1
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Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S. Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1. Nat Commun 2024; 15:1000. [PMID: 38307862 PMCID: PMC10837151 DOI: 10.1038/s41467-024-45237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited to ADP-ribosylated nucleosomes to affect their positioning near DNA breaks is unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest to the DNA break. To dissect the consequences of such asymmetry, we generate nucleosomes with a defined ADP-ribosylated H2B tail on one side only. The cryo-electron microscopy structure of ALC1 bound to such an asymmetric nucleosome indicates preferential engagement on one side. Using single-molecule FRET, we demonstrate that this asymmetric recruitment gives rise to directed sliding away from the DNA linker closest to the ADP-ribosylation site. Our data suggest a mechanism by which ALC1 slides nucleosomes away from a DNA break to render it more accessible to repair factors.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
- Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden
| | - Jugal Mohapatra
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Mikhail Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Glen Liszczak
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
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2
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Wilson CS, Vashi B, Genzor P, Gregory MK, Yau J, Wolfe L, Lochhead MJ, Papst P, Pettrone K, Blair PW, Krishnan S, Chenoweth JG, Clark DV. Point-of-care biomarker assay for rapid multiplexed detection of CRP and IP-10. SLAS Technol 2023; 28:442-448. [PMID: 37844868 DOI: 10.1016/j.slast.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Rapid and accurate measurements of immune protein markers are essential for diagnosis and treatment in all clinical settings. The recent pandemic has revealed a stark need for developing new tools and assays that could be rapidly used in diverse settings and provide useful information to clinicians. Here, we describe the development and test application of a novel one-step CRP/IP-10 duplex assay for the LightDeck platform capable of delivering reproducible and accurate measurements in under eight minutes. We used the optimized assay to measure CRP and IP-10 levels in human blood and serum samples from healthy, SARS-CoV-2 (COVID-19) positive, and influenza-like illness (ILI) presenting patients. Our results agreed with previously published analyte levels and enabled us to make statistically significant comparisons relevant to multiple clinical parameters. Our duplex assay is a simple and powerful tool for aiding prognostic decision-making in diverse settings.
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Affiliation(s)
- Claire S Wilson
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Bhavya Vashi
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Pavol Genzor
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Melissa K Gregory
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Jason Yau
- LightDeck Diagnostics, Inc., Boulder, CO, USA
| | | | | | - Phil Papst
- LightDeck Diagnostics, Inc., Boulder, CO, USA
| | - Kristen Pettrone
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Paul W Blair
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Subramaniam Krishnan
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Josh G Chenoweth
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Danielle V Clark
- The Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
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3
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Spatiotemporally controlled generation of NTPs for single-molecule studies. Nat Chem Biol 2022; 18:1144-1151. [PMID: 36131148 PMCID: PMC9512701 DOI: 10.1038/s41589-022-01100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 12/22/2022]
Abstract
Many essential processes in the cell depend on proteins that use nucleoside triphosphates (NTPs). Methods that directly monitor the often-complex dynamics of these proteins at the single-molecule level have helped to uncover their mechanisms of action. However, the measurement throughput is typically limited for NTP-utilizing reactions, and the quantitative dissection of complex dynamics over multiple sequential turnovers remains challenging. Here we present a method for controlling NTP-driven reactions in single-molecule experiments via the local generation of NTPs (LAGOON) that markedly increases the measurement throughput and enables single-turnover observations. We demonstrate the effectiveness of LAGOON in single-molecule fluorescence and force spectroscopy assays by monitoring DNA unwinding, nucleosome sliding and RNA polymerase elongation. LAGOON can be readily integrated with many single-molecule techniques, and we anticipate that it will facilitate studies of a wide range of crucial NTP-driven processes. ![]()
A new method for controlling NTP-driven reactions in single-molecule experiments via the local generation of NTPs (LAGOON) markedly increases the measurement throughput and enables single-turnover observations.
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4
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Measurement of Nucleotide Hydrolysis Using Fluorescent Biosensors for Phosphate. Methods Mol Biol 2021; 2263:289-318. [PMID: 33877604 DOI: 10.1007/978-1-0716-1197-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Assays for the detection of inorganic phosphate (Pi) are widely used to measure the activity of nucleotide hydrolyzing enzymes, such as ATPases and GTPases. The fluorescent biosensors for Pi, described here, are based on fluorescently labeled versions of E. coli phosphate-binding protein (PBP), which translates Pi binding into a large change in fluorescence intensity. In comparison with other Pi-detection systems, these biosensors are characterized by a high sensitivity (sub-micromolar Pi concentrations) and high time resolution (tens of milliseconds), and they are therefore particularly well suited for measurements of phosphate ester hydrolysis in real time. In this chapter, it is described how the Pi biosensors can be used to measure kinetics of ATPase and GTPase reactions, both under steady state and pre-steady state conditions. An example protocol is given for determining steady state kinetic parameters, Km and kcat, of the ATP-dependent chromatin remodeler Chd1, in a plate reader format. In addition, the measurement of Pi release kinetics under pre-steady state conditions is described, including a detailed experimental procedure for a single turnover measurement of ATP hydrolysis by the ABC-type ATPase SufBC using rapid mixing.
