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Meanor JN, Keung AJ, Rao BM. Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity. Int J Mol Sci 2022; 23:ijms23031691. [PMID: 35163614 PMCID: PMC8836101 DOI: 10.3390/ijms23031691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/03/2022] Open
Abstract
Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.
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Affiliation(s)
- Jenna N. Meanor
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
| | - Albert J. Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Correspondence: (A.J.K.); (B.M.R.)
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Golden LEAF Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, USA
- Correspondence: (A.J.K.); (B.M.R.)
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2
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Ghoneim M, Fuchs HA, Musselman CA. Histone Tail Conformations: A Fuzzy Affair with DNA. Trends Biochem Sci 2021; 46:564-578. [PMID: 33551235 DOI: 10.1016/j.tibs.2020.12.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022]
Abstract
The core histone tails are critical in chromatin structure and signaling. Studies over the past several decades have provided a wealth of information on the histone tails and their interaction with chromatin factors. However, the conformation of the histone tails in a chromatin relevant context has remained elusive. Only recently has enough evidence emerged to start to build a structural model of the tails in the context of nucleosomes and nucleosome arrays. Here, we review these studies and propose that the histone tails adopt a high-affinity fuzzy complex with DNA, characterized by robust but dynamic association. Furthermore, we discuss how these DNA-bound conformational ensembles promote distinct chromatin structure and signaling, and that their fuzzy nature is important in transitioning between functional states.
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Affiliation(s)
- Mohamed Ghoneim
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Harrison A Fuchs
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine A Musselman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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3
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Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Sci Rep 2021; 11:380. [PMID: 33432055 PMCID: PMC7801413 DOI: 10.1038/s41598-020-79654-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023] Open
Abstract
Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.
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Huang YC, Su CJ, Korolev N, Berezhnoy NV, Wang S, Soman A, Chen CY, Chen HL, Jeng US, Nordenskiöld L. The effect of linker DNA on the structure and interaction of nucleosome core particles. SOFT MATTER 2018; 14:9096-9106. [PMID: 30215440 DOI: 10.1039/c8sm00998h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In eukaryotes, the compaction of chromatin fibers composed of nucleosome core particles (NCPs) connected by a linker DNA into chromosomes is highly efficient; however, the underlying folding mechanisms remain elusive. We used small angle X-ray scattering (SAXS) to investigate the influence of linker DNA length on the local structure and the interparticle interactions of the NCPs. In the presence of the linker DNA of 30 bp or less in length, the results suggest partial unwrapping of nucleosomal DNA on the NCP irrespective of the linker DNA length. Moreover, the presence of 15 bp linker DNA alleviated the electrostatic repulsion between the NCPs and prevented the formation of an ordered columnar hexagonal phase, demonstrating that the linker DNA plays an active role in chromatin folding.
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Affiliation(s)
- Yen-Chih Huang
- Department of Chemical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsin-Chu 30013, Taiwan.
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5
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Berezhnoy NV, Liu Y, Allahverdi A, Yang R, Su CJ, Liu CF, Korolev N, Nordenskiöld L. The Influence of Ionic Environment and Histone Tails on Columnar Order of Nucleosome Core Particles. Biophys J 2017; 110:1720-1731. [PMID: 27119633 DOI: 10.1016/j.bpj.2016.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/04/2016] [Accepted: 03/07/2016] [Indexed: 01/08/2023] Open
Abstract
The nucleosome core particle (NCP) is the basic building block of chromatin. Nucleosome-nucleosome interactions are instrumental in chromatin compaction, and understanding NCP self-assembly is important for understanding chromatin structure and dynamics. Recombinant NCPs aggregated by multivalent cations form various ordered phases that can be studied by x-ray diffraction (small-angle x-ray scattering). In this work, the effects on the supramolecular structure of aggregated NCPs due to lysine histone H4 tail acetylations, histone H2A mutations (neutralizing the acidic patch of the histone octamer), and the removal of histone tails were investigated. The formation of ordered mainly hexagonal columnar NCP phases is in agreement with earlier studies; however, the highly homogeneous recombinant NCP systems used in this work display a more compact packing. The long-range order of the NCP columnar phase was found to be abolished or reduced by acetylation of the H4 tails, acidic patch neutralization, and removal of the H3 and H2B tails. Loss of nucleosome stacking upon removal of the H3 tails in combination with other tails was observed. In the absence of the H2A tails, the formation of an unknown highly ordered phase was observed.
