1
|
Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
Collapse
|
2
|
Nosella ML, Kim TH, Huang SK, Harkness RW, Goncalves M, Pan A, Tereshchenko M, Vahidi S, Rubinstein JL, Lee HO, Forman-Kay JD, Kay LE. Poly(ADP-ribosyl)ation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates. Mol Cell 2024; 84:429-446.e17. [PMID: 38215753 DOI: 10.1016/j.molcel.2023.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl)ation (PARylation) of proteins near damage sites is an essential initiation step in several DNA-repair pathways; however, its effects on nucleosome structural dynamics and organization are unclear. Using NMR, cryoelectron microscopy (cryo-EM), and biochemical assays, we show that PARylation enhances motions of the histone H3 tail and DNA, leaving the configuration of the core intact while also stimulating nuclease digestion and ligation of nicked nucleosomal DNA by LIG3. PARylation disrupted interactions between nucleosomes, preventing self-association. Addition of LIG3 and XRCC1 to PARylated nucleosomes generated condensates that selectively partition DNA repair-associated proteins in a PAR- and phosphorylation-dependent manner in vitro. Our results establish that PARylation influences nucleosomes across different length scales, extending from the atom-level motions of histone tails to the mesoscale formation of condensates with selective compositions.
Collapse
Affiliation(s)
- Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Tae Hun Kim
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuya Kate Huang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert W Harkness
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Monica Goncalves
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alisia Pan
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Lewis E Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
3
|
Cleri F, Giordano S, Blossey R. Nucleosome Array Deformation in Chromatin is Sustained by Bending, Twisting and Kinking of Linker DNA. J Mol Biol 2023; 435:168263. [PMID: 37678705 DOI: 10.1016/j.jmb.2023.168263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Chromatin in the nucleus undergoes mechanical stresses from different sources during the various stages of cell life. Here a trinucleosome array is used as the minimal model to study the mechanical response to applied stress at the molecular level. By using large-scale, all-atom steered-molecular dynamics simulations, we show that the largest part of mechanical stress in compression is accommodated by the DNA linkers joining pairs of nucleosomes, which store the elastic energy accumulated by the applied force. Different mechanical instabilities (Euler bending, Brazier kinking, twist-bending) can deform the DNA canonical structure, as a function of the increasing force load. An important role of the histone tails in assisting the DNA deformation is highlighted. The overall response of the smallest chromatin fragment to compressive stress leaves the nucleosome assembly with a substantial plastic deformation and localised defects, which can have a potential impact on DNA transcription, downstream signaling pathways, the regulation of gene expression, and DNA repair.
Collapse
Affiliation(s)
- Fabrizio Cleri
- Université de Lille, Institut d'Electronique Microelectronique et Nanotechnologie (IEMN CNRS UMR8520) and Département de Physique, 59652 Villeneuve d'Ascq, France.
| | - Stefano Giordano
- University of Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN - Institut d'Électronique de Microélectronique et de Nanotechnologie, F-59000 Lille, France
| | - Ralf Blossey
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| |
Collapse
|
4
|
Abstract
Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein-DNA complexes comprising octameric histone core proteins and ∼150 base pairs of DNA. In addition to acting as a DNA compaction vehicle, the dynamics of nucleosomes regulate the DNA site accessibility for the nonhistone proteins, thereby controlling regulatory processes involved in determining the cell identity and cell fate. Here, we propose an analytical framework to analyze the role of nucleosome dynamics on the target search process of transcription factors through a simple discrete-state stochastic description of the search process. By considering the experimentally determined kinetic rates associated with protein and nucleosome dynamics as the only inputs, we estimate the target search time of a protein via first-passage probability calculations separately during nucleosome breathing and sliding dynamics. Although both the nucleosome dynamics permit transient access to the DNA sites that are otherwise occluded by the histone proteins, our result suggests substantial differences between the protein search mechanism on a nucleosome performing breathing and sliding dynamics. Furthermore, we identify the molecular factors that influence the search efficiency and demonstrate how these factors together portray a highly dynamic landscape of gene regulation. Our analytical results are validated using extensive Monte Carlo simulations.
Collapse
Affiliation(s)
- Sujeet Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
5
|
Donovan BT, Chen H, Eek P, Meng Z, Jipa C, Tan S, Bai L, Poirier MG. Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions. Mol Cell 2023; 83:1251-1263.e6. [PMID: 36996811 PMCID: PMC10182836 DOI: 10.1016/j.molcel.2023.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 01/13/2023] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
Nucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding of two conserved S. cerevisiae basic helix-loop-helix (bHLH) TFs, Cbf1 and Pho4. A cryo-EM structure of Cbf1 in complex with the nucleosome reveals that the Cbf1 HLH region can electrostatically interact with exposed histone residues within a partially unwrapped nucleosome. Single-molecule fluorescence studies show that the Cbf1 HLH region facilitates efficient nucleosome invasion by slowing its dissociation rate relative to DNA through interactions with histones, whereas the Pho4 HLH region does not. In vivo studies show that this enhanced binding provided by the Cbf1 HLH region enables nucleosome invasion and ensuing repositioning. These structural, single-molecule, and in vivo studies reveal the mechanistic basis of dissociation rate compensation by PFs and how this translates to facilitating chromatin opening inside cells.