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5
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Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome. Proc Natl Acad Sci U S A 2021; 118:2014498118. [PMID: 33468676 DOI: 10.1073/pnas.2014498118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin remodelers are ATP (adenosine triphosphate)-powered motors that reposition nucleosomes throughout eukaryotic chromosomes. Remodelers possess autoinhibitory elements that control the direction of nucleosome sliding, but underlying mechanisms of inhibition have been unclear. Here, we show that autoinhibitory elements of the yeast Chd1 remodeler block nucleosome sliding by preventing initiation of twist defects. We show that two autoinhibitory elements-the chromodomains and bridge-reinforce each other to block sliding when the DNA-binding domain is not bound to entry-side DNA. Our data support a model where the chromodomains and bridge target nucleotide-free and ADP-bound states of the ATPase motor, favoring a partially disengaged state of the ATPase motor on the nucleosome. By bypassing distortions of nucleosomal DNA prior to ATP binding, we propose that autoinhibitory elements uncouple the ATP binding/hydrolysis cycle from DNA translocation around the histone core.
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6
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Oberbeckmann E, Niebauer V, Watanabe S, Farnung L, Moldt M, Schmid A, Cramer P, Peterson CL, Eustermann S, Hopfner KP, Korber P. Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nat Commun 2021; 12:3232. [PMID: 34050140 PMCID: PMC8163753 DOI: 10.1038/s41467-021-23015-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 03/13/2021] [Indexed: 01/09/2023] Open
Abstract
Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the 'ruler' that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.
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Affiliation(s)
- Elisa Oberbeckmann
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vanessa Niebauer
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shinya Watanabe
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Lucas Farnung
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Manuela Moldt
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea Schmid
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Sebastian Eustermann
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Philipp Korber
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany.
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7
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The Role of Non-Catalytic Domains of Hrp3 in Nucleosome Remodeling. Int J Mol Sci 2021; 22:ijms22041793. [PMID: 33670267 PMCID: PMC7918567 DOI: 10.3390/ijms22041793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/23/2022] Open
Abstract
The Helicase-related protein 3 (Hrp3), an ATP-dependent chromatin remodeling enzyme from the CHD family, is crucial for maintaining global nucleosome occupancy in Schizosaccharomyces pombe (S. pombe). Although the ATPase domain of Hrp3 is essential for chromatin remodeling, the contribution of non-ATPase domains of Hrp3 is still unclear. Here, we investigated the role of non-ATPase domains using in vitro methods. In our study, we expressed and purified recombinant S. pombe histone proteins, reconstituted them into histone octamers, and assembled nucleosome core particles. Using reconstituted nucleosomes and affinity-purified wild type and mutant Hrp3 from S. pombe we created a homogeneous in vitro system to evaluate the ATP hydrolyzing capacity of truncated Hrp3 proteins. We found that all non-ATPase domain deletions (∆chromo, ∆SANT, ∆SLIDE, and ∆coupling region) lead to reduced ATP hydrolyzing activities in vitro with DNA or nucleosome substrates. Only the coupling region deletion showed moderate stimulation of ATPase activity with the nucleosome. Interestingly, affinity-purified Hrp3 showed co-purification with all core histones suggesting a strong association with the nucleosomes in vivo. However, affinity-purified Hrp3 mutant with SANT and coupling regions deletion showed complete loss of interactions with the nucleosomes, while SLIDE and chromodomain deletions reduced Hrp3 interactions with the nucleosomes. Taken together, nucleosome association and ATPase stimulation by DNA or nucleosomes substrate suggest that the enzymatic activity of Hrp3 is fine-tuned by unique contributions of all four non-catalytic domains.
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8
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Levendosky RF, Bowman GD. Asymmetry between the two acidic patches dictates the direction of nucleosome sliding by the ISWI chromatin remodeler. eLife 2019; 8:45472. [PMID: 31094676 PMCID: PMC6546392 DOI: 10.7554/elife.45472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/16/2019] [Indexed: 01/15/2023] Open
Abstract
The acidic patch is a functionally important epitope on each face of the nucleosome that affects chromatin remodeling. Although related by 2-fold symmetry of the nucleosome, each acidic patch is uniquely positioned relative to a bound remodeler. An open question is whether remodelers are distinctly responsive to each acidic patch. Previously we reported a method for homogeneously producing asymmetric nucleosomes with distinct H2A/H2B dimers (Levendosky et al., 2016). Here, we use this methodology to show that the Chd1 remodeler from Saccharomyces cerevisiae and ISWI remodelers from human and Drosophila have distinct spatial requirements for the acidic patch. Unlike Chd1, which is equally affected by entry- and exit-side mutations, ISWI remodelers strongly depend on the entry-side acidic patch. Remarkably, asymmetry in the two acidic patches stimulates ISWI to slide mononucleosomes off DNA ends, overriding the remodeler’s preference to shift the histone core toward longer flanking DNA.
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Affiliation(s)
- Robert F Levendosky
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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9
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Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling. Nat Commun 2019; 10:1720. [PMID: 30979890 PMCID: PMC6461674 DOI: 10.1038/s41467-019-09657-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/20/2019] [Indexed: 11/11/2022] Open
Abstract
ATP-dependent chromatin remodelling enzymes (remodellers) regulate DNA accessibility in eukaryotic genomes. Many remodellers reposition (slide) nucleosomes, however, how DNA is propagated around the histone octamer during this process is unclear. Here we examine the real-time coordination of remodeller-induced DNA movements on both sides of the nucleosome using three-colour single-molecule FRET. During sliding by Chd1 and SNF2h remodellers, DNA is shifted discontinuously, with movement of entry-side DNA preceding that of exit-side DNA. The temporal delay between these movements implies a single rate-limiting step dependent on ATP binding and transient absorption or buffering of at least one base pair. High-resolution cross-linking experiments show that sliding can be achieved by buffering as few as 3 bp between entry and exit sides of the nucleosome. We propose that DNA buffering ensures nucleosome stability during ATP-dependent remodelling, and provides a means for communication between remodellers acting on opposite sides of the nucleosome. Chromatin remodelling enzymes (remodellers) regulate DNA accessibility of eukaryotic genomes, which rely in large part on an ability to reposition nucleosomes. Here the authors use three-colour single-molecule FRET to simultaneously monitor remodeller-induced DNA movements on both sides of the nucleosome in real-time.