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Affiliation(s)
- Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ying Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Abdollah Allahverdi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Zhang R, Erler J, Langowski J. Histone Acetylation Regulates Chromatin Accessibility: Role of H4K16 in Inter-nucleosome Interaction. Biophys J 2017; 112:450-459. [PMID: 27931745 PMCID: PMC5300776 DOI: 10.1016/j.bpj.2016.11.015] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/30/2016] [Accepted: 11/14/2016] [Indexed: 12/17/2022] Open
Abstract
The N-terminal tail of histone H4 is an indispensable mediator for inter-nucleosome interaction, which is required for chromatin fiber condensation. H4K16 acetylation (H4K16Ac) activates gene transcription by influencing both chromatin structure and interplay with nonhistone proteins. To understand the influence of H4K16Ac on inter-nucleosome interaction, we performed a simulation study for the H4 tail in the context of two nucleosomes in neighboring unit cells in the crystal structure. The binding conformation of H4 tail with/without K16Ac was sampled by replica exchange with solute tempering, and the free energy landscape was explored by metadynamics. The results indicate two important features of H4K16: 1) it is the first button to anchor the H4 tail on the adjacent nucleosome; and 2) it is the only acetylation site interacting with the acidic patch. H4K16Ac disrupts the electrostatic interactions of K16, weakens H4 tail-acidic patch binding, and significantly increases H4 tail conformation diversity. Our study suggests that H4K16Ac directly reduces the inter-nucleosome interaction mediated by the H4 tail, which might further encourage the binding of nonhistone proteins on the acidic patch.
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Affiliation(s)
- Ruihan Zhang
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jochen Erler
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany.
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7
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Saurabh S, Glaser MA, Lansac Y, Maiti PK. Atomistic Simulation of Stacked Nucleosome Core Particles: Tail Bridging, the H4 Tail, and Effect of Hydrophobic Forces. J Phys Chem B 2016; 120:3048-60. [DOI: 10.1021/acs.jpcb.5b11863] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suman Saurabh
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Matthew A. Glaser
- Department
of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, United States
| | - Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
- School
of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Prabal K. Maiti
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560012, India
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8
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Buning R, Kropff W, Martens K, van Noort J. spFRET reveals changes in nucleosome breathing by neighboring nucleosomes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064103. [PMID: 25564102 DOI: 10.1088/0953-8984/27/6/064103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chromatin, the structure in which DNA is compacted in eukaryotic cells, plays a key role in regulating DNA accessibility. FRET experiments on single nucleosomes, the basic units in chromatin, have revealed a dynamic nucleosome where spontaneous DNA unwrapping from the ends provides access to the nucleosomal DNA. Here we investigated how this DNA breathing is affected by extension of the linker DNA and by the presence of a neighboring nucleosome. We found that both electrostatic interactions between the entering and exiting linker DNA and nucleosome-nucleosome interactions increase unwrapping. Interactions between neighboring nucleosomes are more likely in dinucleosomes spaced by 55 bp of linker DNA than in dinucleosomes spaced by 50 bp of linker DNA. Such increased unwrapping may not only increase the accessibility of nucleosomal DNA in chromatin fibers, it may also be key to folding of nucleosomes into higher order structures.