Collapse
Affiliation(s)
- Benjamin T Donovan
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Hengye Chen
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Priit Eek
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Zhiyuan Meng
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Caroline Jipa
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Song Tan
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA; Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Department of Physics, The Ohio State University, Columbus, OH 43210, USA; Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
6
|
Lorch Y, Kornberg RD, Maier-Davis B. Role of the histone tails in histone octamer transfer. Nucleic Acids Res 2023; 51:3671-3678. [PMID: 36772826 PMCID: PMC10164550 DOI: 10.1093/nar/gkad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 02/12/2023] Open
Abstract
The exceptionally high positive charge of the histones, concentrated in the N- and C-terminal tails, is believed to contribute to the stability of the nucleosome by neutralizing the negative charge of the nucleosomal DNA. We find, on the contrary, that the high positive charge contributes to instability, performing an essential function in chromatin remodeling. We show that the tails are required for removal of the histone octamer by the RSC chromatin remodeling complex, and this function is not due to direct RSC-tail interaction. We also show that the tails are required for histone octamer transfer from nucleosomes to DNA, and this activity of the tails is a consequence of their positive charge. Thus, the histone tails, intrinsically disordered protein regions, perform a critical role in chromatin structure and transcription, unrelated to their well-known role in regulation through posttranscriptional modification.
Collapse
Affiliation(s)
- Yahli Lorch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Barbara Maier-Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
7
|
Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sevastyan O. Rabdano
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | - Matthew D. Shannon
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Sergei A. Izmailov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Rudra N. Purusottam
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | | | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
- Department of Chemistry Purdue University West Lafayette IN 47906 USA
| | | |
Collapse
|
8
|
Strohkendl I, Saifuddin FA, Gibson BA, Rosen MK, Russell R, Finkelstein IJ. Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin. SCIENCE ADVANCES 2021; 7:7/11/eabd6030. [PMID: 33692102 PMCID: PMC7946368 DOI: 10.1126/sciadv.abd6030] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/22/2021] [Indexed: 06/10/2023]
Abstract
Genome engineering nucleases must access chromatinized DNA. Here, we investigate how AsCas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome arrays. Using quantitative kinetics approaches, we show that dynamic nucleosome unwrapping regulates target accessibility to Cas12a and determines the extent to which both steps of binding-PAM recognition and R-loop formation-are inhibited by the nucleosome. Relaxing DNA wrapping within the nucleosome by reducing DNA bendability, adding histone modifications, or introducing target-proximal dCas9 enhances DNA cleavage rates over 10-fold. Unexpectedly, Cas12a readily cleaves internucleosomal linker DNA within chromatin-like, phase-separated nucleosome arrays. DNA targeting is reduced only ~5-fold due to neighboring nucleosomes and chromatin compaction. This work explains the observation that on-target cleavage within nucleosomes occurs less often than off-target cleavage within nucleosome-depleted genomic regions in cells. We conclude that nucleosome unwrapping regulates accessibility to CRISPR-Cas nucleases and propose that increasing nucleosome breathing dynamics will improve DNA targeting in eukaryotic cells.
Collapse
Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Fatema A Saifuddin
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143, USA
| | - Bryan A Gibson
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rick Russell
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
9
|
Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021; 60:6480-6487. [PMID: 33522067 DOI: 10.1002/anie.202012046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/15/2020] [Indexed: 12/21/2022]
Abstract
The interaction of positively charged N-terminal histone tails with nucleosomal DNA plays an important role in chromatin assembly and regulation, modulating their susceptibility to post-translational modifications and recognition by chromatin-binding proteins. Here, we report residue-specific 15 N NMR relaxation rates for histone H4 tails in reconstituted nucleosomes. These data indicate that H4 tails are strongly dynamically disordered, albeit with reduced conformational flexibility compared to a free peptide with the same sequence. Remarkably, the NMR observables were successfully reproduced in a 2-μs MD trajectory of the nucleosome. This is an important step toward resolving an apparent inconsistency where prior simulations were generally at odds with experimental evidence on conformational dynamics of histone tails. Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).
