with biological molecules as well as rapid developments in novel fluorophores and optical detection techniques. A wide variety of FRET approaches have been devised, each with its own advantages and drawbacks. Especially in the last decade or so, we are witnessing a flourish of FRET applications in biological investigations, many of which exemplify clever experimental design and rigorous analysis. Here we review the current stage of FRET methods development with the main focus on its applications in protein studies in biological systems, by summarizing the basic components of FRET techniques, most established quantification methods, as well as potential pitfalls, illustrated by example applications.
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Affiliation(s)
- Linlin Ma
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Fan Yang
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
| | - Jie Zheng
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
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111
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Abstract
ISWI family chromatin remodeling enzymes generate regularly spaced nucleosome arrays. In a recent Nature report, Hwang et al. (2014) describe how ACF gauges the length of linker DNA when deciding to accelerate nucleosome sliding or to put on the brakes.
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Affiliation(s)
- Hari R Singh
- Department of Physiological Chemistry, Butenandt Institute and LMU Biomedical Center, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5, 81377 Munich, Germany
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Butenandt Institute and LMU Biomedical Center, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5, 81377 Munich, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Martinsried, Germany; Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany.
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112
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Luo Y, North JA, Poirier MG. Single molecule fluorescence methodologies for investigating transcription factor binding kinetics to nucleosomes and DNA. Methods 2014; 70:108-18. [PMID: 25304387 DOI: 10.1016/j.ymeth.2014.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 09/03/2014] [Accepted: 09/30/2014] [Indexed: 11/20/2022] Open
Abstract
Site specific DNA binding complexes must bind their DNA target sites and then reside there for a sufficient amount of time for proper regulation of DNA processing including transcription, replication and DNA repair. In eukaryotes, the occupancy of DNA binding complexes at their target sites is regulated by chromatin structure and dynamics. Methodologies that probe both the binding and dissociation kinetics of DNA binding proteins with naked and nucleosomal DNA are essential for understanding the mechanisms by which these complexes function. Here, we describe single-molecule fluorescence methodologies for quantifying the binding and dissociation kinetics of transcription factors at a target site within DNA, nucleosomes and nucleosome arrays. This approach allowed for the unexpected observation that nucleosomes impact not only binding but also dissociation kinetics of transcription factors and is well-suited for the investigation of numerous DNA processing complexes that directly interact with DNA organized into chromatin.
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Affiliation(s)
- Yi Luo
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Justin A North
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States.
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113
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Al-Ani G, Malik SS, Eastlund A, Briggs K, Fischer CJ. ISWI remodels nucleosomes through a random walk. Biochemistry 2014; 53:4346-57. [PMID: 24898619 PMCID: PMC4100782 DOI: 10.1021/bi500226b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromatin remodeler ISWI is capable of repositioning clusters of nucleosomes to create well-ordered arrays or moving single nucleosomes from the center of DNA fragments toward the ends without disrupting their integrity. Using standard electrophoresis assays, we have monitored the ISWI-catalyzed repositioning of different nucleosome samples each containing a different length of DNA symmetrically flanking the initially centrally positioned histone octamer. We find that ISWI moves the histone octamer between distinct and thermodynamically stable positions on the DNA according to a random walk mechanism. Through the application of a spectrophotometric assay for nucleosome repositioning, we further characterized the repositioning activity of ISWI using short nucleosome substrates and were able to determine the macroscopic rate of nucleosome repositioning by ISWI. Additionally, quantitative analysis of repositioning experiments performed at various ISWI concentrations revealed that a monomeric ISWI is sufficient to obtain the observed repositioning activity as the presence of a second ISWI bound had no effect on the rate of nucleosome repositioning. We also found that ATP hydrolysis is poorly coupled to nucleosome repositioning, suggesting that DNA translocation by ISWI is not energetically rate-limiting for the repositioning reaction. This is the first calculation of a microscopic ATPase coupling efficiency for nucleosome repositioning and also further supports our conclusion that a second bound ISWI does not contribute to the repositioning reaction.