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10
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Verma K, Patel A. Pyruvate Kinase M2 serves as blockade for nucleosome repositioning and abrogates Chd7 remodeling activity. PLoS One 2019; 14:e0211515. [PMID: 30735509 PMCID: PMC6368300 DOI: 10.1371/journal.pone.0211515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/15/2019] [Indexed: 01/10/2023] Open
Abstract
Pyruvate Kinase M2 (PKM2) mediates metabolic reshuffling and is ubiquitously upregulated in several cancer types. The non-metabolic function of PKM2 as key nuclear kinase and modulator of gene expression is instrumental in cancer progression and tumorigenesis. Here, we attempt to discern the non-canonical function of PKM2 as an epigenetic modulator and the underlying implication of this activity. Using 5'-FAM labelled reconstituted mononucleosome we have shown that PKM2 interacts with the complex through Histone H3 and possibly obstruct the access to DNA binding factors. Subsequently, the interaction negatively impacts the ATP dependent remodeling activity of Chromodomain Helicase DNA binding protein-7 (Chd7). Chd7 remodeling activity is required to ameliorate DNA damage and is crucial to genome stability. Our study shows that PKM2 blocks the Chd7 mediated sliding of nucleosome. It can be conjectured that stalling Chd7 may lead to impaired DNA damage and increased genomic instability. We propose a mechanism in which PKM2 negatively regulate nucleosome repositioning in chromatin and may exacerbate cancer by altering the nucleosome architecture. This research is imperative to our understanding of how altered cancer metabolism can potentially modulate the gene expression and sustain incessant proliferation by tweaking the chromatin topography.
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Affiliation(s)
- Kirtika Verma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Ashok Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
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11
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Kovač K, Sauer A, Mačinković I, Awe S, Finkernagel F, Hoffmeister H, Fuchs A, Müller R, Rathke C, Längst G, Brehm A. Tumour-associated missense mutations in the dMi-2 ATPase alters nucleosome remodelling properties in a mutation-specific manner. Nat Commun 2018; 9:2112. [PMID: 29844320 PMCID: PMC5974244 DOI: 10.1038/s41467-018-04503-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/30/2018] [Indexed: 12/20/2022] Open
Abstract
ATP-dependent chromatin remodellers are mutated in more than 20% of human cancers. The consequences of these mutations on enzyme function are poorly understood. Here, we characterise the effects of CHD4 mutations identified in endometrial carcinoma on the remodelling properties of dMi-2, the highly conserved Drosophila homologue of CHD4. Mutations from different patients have surprisingly diverse defects on nucleosome binding, ATPase activity and nucleosome remodelling. Unexpectedly, we identify both mutations that decrease and increase the enzyme activity. Our results define the chromodomains and a novel regulatory region as essential for nucleosome remodelling. Genetic experiments in Drosophila demonstrate that expression of cancer-derived dMi-2 mutants misregulates differentiation of epithelial wing structures and produces phenotypes that correlate with their nucleosome remodelling properties. Our results help to define the defects of CHD4 in cancer at the mechanistic level and provide the basis for the development of molecular approaches aimed at restoring their activity. ATP-dependent chromatin remodelers are often found mutated in human cancers. Here, the authors characterize the nucleosome remodelling properties of cancer-associated mutants of the Drosophila Chd4 homolog dMi-2.
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Affiliation(s)
- Kristina Kovač
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Anja Sauer
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Igor Mačinković
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Stephan Awe
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Florian Finkernagel
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.,Center for Tumour Biology and Immunology, University of Marburg, 35043, Marburg, Germany
| | - Helen Hoffmeister
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Andreas Fuchs
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Rolf Müller
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.,Center for Tumour Biology and Immunology, University of Marburg, 35043, Marburg, Germany
| | - Christina Rathke
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043, Marburg, Germany
| | - Gernot Längst
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Alexander Brehm
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.
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12
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Winger J, Nodelman IM, Levendosky RF, Bowman GD. A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA. eLife 2018; 7:34100. [PMID: 29809147 PMCID: PMC6031429 DOI: 10.7554/elife.34100] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/26/2018] [Indexed: 12/17/2022] Open
Abstract
As superfamily 2 (SF2)-type translocases, chromatin remodelers are expected to use an inchworm-type mechanism to walk along DNA. Yet how they move DNA around the histone core has not been clear. Here we show that a remodeler ATPase motor can shift large segments of DNA by changing the twist and length of nucleosomal DNA at superhelix location 2 (SHL2). Using canonical and variant 601 nucleosomes, we find that the Saccharomyces cerevisiae Chd1 remodeler decreased DNA twist at SHL2 in nucleotide-free and ADP-bound states, and increased twist with transition state analogs. These differences in DNA twist allow the open state of the ATPase to pull in ~1 base pair (bp) by stabilizing a small DNA bulge, and closure of the ATPase to shift the DNA bulge toward the dyad. We propose that such formation and elimination of twist defects underlie the mechanism of nucleosome sliding by CHD-, ISWI-, and SWI/SNF-type remodelers. DNA is shaped like a spiral staircase, twisting around itself to create a double helix. This results in a long string-like molecule that needs to be carefully packaged to fit inside the cells of organisms as diverse as fungi or humans. This packaging process starts when a portion of DNA tightly wraps around a spool-like core of proteins called histones. The resulting structure is known as a nucleosome. Like the beads on a necklace, nucleosomes exist at regular intervals along DNA. The DNA sequence around the histones cannot be accessed by a cell, and so the nucleosomes need to be ‘shifted’ along DNA to free up the genetic information. Enzymes known as chromatin remodelers perform this role by binding to a nucleosome, and then using energy to fuel a change in their structure that makes them ‘crawl’ on DNA like an inchworm. During this process, chromatin remodelers slide nucleosomes along the DNA, but it was unclear how exactly the inchworm motions pushed DNA around the histones. Here, Winger et al. look into the details of this mechanism by focusing on the chromatin remodeler Chd1, which is conserved from yeast to humans. Experiments show that, first, the enzyme slightly untwists the DNA double helix; this untwisting causes the DNA to pucker a little on the nucleosome. The puckering creates tension and ‘pulls’ DNA towards the remodeler. Then, Chd1 changes its structure and twists DNA in the opposite direction, which forces the puckered DNA onto the other side of the remodeler. This extra bit of DNA then propagates around the rest of the nucleosome, like the wave created by flicking the end of a long rope. This sheds light on how these enzymes can ratchet DNA past the histones. As the gatekeepers of our genetic information, chromatin remodelers are key to the health of the cell – in fact, they are often affected in cancers. The work by Winger et al. creates a framework that will help to understand how exactly chromatin remodelers help cells access the genetic information that the body needs to function properly.