Collapse
Affiliation(s)
- Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | - Matthew D Shannon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Rudra N Purusottam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation.,Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| |
Collapse
|
10
|
Gamarra N, Narlikar GJ. Collaboration through chromatin: motors of transcription and chromatin structure. J Mol Biol 2021; 433:166876. [PMID: 33556407 DOI: 10.1016/j.jmb.2021.166876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Packaging of the eukaryotic genome into chromatin places fundamental physical constraints on transcription. Clarifying how transcription operates within these constraints is essential to understand how eukaryotic gene expression programs are established and maintained. Here we review what is known about the mechanisms of transcription on chromatin templates. Current models indicate that transcription through chromatin is accomplished by the combination of an inherent nucleosome disrupting activity of RNA polymerase and the action of ATP-dependent chromatin remodeling motors. Collaboration between these two types of molecular motors is proposed to occur at all stages of transcription through diverse mechanisms. Further investigation of how these two motors combine their basic activities is essential to clarify the interdependent relationship between genome structure and transcription.
Collapse
Affiliation(s)
- Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States; TETRAD Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.
| |
Collapse
|
11
|
Caffrey PJ, Delaney S. Nucleosome Core Particles Lacking H2B or H3 Tails Are Altered Structurally and Have Differential Base Excision Repair Fingerprints. Biochemistry 2021; 60:210-218. [PMID: 33426868 DOI: 10.1021/acs.biochem.0c00877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A recently discovered post-translational modification of histone proteins is the irreversible proteolytic clipping of the histone N-terminal tail domains. This modification is involved in the regulation of various biological processes, including the DNA damage response. In this work, we used chemical footprinting to characterize the structural alterations to nucleosome core particles (NCPs) that result from a lack of a histone H2B or H3 tail. We also examine the influence of these histone tails on excision of the mutagenic lesion 1,N6-ethenoadenine (εA) by the repair enzyme alkyladenine DNA glycosylase. We found that the absence of the H2B or H3 tail results in altered DNA periodicity relative to that of native NCPs. We correlated these structural alterations to εA excision by utilizing a global analysis of 21 εA sites in NCPs and unincorporated duplex DNA. In comparison to native NCPs, there is enhanced excision of εA in tailless H2B NCPs in regions that undergo DNA unwrapping. This enhanced excision is not observed for tailless H3 NCPs; rather, excision is inhibited in more static areas of the NCP not prone to unwrapping. Our results support in vivo observations of alkylation damage profiles and the potential role of tail clipping as a mechanism for overcoming physical obstructions caused by packaging in NCPs but also reveal the potential inhibition of repair by tail clipping in some locations. Taken together, these results further our understanding of how base excision repair can be facilitated or diminished by histone tail removal and contribute to our understanding of the underlying mechanism that leads to mutational hot spots.
Collapse
Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| |
Collapse
|
12
|
Bendandi A, Patelli AS, Diaspro A, Rocchia W. The role of histone tails in nucleosome stability: An electrostatic perspective. Comput Struct Biotechnol J 2020; 18:2799-2809. [PMID: 33133421 PMCID: PMC7575852 DOI: 10.1016/j.csbj.2020.09.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 01/20/2023] Open
Abstract
We propose a methodology for the study of protein-DNA electrostatic interactions and apply it to clarify the effect of histone tails in nucleosomes. This method can be used to correlate electrostatic interactions to structural and functional features of protein-DNA systems, and can be combined with coarse-grained representations. In particular, we focus on the electrostatic field and resulting forces acting on the DNA. We investigate the electrostatic origins of effects such as different stages in DNA unwrapping, nucleosome destabilization upon histone tail truncation, and the role of specific arginines and lysines undergoing Post-Translational Modifications. We find that the positioning of the histone tails can oppose the attractive pull of the histone core, locally deform the DNA, and tune DNA unwrapping. Small conformational variations in the often overlooked H2A C-terminal tails had significant electrostatic repercussions near the DNA entry and exit sites. The H2A N-terminal tail exerts attractive electrostatic forces towards the histone core in positions where Polymerase II halts its progress. We validate our results with comparisons to previous experimental and computational observations.
Collapse
Affiliation(s)
- Artemi Bendandi
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16149 Genoa, Italy.,CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Alessandro S Patelli
- LCVMM, Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Alberto Diaspro
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16149 Genoa, Italy.,CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Walter Rocchia
- Concept Lab, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| |
Collapse
|
13
|
Nizovtseva EV, Polikanov YS, Kulaeva OI, Clauvelin N, Postnikov YV, Olson WK, Studitsky VM. [Opposite Effects of Histone H1 and HMGN5 Protein on Distant Interactions in Chromatin]. Mol Biol (Mosk) 2020; 53:1038-1048. [PMID: 31876282 DOI: 10.1134/s0026898419060132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/14/2019] [Indexed: 11/23/2022]
Abstract
Transcriptional enhancers in the cell nuclei typically interact with the target promoters in cis over long stretches of chromatin, but the mechanism of this communication remains unknown. Previously we have developed a defined in vitro system for quantitative analysis of the rate of distant enhancer-promoter communication (EPC) and have shown that the chromatin fibers maintain efficient distant EPC in cis. Here we investigate the roles of linker histone H1 and HMGN5 protein in EPC. A considerable negative effect of histone H1 on EPC depending on its C- and N-tails was shown. Protein HMGN5 that affects chromatin compaction and is associated with active chromatin counteracts EPC inhibition by H1. The data suggest that the efficiency of the interaction between the enhancer and the promoter depends on the structure and dynamics of the chromatin fiber localized between them and can be regulated by proteins associated with chromatin.