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Affiliation(s)
- Ruth Buning
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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9
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Dhanak D, Jackson P. Development and classes of epigenetic drugs for cancer. Biochem Biophys Res Commun 2014; 455:58-69. [PMID: 25016182 DOI: 10.1016/j.bbrc.2014.07.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 12/16/2022]
Abstract
Emerging evidence supports an important, etiologic role for epigenetic modifications in cancer. Various post translational modifications of histone proteins together with DNA methylation constitute an 'epigenetic code' regulating the transcriptional status of the cell and aberrant writing and/or interpretation of the code can contribute to a dysregulated, hyperproliferative state. In some cases, epigenetic deregulation has also been reported to result in tumor initiation. The discovery of somatic mutations in some chromatin binding proteins associated with subtypes of lymphomas and the ability to regulate expression of proto oncogenes such as Myc has spurred the development of specific small molecule modulators of histone binding proteins. Several of these compounds have entered clinical development for the treatment of heme malignancies. This review summarizes progress in the discovery and advancement of epigenetic therapeutics for cancer and provides a perspective for future development.
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Affiliation(s)
- Dashyant Dhanak
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA.
| | - Paul Jackson
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA
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10
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Chen Y, Tokuda JM, Topping T, Sutton JL, Meisburger SP, Pabit SA, Gloss LM, Pollack L. Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Res 2014; 42:8767-76. [PMID: 24990379 PMCID: PMC4117781 DOI: 10.1093/nar/gku562] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) consists of 147 bp of DNA wrapped around a symmetric octamer of histone proteins. The dynamics of DNA packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including DNA positioning sequence, histone variants and modifications. Although the structure of the intact NCP has been studied by crystallography at atomic resolution, little is known about the structures of the partially unwrapped, transient intermediates relevant to nucleosome dynamics in processes such as transcription, DNA replication and repair. We apply a new experimental approach combining contrast variation with time-resolved small angle X-ray scattering (TR-SAXS) to determine transient structures of protein and DNA constituents of NCPs during salt-induced disassembly. We measure the structures of unwrapping DNA and monitor protein dissociation from Xenopus laevis histones reconstituted with two model NCP positioning constructs: the Widom 601 sequence and the sea urchin 5S ribosomal gene. Both constructs reveal asymmetric release of DNA from disrupted histone cores, but display different patterns of protein dissociation. These kinetic intermediates may be biologically important substrates for gene regulation.
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Affiliation(s)
- Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Joshua M Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Traci Topping
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Julie L Sutton
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Steve P Meisburger
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Lisa M Gloss
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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11
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Hieb AR, Gansen A, Böhm V, Langowski J. The conformational state of the nucleosome entry-exit site modulates TATA box-specific TBP binding. Nucleic Acids Res 2014; 42:7561-76. [PMID: 24829456 PMCID: PMC4081063 DOI: 10.1093/nar/gku423] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is needed. Using bulk and single-molecule FRET, we find that TBP binds a minimal consensus TATA box as a two-state equilibrium process, showing no evidence for intermediate states. However, upon addition of flanking DNA sequence, we observe non-specific cooperative binding to multiple DNA sites that compete for TATA-box specificity. Thus, we conclude that TBP binding is defined by a branched pathway, wherein TBP initially binds with little sequence specificity and is thermodynamically positioned by its kinetic stability to the TATA box. Furthermore, we observed the real-time access of TBP binding to TATA box DNA located within the DNA entry–exit site of the nucleosome. From these data, we determined salt-dependent changes in the nucleosome conformation regulate TBP's access to the TATA box, where access is highly constrained under physiological conditions, but is alleviated by histone acetylation and TFIIA.
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Affiliation(s)
- Aaron R Hieb
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Alexander Gansen
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Vera Böhm
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
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12
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Andresen K, Jimenez-Useche I, Howell SC, Yuan C, Qiu X. Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal. PLoS One 2013; 8:e78587. [PMID: 24265699 PMCID: PMC3827064 DOI: 10.1371/journal.pone.0078587] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.
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Affiliation(s)
- Kurt Andresen
- Department of Physics, Gettysburg College, Gettysburg, Pennsylvania, United States of America
- * E-mail:
| | - Isabel Jimenez-Useche
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Steven C. Howell
- Department of Physics, George Washington University, Washington, District of Columbia, United States of America
| | - Chongli Yuan
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Xiangyun Qiu
- Department of Physics, George Washington University, Washington, District of Columbia, United States of America
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