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Affiliation(s)
- Jessica Winger
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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13
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Qiu Y, Levendosky RF, Chakravarthy S, Patel A, Bowman GD, Myong S. The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer. Mol Cell 2017; 68:76-88.e6. [PMID: 28943314 PMCID: PMC5745159 DOI: 10.1016/j.molcel.2017.08.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/30/2017] [Accepted: 08/18/2017] [Indexed: 11/18/2022]
Abstract
Chromatin remodelers catalyze dynamic packaging of the genome by carrying out nucleosome assembly/disassembly, histone exchange, and nucleosome repositioning. Remodeling results in evenly spaced nucleosomes, which requires probing both sides of the nucleosome, yet the way remodelers organize sliding activity to achieve this task is not understood. Here, we show that the monomeric Chd1 remodeler shifts DNA back and forth by dynamically alternating between different segments of the nucleosome. During sliding, Chd1 generates unstable remodeling intermediates that spontaneously relax to a pre-remodeled position. We demonstrate that nucleosome sliding is tightly controlled by two regulatory domains: the DNA-binding domain, which interferes with sliding when its range is limited by a truncated linking segment, and the chromodomains, which play a key role in substrate discrimination. We propose that active interplay of the ATPase motor with the regulatory domains may promote dynamic nucleosome structures uniquely suited for histone exchange and chromatin reorganization during transcription.
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Affiliation(s)
- Yupeng Qiu
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | - Robert F Levendosky
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ashok Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gregory D Bowman
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL 61801, USA.
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14
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Winger J, Bowman GD. The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler. J Mol Biol 2017; 429:808-822. [PMID: 28189426 DOI: 10.1016/j.jmb.2017.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 10/20/2022]
Abstract
Chromatin remodelers are ATP-dependent enzymes that are critical for reorganizing and repositioning nucleosomes in concert with many basic cellular processes. For the chromodomain helicase DNA-binding protein 1 (Chd1) remodeler, nucleosome sliding has been shown to depend on the DNA flanking the nucleosome, transcription factor binding at the nucleosome edge, and the presence of the histone H2A/H2B dimer on the entry side. Here, we report that Chd1 is also sensitive to the sequence of DNA within the nucleosome and slides nucleosomes made with the 601 Widom positioning sequence asymmetrically. Kinetic and equilibrium experiments show that poly(dA:dT) tracts perturb remodeling reactions if within one and a half helical turns of superhelix location 2 (SHL2), where the Chd1 ATPase engages nucleosomal DNA. These sequence-dependent effects do not rely on the Chd1 DNA-binding domain and are not due to differences in nucleosome affinity. Using site-specific cross-linking, we show that internal poly(dA:dT) tracts do not block the engagement of the ATPase motor with SHL2, yet they promote multiple translational positions of DNA with respect to both Chd1 and the histone core. We speculate that Chd1 senses the sequence-dependent response of DNA as the remodeler ATPase perturbs the duplex at SHL2. These results suggest that the sequence sensitivity of histones and remodelers occur at unique segments of DNA on the nucleosome, allowing them to work together or in opposition to determine nucleosome positions throughout the genome.