Collapse
Affiliation(s)
- E V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19422 USA
| | - Y S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - O I Kulaeva
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19422 USA
| | - N Clauvelin
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Y V Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - W K Olson
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854 USA
| | - V M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19422 USA.,Faculty of Biology, Moscow State University, Moscow, 119991 Russia.,
| |
Collapse
|
14
|
Nizovtseva EV, Polikanov YS, Kulaeva OI, Clauvelin N, Postnikov YV, Olson WK, Studitsky VM. Opposite Effects of Histone H1 and HMGN5 Protein on Distant Interactions in Chromatin. Mol Biol 2019. [DOI: 10.1134/s002689331906013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Ensembles of Breathing Nucleosomes: A Computational Study. Biophys J 2019; 118:2297-2308. [PMID: 31882248 DOI: 10.1016/j.bpj.2019.11.3395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In this study, we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent DNA mechanics. Our analysis gives detailed insights into the sequence dependence of nucleosome breathing observed in the experiment and allows us to determine the adsorption energy of the DNA bound to the protein core as a function of the ionic strength. Moreover, we predict the breathing behavior of other potentially interesting sequences and compare the findings to earlier related experiments.
Collapse
|
16
|
Mahadevan IA, Pentakota S, Roy R, Bhaduri U, Satyanarayana Rao MR. TH2BS11ph histone mark is enriched in the unsynapsed axes of the XY body and predominantly associates with H3K4me3-containing genomic regions in mammalian spermatocytes. Epigenetics Chromatin 2019; 12:53. [PMID: 31493790 PMCID: PMC6731575 DOI: 10.1186/s13072-019-0300-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023] Open
Abstract
Background TH2B is a major histone variant that replaces about 80–85% of somatic H2B in mammalian spermatocytes and spermatids. The post-translational modifications (PTMs) on TH2B have been well characterised in spermatocytes and spermatids. However, the biological function(s) of these PTMs on TH2B have not been deciphered in great detail. In our attempt to decipher the unique function(s) of histone variant TH2B, we detected the modification in the N-terminal tail, Serine 11 phosphorylation on TH2B (TH2BS11ph) in spermatocytes. Results The current study is aimed at understanding the function of the TH2BS11ph modification in the context of processes that occur during meiotic prophase I. Immunofluorescence studies with the highly specific antibodies revealed that TH2BS11ph histone mark is enriched in the unsynapsed axes of the sex body and is associated with XY body-associated proteins like Scp3, γH2AX, pATM, ATR, etc. Genome-wide occupancy studies as determined by ChIP sequencing experiments in P20 C57BL6 mouse testicular cells revealed that TH2BS11ph is enriched in X and Y chromosomes confirming the immunofluorescence staining pattern in the pachytene spermatocytes. Apart from the localisation of this modification in the XY body, TH2BS11ph is majorly associated with H3K4me3-containing genomic regions like gene promoters, etc. These data were also found to corroborate with the ChIP sequencing data of TH2BS11ph histone mark carried out in P12 C57BL6 mouse testicular cells, wherein we found the predominant localisation of this modification at H3K4me3-containing genomic regions. Mass spectrometry analysis of proteins that associate with TH2BS11ph-containing mononucleosomes revealed key proteins linked with the functions of XY body, pericentric heterochromatin and transcription. Conclusions TH2BS11ph modification is densely localised in the unsynapsed axes of the XY body of the pachytene spermatocyte. By ChIP sequencing studies in mouse P12 and P20 testicular cells, we demonstrate that TH2BS11ph is predominantly associated with H3K4me3 positive genomic regions like gene promoters, etc. We propose that TH2BS11ph modification could act alone or in concert with other histone modifications to recruit the appropriate transcription or XY body recombination protein machinery at specific genomic loci.