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Affiliation(s)
- Gada Al-Ani
- Department of Molecular Biosciences, University of Kansas , 2034 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
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114
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Hwang WL, Deindl S, Harada BT, Zhuang X. Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA. Nature 2014; 512:213-7. [PMID: 25043036 PMCID: PMC4134374 DOI: 10.1038/nature13380] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 04/14/2014] [Indexed: 12/05/2022]
Abstract
ISWI-family remodelling enzymes regulate access to genomic DNA by mobilizing nucleosomes1. These ATP-dependent chromatin remodellers promote heterochromatin formation and transcriptional silencing1 by generating regularly-spaced nucleosome arrays2-5. The nucleosome-spacing activity arises from regulation of nucleosome translocation by the length of extranucleosomal linker DNA6-10, but the underlying mechanism remains unclear. Here, we studied nucleosome remodelling by human ACF, an ISWI enzyme comprised of a catalytic subunit, Snf2h, and an accessory subunit, Acf12,11-13. We found that ACF senses linker DNA length through an interplay between its accessory and catalytic subunits mediated by the histone H4 tail of the nucleosome. Mutation of AutoN, an auto-inhibitory domain within Snf2h that bears sequence homology to the H4 tail14, abolished the linker-length sensitivity in remodelling. Addition of exogenous H4-tail peptide or deletion of the nucleosomal H4 tail also diminished the linker-length sensitivity. Moreover, the accessory subunit Acf1 bound the H4-tail peptide and DNA in a manner that depended on its N-terminal domain, and lengthening the linker DNA in the nucleosome reduced the proximity between Acf1 and the H4 tail. Deletion of the N-terminal portion of Acf1 (or its homologue in yeast) abolished linker-length sensitivity in nucleosome remodeling and led to severe growth defects in vivo. Taken together, our results suggest a mechanism for nucleosome spacing where linker DNA sensing by Acf1 is allosterically transmitted to Snf2h through the H4 tail of the nucleosome. For nucleosomes with short linker DNA, Acf1 preferentially binds to the H4 tail, allowing AutoN to inhibit the ATPase activity of Snf2h. As the linker DNA lengthens, Acf1 shifts its binding preference to the linker DNA, freeing the H4 tail to compete AutoN off the ATPase and thereby activating ACF.
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Affiliation(s)
- William L Hwang
- 1] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA [2] Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA [3] Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, Massachusetts 02115, USA [4]
| | - Sebastian Deindl
- 1] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA [2] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [3]
| | - Bryan T Harada
- 1] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA [2] Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Xiaowei Zhuang
- 1] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA [2] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [3] Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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115
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Manelyte L, Strohner R, Gross T, Längst G. Chromatin targeting signals, nucleosome positioning mechanism and non-coding RNA-mediated regulation of the chromatin remodeling complex NoRC. PLoS Genet 2014; 10:e1004157. [PMID: 24651573 PMCID: PMC3961174 DOI: 10.1371/journal.pgen.1004157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 12/17/2013] [Indexed: 11/21/2022] Open
Abstract
Active and repressed ribosomal RNA (rRNA) genes are characterised by specific epigenetic marks and differentially positioned nucleosomes at their promoters. Repression of the rRNA genes requires a non-coding RNA (pRNA) and the presence of the nucleolar remodeling complex (NoRC). ATP-dependent chromatin remodeling enzymes are essential regulators of DNA-dependent processes, and this regulation occurs via the modulation of DNA accessibility in chromatin. We have studied the targeting of NoRC to the rRNA gene promoter; its mechanism of nucleosome positioning, in which a nucleosome is placed over the transcription initiation site; and the functional role of the pRNA. We demonstrate that NoRC is capable of recognising and binding to the nucleosomal rRNA gene promoter on its own and binds with higher affinity the nucleosomes positioned at non-repressive positions. NoRC recognises the promoter nucleosome within a chromatin array and positions the nucleosomes, as observed in vivo. NoRC uses the release mechanism of positioning, which is characterised by a reduced affinity for the remodeled substrate. The pRNA specifically binds to NoRC and regulates the enzyme by switching off its ATPase activity. Given the known role of pRNA in tethering NoRC to the rDNA, we propose that pRNA is a key factor that links the chromatin modification activity and scaffolding function of NoRC. Tumour cells overexpress ribosomal RNA (rRNA), which is required for ribosome assembly and cell growth. rRNA gene repression is mediated by the chromatin remodeling complex (NoRC) and a non-coding RNA that binds to this enzyme. This study addresses the mechanism of nucleosome positioning by NoRC and the functional role of the non-coding RNA, which is termed pRNA because it corresponds to the promoter sequence. NoRC recognises the promoter nucleosome in a chromatin array with high affinity and uses a release mechanism to position the nucleosome over the transcription initiation site. The pRNA binds specifically to NoRC and inhibits its ATPase activity. We suggest that the RNA retains NoRC at the gene promoter after remodeling, linking its chromatin modification and scaffolding activity to inactive rDNA copies.
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Affiliation(s)
- Laura Manelyte
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Ralf Strohner
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Thomas Gross
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
- * E-mail:
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116
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Abstract
A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).
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Affiliation(s)
- Blaine Bartholomew
- University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, Texas 78957;
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117
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Bartholomew B. ISWI chromatin remodeling: one primary actor or a coordinated effort? Curr Opin Struct Biol 2014; 24:150-5. [PMID: 24561830 DOI: 10.1016/j.sbi.2014.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 01/14/2014] [Accepted: 01/16/2014] [Indexed: 01/20/2023]
Abstract
The ISWI family of ATP-dependent chromatin remodelers regulates transcription of coding and noncoding RNA by mobilizing nucleosomes and controlling the length of linker DNA separating nucleosomes (spacing). Nucleosome movement is tightly coupled to the DNA translocation activity of the helicase domain in the catalytic subunit. There may be other domains besides the helicase domain needed to move DNA in and out of nucleosomes. The C terminus of the ISWI catalytic subunit with the conserved HAND, SANT, and SLIDE domains may be involved in nucleosome spacing. There are several models of how the C terminus may facilitate in ISWI remodeling such as regulating the activity of the helicase domain and causing the helicase domain to translocate more efficiently on DNA or to enhance its selectivity for nucleosomes. Another possibility is that domains like SLIDE promote linker DNA entering into nucleosomes in a coordinated manner with the helicase domain.