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Affiliation(s)
- Jessica Winger
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregory D Bowman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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15
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Nodelman IM, Bleichert F, Patel A, Ren R, Horvath KC, Berger JM, Bowman GD. Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome. Mol Cell 2017; 65:447-459.e6. [PMID: 28111016 DOI: 10.1016/j.molcel.2016.12.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/24/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022]
Abstract
Chromatin remodelers use a helicase-like ATPase motor to reposition and reorganize nucleosomes along genomic DNA. Yet, how the ATPase motor communicates with other remodeler domains in the context of the nucleosome has so far been elusive. Here, we report for the Chd1 remodeler a unique organization of domains on the nucleosome that reveals direct domain-domain communication. Site-specific cross-linking shows that the chromodomains and ATPase motor bind to adjacent SHL1 and SHL2 sites, respectively, on nucleosomal DNA and pack against the DNA-binding domain on DNA exiting the nucleosome. This domain arrangement spans the two DNA gyres of the nucleosome and bridges both ends of a wrapped, ∼90-bp nucleosomal loop of DNA, suggesting a means for nucleosome assembly. This architecture illustrates how Chd1 senses DNA outside the nucleosome core and provides a basis for nucleosome spacing and directional sliding away from transcription factor barriers.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Franziska Bleichert
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ashok Patel
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Ren Ren
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Kyle C Horvath
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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16
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Levendosky RF, Sabantsev A, Deindl S, Bowman GD. The Chd1 chromatin remodeler shifts hexasomes unidirectionally. eLife 2016; 5. [PMID: 28032848 PMCID: PMC5226652 DOI: 10.7554/elife.21356] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022] Open
Abstract
Despite their canonical two-fold symmetry, nucleosomes in biological contexts are often asymmetric: functionalized with post-translational modifications (PTMs), substituted with histone variants, and even lacking H2A/H2B dimers. Here we show that the Widom 601 nucleosome positioning sequence can produce hexasomes in a specific orientation on DNA, providing a useful tool for interrogating chromatin enzymes and allowing for the generation of nucleosomes with precisely defined asymmetry. Using this methodology, we demonstrate that the Chd1 chromatin remodeler from Saccharomyces cerevisiae requires H2A/H2B on the entry side for sliding, and thus, unlike the back-and-forth sliding observed for nucleosomes, Chd1 shifts hexasomes unidirectionally. Chd1 takes part in chromatin reorganization surrounding transcribing RNA polymerase II (Pol II), and using asymmetric nucleosomes we show that ubiquitin-conjugated H2B on the entry side stimulates nucleosome sliding by Chd1. We speculate that biased nucleosome and hexasome sliding due to asymmetry contributes to the packing of arrays observed in vivo. DOI:http://dx.doi.org/10.7554/eLife.21356.001
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Affiliation(s)
- Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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17
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Nodelman IM, Horvath KC, Levendosky RF, Winger J, Ren R, Patel A, Li M, Wang MD, Roberts E, Bowman GD. The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome. Nucleic Acids Res 2016; 44:7580-91. [PMID: 27174939 PMCID: PMC5027475 DOI: 10.1093/nar/gkw406] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 04/29/2016] [Indexed: 12/21/2022] Open
Abstract
Chromatin remodelers are essential for establishing and maintaining the placement of nucleosomes along genomic DNA. Yet how chromatin remodelers recognize and respond to distinct chromatin environments surrounding nucleosomes is poorly understood. Here, we use Lac repressor as a tool to probe how a DNA-bound factor influences action of the Chd1 remodeler. We show that Chd1 preferentially shifts nucleosomes away from Lac repressor, demonstrating that a DNA-bound factor defines a barrier for nucleosome positioning. Rather than an absolute block in sliding, the barrier effect was achieved by altered rates of nucleosome sliding that biased redistribution of nucleosomes away from the bound Lac repressor site. Remarkably, in addition to slower sliding toward the LacO site, the presence of Lac repressor also stimulated sliding in the opposite direction. These experiments therefore demonstrate that Chd1 responds to the presence of a bound protein on both entry and exit sides of the nucleosome. This sensitivity to both sides of the nucleosome allows for a faster and sharper response than would be possible by responding to only the entry side, and we speculate that dual entry/exit sensitivity is also important for regularly spaced nucleosome arrays generated by Chd1 and the related ISWI remodelers.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kyle C Horvath
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Jessica Winger
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ren Ren
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ashok Patel
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ming Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michelle D Wang
- Department of Physics, LASSP, Cornell University, Ithaca, NY 14853, USA Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA
| | - Elijah Roberts
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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18
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Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife 2016; 5:e12677. [PMID: 26987018 PMCID: PMC4861601 DOI: 10.7554/elife.12677] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/16/2016] [Indexed: 12/23/2022] Open
Abstract
The prokaryotic CRISPR (clustered regularly interspaced palindromic repeats)-associated protein, Cas9, has been widely adopted as a tool for editing, imaging, and regulating eukaryotic genomes. However, our understanding of how to select single-guide RNAs (sgRNAs) that mediate efficient Cas9 activity is incomplete, as we lack insight into how chromatin impacts Cas9 targeting. To address this gap, we analyzed large-scale genetic screens performed in human cell lines using either nuclease-active or nuclease-dead Cas9 (dCas9). We observed that highly active sgRNAs for Cas9 and dCas9 were found almost exclusively in regions of low nucleosome occupancy. In vitro experiments demonstrated that nucleosomes in fact directly impede Cas9 binding and cleavage, while chromatin remodeling can restore Cas9 access. Our results reveal a critical role of eukaryotic chromatin in dictating the targeting specificity of this transplanted bacterial enzyme, and provide rules for selecting Cas9 target sites distinct from and complementary to those based on sequence properties.
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Affiliation(s)
- Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Lea B Witkowsky
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Benjamin Guglielmi
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Sharon E Torigoe
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
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19
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Yao W, Beckwith SL, Zheng T, Young T, Dinh VT, Ranjan A, Morrison AJ. Assembly of the Arp5 (Actin-related Protein) Subunit Involved in Distinct INO80 Chromatin Remodeling Activities. J Biol Chem 2015; 290:25700-9. [PMID: 26306040 DOI: 10.1074/jbc.m115.674887] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/06/2022] Open
Abstract
ATP-dependent chromatin remodeling, which repositions and restructures nucleosomes, is essential to all DNA-templated processes. The INO80 chromatin remodeling complex is an evolutionarily conserved complex involved in diverse cellular processes, including transcription, DNA repair, and replication. The functional diversity of the INO80 complex can, in part, be attributed to specialized activities of distinct subunits that compose the complex. Furthermore, structural analyses have identified biochemically discrete subunit modules that assemble along the Ino80 ATPase scaffold. Of particular interest is the Saccharomyces cerevisiae Arp5-Ies6 module located proximal to the Ino80 ATPase and the Rvb1-Rvb2 helicase module needed for INO80-mediated in vitro activity. In this study we demonstrate that the previously uncharacterized Ies2 subunit is required for Arp5-Ies6 association with the catalytic components of the INO80 complex. In addition, Arp5-Ies6 module assembly with the INO80 complex is dependent on distinct conserved domains within Arp5, Ies6, and Ino80, including the spacer region within the Ino80 ATPase domain. Arp5-Ies6 interacts with chromatin via assembly with the INO80 complex, as IES2 and INO80 deletion results in loss of Arp5-Ies6 chromatin association. Interestingly, ectopic addition of the wild-type Arp5-Ies6 module stimulates INO80-mediated ATP hydrolysis and nucleosome sliding in vitro. However, the addition of mutant Arp5 lacking unique insertion domains facilitates ATP hydrolysis in the absence of nucleosome sliding. Collectively, these results define the requirements of Arp5-Ies6 assembly, which are needed to couple ATP hydrolysis to productive nucleosome movement.