Collapse
Affiliation(s)
- Iyer Aditya Mahadevan
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO., Bangalore, 560064, India
| | - Satyakrishna Pentakota
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Raktim Roy
- The Graduate School of the Stowers Institute for Medical Research, 1000E. 50th St., Kansas City, MO, 64110, USA
| | - Utsa Bhaduri
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO., Bangalore, 560064, India
| | - Manchanahalli R Satyanarayana Rao
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO., Bangalore, 560064, India.
| |
Collapse
|
17
|
Abstract
Repair of damaged DNA plays a crucial role in maintaining genomic integrity and normal cell function. The base excision repair (BER) pathway is primarily responsible for removing modified nucleobases that would otherwise cause deleterious and mutagenic consequences and lead to disease. The BER process is initiated by a DNA glycosylase, which recognizes and excises the target nucleobase lesion, and is completed via downstream enzymes acting in a well-coordinated manner. A majority of our current understanding about how BER enzymes function comes from in vitro studies using free duplex DNA as a simplified model. In eukaryotes, however, BER is challenged by the packaging of genomic DNA into chromatin. The fundamental structural repeating unit of chromatin is the nucleosome, which presents a more complex substrate context than free duplex DNA for repair. In this chapter, we discuss how BER enzymes, particularly glycosylases, engage in the context of packaged DNA with insights obtained from both in vivo and in vitro studies. Furthermore, we review factors and mechanisms that can modify chromatin architecture and/or influence DNA accessibility to BER machinery, such as the geometric location of the damage site, nucleosomal DNA unwrapping, histone post-translational modifications, histone variant incorporation, and chromatin remodeling.
Collapse
Affiliation(s)
- Chuxuan Li
- Department of Chemistry, Brown University, Providence, RI, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, United States.
| |
Collapse
|
18
|
Abstract
Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.
Collapse
Affiliation(s)
- Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael G. Poirier
- Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210-1117, USA
| |
Collapse
|
19
|
Kurup JT, Campeanu IJ, Kidder BL. Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing. Epigenetics Chromatin 2019; 12:20. [PMID: 30940185 PMCID: PMC6444878 DOI: 10.1186/s13072-019-0266-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Positioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how histone demethylases including the histone 3 lysine 4 (H3K4) demethylase, KDM5B, impacts nucleosome positioning around transcriptional start sites (TSS) of active genes is poorly understood. RESULTS Here, we report that KDM5B is a critical regulator of nucleosome positioning in embryonic stem (ES) cells. Micrococcal nuclease sequencing (MNase-Seq) revealed increased enrichment of nucleosomes around TSS regions and DNase I hypersensitive sites in KDM5B-depleted ES cells. Moreover, depletion of KDM5B resulted in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner. Dysregulated nucleosome phasing was also evident in KDM5B-depleted ES cells, including asynchronous nucleosome spacing surrounding TSS regions, where nucleosome variance was positively correlated with the degree of asynchronous phasing. The redistribution of nucleosomes around TSS regions in KDM5B-depleted ES cells is correlated with dysregulated gene expression, and altered H3K4me3 and RNA polymerase II occupancy. In addition, we found that DNA shape features varied significantly at regions with shifted nucleosomes. CONCLUSION Altogether, our data support a role for KDM5B in regulating nucleosome positioning in ES cells.
Collapse
Affiliation(s)
- Jiji T. Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
| | - Ion J. Campeanu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
| | - Benjamin L. Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
| |
Collapse
|
20
|
Abstract
Chromatin is an intelligent building block that can express either external or internal needs through structural changes. To date, three methods to change chromatin structure and regulate gene expression have been well-documented: histone modification, histone exchange, and ATP-dependent chromatin remodeling. Recently, a growing body of literature has suggested that histone tail cleavage is related to various cellular processes including stem cell differentiation, osteoclast differentiation, granulocyte differentiation, mammary gland differentiation, viral infection, aging, and yeast sporulation. Although the underlying mechanisms suggesting how histone cleavage affects gene expression in view of chromatin structure are only beginning to be understood, it is clear that this process is a novel transcriptional epigenetic mechanism involving chromatin dynamics. In this review, we describe the functional properties of the known histone tail cleavage with its proteolytic enzymes, discuss how histone cleavage impacts gene expression, and present future directions for this area of study.
Collapse
Affiliation(s)
- Sun-Ju Yi
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea
| | - Kyunghwan Kim
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea
| |
Collapse
|
21
|
Azad GK, Swagatika S, Kumawat M, Kumawat R, Tomar RS. Modifying Chromatin by Histone Tail Clipping. J Mol Biol 2018; 430:3051-3067. [DOI: 10.1016/j.jmb.2018.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022]
|
22
|
Chirico G, Gansen A, Leuba SH, Olins AL, Olins DE, Smith JC, Tóth K. Jörg Langowski: his scientific legacy and the future it promises. BMC BIOPHYSICS 2018; 11:5. [PMID: 30026939 PMCID: PMC6048899 DOI: 10.1186/s13628-018-0045-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/27/2018] [Indexed: 11/10/2022]
Abstract
Background With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for open access publishing and for the creation of effective scientific research networks. Methods Here, after reviewing some of Jörg's key research contributions and ideas, we offer through the personal remembrance of his closest collaborators, a deep analysis of the major results of his research and the future directions they have engendered. Conclusions The legacy of Jörg Langowski has been to propel a way of viewing biological function that considers living systems as dynamic and in three dimensions. This physical view of biology that he pioneered is now, finally, becoming established also because of his great effort.