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Affiliation(s)
- Blaine Bartholomew
- The University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, TX 78957, United States.
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118
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Mueller-Planitz F, Klinker H, Becker PB. Nucleosome sliding mechanisms: new twists in a looped history. Nat Struct Mol Biol 2013; 20:1026-32. [PMID: 24008565 DOI: 10.1038/nsmb.2648] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/12/2013] [Indexed: 01/11/2023]
Abstract
Nucleosomes, the basic organizational units of chromatin, package and regulate eukaryotic genomes. ATP-dependent nucleosome-remodeling factors endow chromatin with structural flexibility by promoting assembly or disruption of nucleosomes and the exchange of histone variants. Furthermore, most remodeling factors induce nucleosome movements through sliding of histone octamers on DNA. We summarize recent progress toward unraveling the basic nucleosome sliding mechanism and the interplay of the remodelers' DNA translocases with accessory domains. Such domains optimize and regulate the basic sliding reaction and exploit sliding to achieve diverse structural effects, such as nucleosome positioning or eviction, or the regular spacing of nucleosomes in chromatin.
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Affiliation(s)
- Felix Mueller-Planitz
- 1] Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität, Munich, Germany. [2] Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität, Munich, Germany
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119
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Narlikar G, Sundaramoorthy R, Owen-Hughes T. Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell 2013; 154:490-503. [PMID: 23911317 PMCID: PMC3781322 DOI: 10.1016/j.cell.2013.07.011] [Citation(s) in RCA: 447] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Indexed: 12/28/2022]
Abstract
Chromatin provides both a means to accommodate a large amount of genetic material in a small space and a means to package the same genetic material in different chromatin states. Transitions between chromatin states are enabled by chromatin-remodeling ATPases, which catalyze a diverse range of structural transformations. Biochemical evidence over the last two decades suggests that chromatin-remodeling activities may have emerged by adaptation of ancient DNA translocases to respond to specific features of chromatin. Here, we discuss such evidence and also relate mechanistic insights to our understanding of how chromatin-remodeling enzymes enable different in vivo processes.
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Affiliation(s)
- Geeta J. Narlikar
- Biochemistry and Biophysics, Genentech Hall 600, 16th Street, University of California, San Francisco, San Francisco, CA 94158, USA
- Corresponding author
| | | | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Corresponding author
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120
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Dutta A, Workman JL. Remodelling without a power stroke. EMBO Rep 2013; 14:1030-1. [PMID: 24157947 DOI: 10.1038/embor.2013.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Arnob Dutta
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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121
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Nucleosome sliding by Chd1 does not require rigid coupling between DNA-binding and ATPase domains. EMBO Rep 2013; 14:1098-103. [PMID: 24126763 DOI: 10.1038/embor.2013.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 11/08/2022] Open
Abstract
Chromatin remodellers are ATP-dependent motor proteins that physically reposition and reorganize nucleosomes. Chd1 and Iswi-type remodellers possess a DNA-binding domain (DBD) needed for efficient nucleosome mobilization; however, it has not been clear how this domain physically contributes to remodelling. Here we show that the Chd1 DBD promotes nucleosome sliding simply by tethering the remodeller to nucleosome substrates. Nucleosome sliding activity was largely resistant to increasing length and flexibility of the linker connecting the DBD and ATPase motor, arguing that the ATPase motor does not shift DNA onto the nucleosome by pulling on the DBD.
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122
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No need for a power stroke in ISWI-mediated nucleosome sliding. EMBO Rep 2013; 14:1092-7. [PMID: 24113208 DOI: 10.1038/embor.2013.160] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/04/2013] [Accepted: 09/16/2013] [Indexed: 11/08/2022] Open
Abstract
Nucleosome remodelling enzymes of the ISWI family reposition nucleosomes in eukaryotes. ISWI contains an ATPase and a HAND-SANT-SLIDE (HSS) domain. Conformational changes between these domains have been proposed to be critical for nucleosome repositioning by pulling flanking DNA into the nucleosome. We inserted flexible linkers at strategic sites in ISWI to disrupt this putative power stroke and assess its functional importance by quantitative biochemical assays. Notably, the flexible linkers did not disrupt catalysis. Instead of engaging in a power stroke, the HSS module might therefore assist DNA to ratchet into the nucleosome. Our results clarify the roles had by the domains and suggest that the HSS domain evolved to optimize a rudimentary remodelling engine.
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