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Affiliation(s)
- Wei Yao
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Sean L Beckwith
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Tina Zheng
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Thomas Young
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Van T Dinh
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Anand Ranjan
- Laboratory of Biochemistry and Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Ashby J Morrison
- From the Department of Biology, Stanford University, Stanford California 94305 and
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20
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Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density. Mol Cell Biol 2015; 35:1588-605. [PMID: 25733687 DOI: 10.1128/mcb.01070-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 02/14/2015] [Indexed: 12/14/2022] Open
Abstract
Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI- and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the Hand-Sant-Slide (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.
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21
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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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22
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Al-Ani G, Briggs K, Malik SS, Conner M, Azuma Y, Fischer CJ. Quantitative determination of binding of ISWI to nucleosomes and DNA shows allosteric regulation of DNA binding by nucleotides. Biochemistry 2014; 53:4334-45. [PMID: 24898734 PMCID: PMC4100786 DOI: 10.1021/bi500224t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
regulation of chromatin structure is controlled by a family
of molecular motors called chromatin remodelers. The ability of these
enzymes to remodel chromatin structure is dependent on their ability
to couple ATP binding and hydrolysis into the mechanical work that
drives nucleosome repositioning. The necessary first step in determining
how these essential enzymes perform this function is to characterize
both how they bind nucleosomes and how this interaction is regulated
by ATP binding and hydrolysis. With this goal in mind, we monitored
the interaction of the chromatin remodeler ISWI with fluorophore-labeled
nucleosomes and DNA through associated changes in fluorescence anisotropy
of the fluorophore upon binding of ISWI to these substrates. We determined
that one ISWI molecule binds to a 20 bp double-stranded DNA substrate
with an affinity of 18 ± 2 nM. In contrast, two ISWI molecules
can bind to the core nucleosome with short linker DNA with stoichiometric
macroscopic equilibrium constants: 1/β1 = 1.3 ±
0.6 nM, and 1/β2 = 13 ± 7 nM2. Furthermore,
to improve our understanding of the mechanism of DNA translocation
by ISWI, and hence nucleosome repositioning, we determined the effect
of nucleotide analogues on substrate binding by ISWI. While the affinity
of ISWI for the nucleosome substrate with short lengths of flanking
DNA was not affected by the presence of nucleotides, the affinity
of ISWI for the DNA substrate is weakened in the presence of nonhydrolyzable
ATP analogues but not by ADP.
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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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23
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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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24
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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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25
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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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26
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Abstract
Biochemical assays reveal that nucleosome maturation and chromatin remodelling by the motor protein Chd1 are distinct, separable enzymatic activities.
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Affiliation(s)
- Karim Bouazoune
- is in the Department of Molecular Biology and the Department of Genetics , Massachusetts General Hospital, Harvard Medical School , Boston , United States
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27
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Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. eLife 2013; 2:e00863. [PMID: 23986862 PMCID: PMC3748710 DOI: 10.7554/elife.00863] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/16/2013] [Indexed: 11/23/2022] Open
Abstract
Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI:http://dx.doi.org/10.7554/eLife.00863.001 In many cells, genomic DNA is wrapped around proteins known as histones to produce particles called nucleosomes. These particles then join together—like beads on a string—to form a highly periodic structure called chromatin. In the nucleus, chromatin is further folded and condensed into chromosomes. However, many important processes, including the replication of DNA and the transcription of genes, require access to the DNA. The cell must therefore be able to disassemble chromatin and remove the histones, and then, once these processes are complete, to reassemble the chromatin. Enzymes known as chromatin assembly factors are responsible for the disassembly and reassembly of chromatin. There are two main types of chromatin assembly factors in eukaryotic cells (i.e., cells with nuclei)—histone chaperones and motor proteins. The histone chaperones escort histones from the cytoplasm, where they are made, to the nucleus. The motor proteins—using energy supplied by ATP molecules—then catalyze the formation of nucleosomes. This involves two activities: the motor proteins assemble nucleosomes by helping the DNA to wrap around the histones, and they also remodel chromatin by altering the positions of nucleosomes along the DNA to ensure that they are periodic—that is, regularly spaced. A conserved motor protein called Chd1 performs chromatin assembly and remodeling in eukaryotic cells. Chd1 works in conjunction with histone chaperones—both are needed for chromatin assembly, and so are DNA, histones and ATP. However, whether or not chromatin assembly and chromatin remodeling by Chd1 are identical or distinct processes is not well understood. Torigoe et al. have now discovered a mutant Chd1 protein that has nucleosome assembly activity (i.e., it can make nucleosomes) but cannot remodel chromatin (i.e., it is unable to move nucleosomes), and thus have demonstrated that these two processes are functionally distinct. Torigoe et al. additionally have found that the mutant Chd1 proteins produce randomly distributed nucleosomes rather than the periodic arrays normally found in chromatin. Further analysis then revealed that the wild-type Chd1 protein, which can remodel chromatin, is able to convert randomly distributed nucleosomes into periodic arrays. These findings have led to a new model for chromatin assembly in which Chd1 initially generates randomly distributed nucleosomes (via its assembly function), and then converts them into periodic arrays of nucleosomes (via its remodeling function). Together, these studies shed light on the mechanisms by which chromatin is created and manipulated in cells. DOI:http://dx.doi.org/10.7554/eLife.00863.002
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Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology , University of California, San Diego , La Jolla , United States
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Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. eLife 2013. [PMID: 23986862 DOI: 10.7554/elife.00863.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI:http://dx.doi.org/10.7554/eLife.00863.001.