Collapse
Affiliation(s)
- Giuseppe Chirico
- 1Dipartimento di Fisica, Università di Milano-Bicocca, Milan, Italy
| | - Alexander Gansen
- 2Biophysics of Macromolecules (B040), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sanford H Leuba
- 3Departments of Cell Biology and Bioengineering, 2.26a UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Ada L Olins
- 4Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME USA
| | - Donald E Olins
- 4Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME USA
| | - Jeremy C Smith
- 5Oak Ridge National Laboratory, P.O. Box 2008 MS6309, Oak Ridge, TN 37831-6309 USA.,6Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
| | - Katalin Tóth
- 2Biophysics of Macromolecules (B040), Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| |
Collapse
|
23
|
Morrison EA, Bowerman S, Sylvers KL, Wereszczynski J, Musselman CA. The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome. eLife 2018; 7:31481. [PMID: 29648537 PMCID: PMC5953545 DOI: 10.7554/elife.31481] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/11/2018] [Indexed: 01/08/2023] Open
Abstract
Histone tails harbor a plethora of post-translational modifications that direct the function of chromatin regulators, which recognize them through effector domains. Effector domain/histone interactions have been broadly studied, but largely using peptide fragments of histone tails. Here, we extend these studies into the nucleosome context and find that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding. Using NMR spectroscopy and MD simulations, we show that the H3 tails interact robustly but dynamically with nucleosomal DNA, substantially reducing PHD finger association. Altering the electrostatics of the H3 tail via modification or mutation increases accessibility to the PHD finger, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation. Together, our results demonstrate that the nucleosome context has a dramatic impact on signaling events at the histone tails, and highlights the importance of studying histone binding in the context of the nucleosome.
Collapse
Affiliation(s)
- Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Samuel Bowerman
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Kelli L Sylvers
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| |
Collapse
|
24
|
Morgan AM, LeGresley SE, Briggs K, Al-Ani G, Fischer CJ. Effects of nucleosome stability on remodeler-catalyzed repositioning. Phys Rev E 2018; 97:032422. [PMID: 29776169 DOI: 10.1103/physreve.97.032422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 06/08/2023]
Abstract
Chromatin remodelers are molecular motors that play essential roles in the regulation of nucleosome positioning and chromatin accessibility. These machines couple the energy obtained from the binding and hydrolysis of ATP to the mechanical work of manipulating chromatin structure through processes that are not completely understood. Here we present a quantitative analysis of nucleosome repositioning by the imitation switch (ISWI) chromatin remodeler and demonstrate that nucleosome stability significantly impacts the observed activity. We show how DNA damage induced changes in the affinity of DNA wrapping within the nucleosome can affect ISWI repositioning activity and demonstrate how assay-dependent limitations can bias studies of nucleosome repositioning. Together, these results also suggest that some of the diversity seen in chromatin remodeler activity can be attributed to the variations in the thermodynamics of interactions between the remodeler, the histones, and the DNA, rather than reflect inherent properties of the remodeler itself.
Collapse
Affiliation(s)
- Aaron M Morgan
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Koan Briggs
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Gada Al-Ani
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Christopher J Fischer
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| |
Collapse
|
25
|
Culkin J, de Bruin L, Tompitak M, Phillips R, Schiessel H. The role of DNA sequence in nucleosome breathing. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:106. [PMID: 29185124 PMCID: PMC7001874 DOI: 10.1140/epje/i2017-11596-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/14/2017] [Indexed: 05/05/2023]
Abstract
Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so.
Collapse
Affiliation(s)
- Jamie Culkin
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Lennart de Bruin
- Laboratory for Computation and Visualization in Mathematics and Mechanics, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Tompitak
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Rob Phillips
- Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology, 91125, Pasadena, CA, USA
| | - Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands.
| |
Collapse
|
26
|
Chakraborty K, Loverde SM. Asymmetric breathing motions of nucleosomal DNA and the role of histone tails. J Chem Phys 2017; 147:065101. [DOI: 10.1063/1.4997573] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
27
|
Fu I, Cai Y, Geacintov NE, Zhang Y, Broyde S. Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. Biochemistry 2017; 56:1963-1973. [PMID: 28304160 DOI: 10.1021/acs.biochem.6b01208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Histone tails in nucleosomes play critical roles in regulation of many biological processes, including chromatin compaction, transcription, and DNA repair. Moreover, post-translational modifications, notably lysine acetylation, are crucial to these functions. While the tails have been intensively studied, how the structures and dynamics of tails are impacted by the presence of a nearby bulky DNA lesion is a frontier research area, and how these properties are impacted by tail lysine acetylation remains unexplored. To obtain molecular insight, we have utilized all atom 3 μs molecular dynamics simulations of nucleosome core particles (NCPs) to determine the impact of a nearby DNA lesion, 10S (+)-trans-anti-B[a]P-N2-dG-the major adduct derived from the procarcinogen benzo[a]pyrene-on H2B tail behavior in unacetylated and acetylated states. We similarly studied lesion-free NCPs to investigate the normal properties of the H2B tail in both states. In the lesion-free NCPs, charge neutralization upon lysine acetylation causes release of the tail from the DNA. When the lesion is present, it stably engulfs part of the nearby tail, impairing the interactions between DNA and tail. With the tail in an acetylated state, the lesion still interacts with part of it, although unstably. The lesion's partial entrapment of the tail should hinder the tail from interacting with other nucleosomes, and other proteins such as acetylases, deacetylases, and acetyl-lysine binding proteins, and thus disrupt critical tail-governed processes. Hence, the lesion would impede tail functions modulated by acetylation or deacetylation, causing aberrant chromatin structures and impaired biological transactions such as transcription and DNA repair.
Collapse
Affiliation(s)
| | | | | | - Yingkai Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
| | | |
Collapse
|
28
|
Stephens AD, Banigan EJ, Adam SA, Goldman RD, Marko JF. Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Mol Biol Cell 2017; 28:1984-1996. [PMID: 28057760 PMCID: PMC5541848 DOI: 10.1091/mbc.e16-09-0653] [Citation(s) in RCA: 281] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/04/2016] [Accepted: 12/29/2016] [Indexed: 02/02/2023] Open
Abstract
The cell nucleus must continually resist and respond to intercellular and intracellular mechanical forces to transduce mechanical signals and maintain proper genome organization and expression. Altered nuclear mechanics is associated with many human diseases, including heart disease, progeria, and cancer. Chromatin and nuclear envelope A-type lamin proteins are known to be key nuclear mechanical components perturbed in these diseases, but their distinct mechanical contributions are not known. Here we directly establish the separate roles of chromatin and lamin A/C and show that they determine two distinct mechanical regimes via micromanipulation of single isolated nuclei. Chromatin governs response to small extensions (<3 μm), and euchromatin/heterochromatin levels modulate the stiffness. In contrast, lamin A/C levels control nuclear strain stiffening at large extensions. These results can be understood through simulations of a polymeric shell and cross-linked polymer interior. Our results provide a framework for understanding the differential effects of chromatin and lamin A/C in cell nuclear mechanics and their alterations in disease.
Collapse
Affiliation(s)
- Andrew D Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Edward J Banigan
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
| |
Collapse
|
29
|
Li Z, Kono H. Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability. Sci Rep 2016; 6:31437. [PMID: 27527579 PMCID: PMC4985630 DOI: 10.1038/srep31437] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/21/2016] [Indexed: 01/06/2023] Open
Abstract
Nucleosome breathing potentially increases the DNA exposure, which in turn recruits DNA-binding protein and regulates gene transcription. Numerous studies have shown the critical roles of N-terminal tails of histones H3 and H4 in gene expression; however, few studies have focused on the H2A C-terminal tail. Here we present thorough computational studies on a single nucleosome particle showing the linker DNA closing and opening, which is thought to be nucleosome breathing. With our simulation, the H2A C-terminal and H3 N-terminal tails were found to modulate the nucleosome conformation differently. The H2A C-terminal tail regulates nucleosome conformation by binding to linker DNA at different locations, whereas the H3 N-terminal tail regulates linker DNA by binding to it in different patterns. Further MD simulation on tail truncated structures corroborates this analysis. These findings replenish our understanding of the histone tail regulation mechanism on atomic level.
Collapse
Affiliation(s)
- Zhenhai Li
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| |
Collapse
|
30
|
Eslami-Mossallam B, Schiessel H, van Noort J. Nucleosome dynamics: Sequence matters. Adv Colloid Interface Sci 2016; 232:101-113. [PMID: 26896338 DOI: 10.1016/j.cis.2016.01.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 02/06/2023]
Abstract
About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly conserved in evolution, nucleosomes can be very different from each other due to posttranslational modifications of the histones. Another crucial factor in making nucleosomes unique has so far been underappreciated: the sequence of their DNA. This review provides an overview of the experimental and theoretical progress that increasingly points to the importance of the nucleosomal base pair sequence. Specifically, we discuss the role of the underlying base pair sequence in nucleosome positioning, sliding, breathing, force-induced unwrapping, dissociation and partial assembly and also how the sequence can influence higher-order structures. A new view emerges: the physical properties of nucleosomes, especially their dynamical properties, are determined to a large extent by the mechanical properties of their DNA, which in turn depends on DNA sequence.