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Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology , University of California, San Diego , La Jolla , United States
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29
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Balancing chromatin remodeling and histone modifications in transcription. Trends Genet 2013; 29:621-9. [PMID: 23870137 DOI: 10.1016/j.tig.2013.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/29/2013] [Accepted: 06/18/2013] [Indexed: 11/24/2022]
Abstract
Chromatin remodelers use the energy of ATP hydrolysis to reposition or evict nucleosomes or to replace canonical histones with histone variants. By regulating nucleosome dynamics, remodelers gate access to the underlying DNA for replication, repair, and transcription. Nucleosomes are subject to extensive post-translational modifications that can recruit regulatory proteins or alter the local chromatin structure. Just as extensive crosstalk has been observed between different histone post-translational modifications, there is growing evidence for both coordinated and antagonistic functional relations between nucleosome remodeling and modifying machineries. Defining the combined functions of the complexes that alter nucleosome interactions, position, and stability is key to understanding processes that require access to DNA, particularly with growing appreciation of their contributions to human health and disease. Here, we highlight recent advances in the interactions between histone modifications and the imitation-switch (ISWI) and chromodomain helicase DNA-binding protein 1 (CHD1) chromatin remodelers from studies in budding yeast, fission yeast, flies, and mammalian cells, with a focus on yeast.
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Manning BJ, Peterson CL. Releasing the brakes on a chromatin-remodeling enzyme. Nat Struct Mol Biol 2013; 20:5-7. [PMID: 23288358 DOI: 10.1038/nsmb.2482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatin-remodeling enzymes use the energy from ATP hydrolysis to mobilize, disrupt or change the histone composition of nucleosomes, facilitating nearly every nuclear event. Two recent studies indicate that remodeling enzymes harness the power of an ancient constitutively active DNA translocase and that different remodeling enzymes may use specialized coupling domains that communicate the presence of nucleosomal epitopes to regulate translocase and remodeling activity.
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Affiliation(s)
- Benjamin J Manning
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Patel A, Chakravarthy S, Morrone S, Nodelman IM, McKnight JN, Bowman GD. Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler. Nucleic Acids Res 2012; 41:1637-48. [PMID: 23275572 PMCID: PMC3561990 DOI: 10.1093/nar/gks1440] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Chromatin remodelers can either organize or disrupt nucleosomal arrays, yet the mechanisms specifying these opposing actions are not clear. Here, we show that the outcome of nucleosome sliding by Chd1 changes dramatically depending on how the chromatin remodeler is targeted to nucleosomes. Using a Chd1–streptavidin fusion remodeler, we found that targeting via biotinylated DNA resulted in directional sliding towards the recruitment site, whereas targeting via biotinylated histones produced a distribution of nucleosome positions. Remarkably, the fusion remodeler shifted nucleosomes with biotinylated histones up to 50 bp off the ends of DNA and was capable of reducing negative supercoiling of plasmids containing biotinylated chromatin, similar to remodelling characteristics observed for SWI/SNF-type remodelers. These data suggest that forming a stable attachment to nucleosomes via histones, and thus lacking sensitivity to extranucleosomal DNA, seems to be sufficient for allowing a chromatin remodeler to possess SWI/SNF-like disruptive properties.
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Affiliation(s)
- Ashok Patel
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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Use of biotinylated plasmid DNA as a surrogate for HSV DNA to identify proteins that repress or activate viral gene expression. Proc Natl Acad Sci U S A 2012; 109:E3549-57. [PMID: 23223531 DOI: 10.1073/pnas.1218783109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ICP0, a key herpes simplex virus regulatory protein, functions first in the nucleus and then in the cytoplasm. The duration of its nuclear sojourn in cells transfected with DNA and then infected is related to the quantity of transfected DNA. Furthermore, ICP0 transactivates both viral genes and genes encoded by the transfected DNA. The data support the hypothesis that ICP0 is retained in the nucleus until it completes the replacement of repressive chromatin with effector proteins that enable transcription of both DNA templates.To identify the effector proteins, we transfected cells with biotinylated DNA encoding a nonviral gene and then infected the cells with wild-type virus. Proteins bound to transfected biotinylated plasmid recovered from mock-treated and infected cells were identified using mass spectrometry followed by appropriate database search. The transfected DNA from mock-infected cells yielded proteins associated with repression, whereas DNA recovered from infected cells included proteins known to enable transcription and proteins that have not been previously associated with that role. To test the hypothesis that the proteins hitherto not known to associate with viral gene expression are nevertheless essential, we tested the role of the DEAD-box helicase Ddx17. We report that Ddx17 plays a critical role in the expression of early and late viral genes. Thus, biotinylated DNA recovered from transfected infected cells can function as a surrogate for viral DNA and is a rich source of proteins that play a role in viral gene expression but which have not been previously identified in that role.
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Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 2012; 492:280-4. [PMID: 23143334 PMCID: PMC3631562 DOI: 10.1038/nature11625] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 09/27/2012] [Indexed: 12/25/2022]
Abstract
Chromatin remodeling complexes (CRCs) mobilize nucleosomes to mediate the access of DNA-binding factors to their sites in vivo. These CRCs contain a catalytic subunit that bears an ATPase/DNA translocase domain, and flanking regions that bind nucleosomal epitopes1. A central question is whether and how these flanking regions regulate ATP hydrolysis or the coupling of hydrolysis to DNA translocation, to affect nucleosome sliding efficiency. ISWIfamily CRCs contain ISWI2, which utilizes its ATPase/DNA translocase domain to pump DNA around the histone octamer to enable sliding3-7_ENREF_13. ISWI is positively regulated by two ‘activating’ nucleosomal epitopes: the ‘basic patch’ on the H4 tail, and extranucleosomal (linker) DNA8-13. Previous work defined the HSS domain in the ISWI C-terminus that binds linker DNA, needed for ISWI activity14,15. Here, we define two new, conserved, and separate regulatory regions on Drosophila ISWI, AutoN and NegC, that negatively regulate ATP hydrolysis (AutoN) or the coupling of ATP hydrolysis to productive DNA translocation (NegC). Rather than ‘activating’, the two aforementioned nucleosomal epitopes actually inhibit the negative regulation of AutoN and NegC. Remarkably, mutation/removal of AutoN and NegC enables significant nucleosome sliding without the H4 ‘basic patch’ or extranucleosomal DNA, or the HSS domain – converting ISWI to biochemical attributes of SWI/SNF-family ATPases. Thus, the ISWI ATPase catalytic core is an intrinsically-active DNA translocase which conducts nucleosome sliding, onto which selective ‘inhibition-of-inhibition’ modules are placed, to help ensure that remodeling occurs only in the presence of proper nucleosomal epitopes. This supports a general concept for the specialization of chromatin remodeling ATPases, where specific regulatory modules adapt an ancient active DNA translocase to conduct particular tasks only on the appropriate chromatin landscape.
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Chakravarthy S, Patel A, Bowman GD. The basic linker of macroH2A stabilizes DNA at the entry/exit site of the nucleosome. Nucleic Acids Res 2012; 40:8285-95. [PMID: 22753032 PMCID: PMC3458575 DOI: 10.1093/nar/gks645] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MacroH2A is a histone H2A variant that is typically found in heterochromatic regions of the genome. A positively charged linker that connects the histone-fold with the macro-domain was suggested to have DNA-binding properties, and has been shown to promote oligomerization of chromatin fibers. Here we examine the influence of this basic linker on DNA of mononucleosomes. We find that the macro-linker reduces accessibility to extranucleosomal DNA, and appears to increase compaction of the nucleosome. These properties arise from interactions between the H1-like basic linker region and DNA around the entry/exit site, which increases protection of nucleosomal DNA from exonuclease III digestion by ∼10 bp. By stabilizing the wrapping of DNA around the histone core, this basic linker of macroH2A may alter the distribution of nucleosome-associated factors, and potentially contribute to the more compacted nature of heterochromatin.
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Affiliation(s)
- Srinivas Chakravarthy
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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Chavez MS, Scorgie JK, Dennehey BK, Noone S, Tyler JK, Churchill ME. The conformational flexibility of the C-terminus of histone H4 promotes histone octamer and nucleosome stability and yeast viability. Epigenetics Chromatin 2012; 5:5. [PMID: 22541333 PMCID: PMC3439350 DOI: 10.1186/1756-8935-5-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 03/19/2012] [Indexed: 01/10/2023] Open
Abstract
Background The protein anti-silencing function 1 (Asf1) chaperones histones H3/H4 for assembly into nucleosomes every cell cycle as well as during DNA transcription and repair. Asf1 interacts directly with H4 through the C-terminal tail of H4, which itself interacts with the docking domain of H2A in the nucleosome. The structure of this region of the H4 C-terminus differs greatly in these two contexts. Results To investigate the functional consequence of this structural change in histone H4, we restricted the available conformations of the H4 C-terminus and analyzed its effect in vitro and in vivo in Saccharomyces cerevisiae. One such mutation, H4 G94P, had modest effects on the interaction between H4 and Asf1. However, in yeast, flexibility of the C-terminal tail of H4 has essential functions that extend beyond chromatin assembly and disassembly. The H4 G94P mutation resulted in severely sick yeast, although nucleosomes still formed in vivo albeit yielding diffuse micrococcal nuclease ladders. In vitro, H4G4P had modest effects on nucleosome stability, dramatically reduced histone octamer stability, and altered nucleosome sliding ability. Conclusions The functional consequences of altering the conformational flexibility in the C-terminal tail of H4 are severe. Interestingly, despite the detrimental effects of the histone H4 G94P mutant on viability, nucleosome formation was not markedly affected in vivo. However, histone octamer stability and nucleosome stability as well as nucleosome sliding ability were altered in vitro. These studies highlight an important role for correct interactions of the histone H4 C-terminal tail within the histone octamer and suggest that maintenance of a stable histone octamer in vivo is an essential feature of chromatin dynamics.
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Affiliation(s)
- Myrriah S Chavez
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jean K Scorgie
- Department of Pharmacology and Structural Biology and Biophysics Program, University of Colorado, School of Medicine, 12801 East 17th Avenue, Aurora, CO, 80045-0511, USA
| | - Briana K Dennehey
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Seth Noone
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jessica K Tyler
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mair Ea Churchill
- Department of Pharmacology and Structural Biology and Biophysics Program, University of Colorado, School of Medicine, 12801 East 17th Avenue, Aurora, CO, 80045-0511, USA
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