Collapse
|
31
|
Scovell WM. High mobility group protein 1: A collaborator in nucleosome dynamics and estrogen-responsive gene expression. World J Biol Chem 2016; 7:206-222. [PMID: 27247709 PMCID: PMC4877529 DOI: 10.4331/wjbc.v7.i2.206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 02/19/2016] [Accepted: 03/14/2016] [Indexed: 02/05/2023] Open
Abstract
High mobility group protein 1 (HMGB1) is a multifunctional protein that interacts with DNA and chromatin to influence the regulation of transcription, DNA replication and repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome (N) in a nonenzymatic, adenosine triphosphate-independent manner. As a result, the canonical nucleosome is converted to two stable, physically distinct nucleosome conformers. Although estrogen receptor (ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding. The isolated HMGB1-restructured nucleosomes (N’ and N’’) remain stable and exhibit a number of characteristics that are distinctly different from the canonical nucleosome. These findings complement previous studies that showed (1) HMGB1 stimulates in vivo transcriptional activation at estrogen response elements and (2) knock down of HMGB1 expression by siRNA precipitously reduced transcriptional activation. The findings indicate that a major facet of the mechanism of HMGB1 action involves a restructuring of aspects of the nucleosome that appear to relax structural constraints within the nucleosome. The findings are extended to reveal the differences between ER and the other steroid hormone receptors. A working proposal outlines mechanisms that highlight the multiple facets that HMGB1 may utilize in restructuring the nucleosome.
Collapse
|
32
|
Ng MK, Cheung P. A brief histone in time: understanding the combinatorial functions of histone PTMs in the nucleosome context. Biochem Cell Biol 2016. [DOI: 10.1139/bcb-2015-0031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
It has been over 50 years since Allfrey et al. proposed that histone acetylation regulates RNA synthesis, and the study of histone modifications has progressed at an extraordinary pace for the past two decades. In this review, we provide a perspective on some key events and advances in our understanding of histone modifications. We also highlight reagents and tools from past to present that facilitated progress in this research field. Using histone H3 phosphorylation as an underlying thread, we review the rationale that led to the proposal of the histone code hypothesis, as well as examples that illustrate the concepts of combinatorial histone modifications and cross-talk pathways. We further highlight the importance of investigating these mechanisms in the context of nucleosomes rather than just at the histone level and present current and developing approaches for such studies. Overall, research on histone modifications has yielded great mechanistic insights into the regulation of genomic functions, and extending these studies using nucleosomes will further elucidate the complexity of these pathways in a more physiologically relevant context.
Collapse
Affiliation(s)
- Marlee K. Ng
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
| | - Peter Cheung
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
| |
Collapse
|
33
|
Linker histone H1 and H3K56 acetylation are antagonistic regulators of nucleosome dynamics. Nat Commun 2015; 6:10152. [PMID: 26648124 PMCID: PMC4682114 DOI: 10.1038/ncomms10152] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 11/08/2015] [Indexed: 11/17/2022] Open
Abstract
H1 linker histones are highly abundant proteins that compact nucleosomes and chromatin to regulate DNA accessibility and transcription. However, the mechanisms that target H1 regulation to specific regions of eukaryotic genomes are unknown. Here we report fluorescence measurements of human H1 regulation of nucleosome dynamics and transcription factor (TF) binding within nucleosomes. H1 does not block TF binding, instead it suppresses nucleosome unwrapping to reduce DNA accessibility within H1-bound nucleosomes. We then investigated H1 regulation by H3K56 and H3K122 acetylation, two transcriptional activating histone post translational modifications (PTMs). Only H3K56 acetylation, which increases nucleosome unwrapping, abolishes H1.0 reduction of TF binding. These findings show that nucleosomes remain dynamic, while H1 is bound and H1 dissociation is not required for TF binding within the nucleosome. Furthermore, our H3K56 acetylation measurements suggest that a single-histone PTM can define regions of the genome that are not regulated by H1. The linker histone H1 is highly abundant and regulates DNA accessibility by compacting chromatin. Here the authors analyze transcription factor binding to nucleosomes and show that histone H1 suppresses unwrapping but does not directly block the binding of transcription factors.
Collapse
|
34
|
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S. Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation. Sci Rep 2015; 5:17204. [PMID: 26607036 PMCID: PMC4660432 DOI: 10.1038/srep17204] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/27/2015] [Indexed: 01/07/2023] Open
Abstract
Post-translational modifications (PTMs) of histones, such as lysine acetylation of the N-terminal tails, play crucial roles in controlling gene expression. Due to the difficulty in reconstituting site-specifically acetylated nucleosomes with crystallization quality, structural analyses of histone acetylation are currently performed using synthesized tail peptides. Through engineering of the genetic code, translation termination, and cell-free protein synthesis, we reconstituted human H4-mono- to tetra-acetylated nucleosome core particles (NCPs), and solved the crystal structures of the H4-K5/K8/K12/K16-tetra-acetylated NCP and unmodified NCP at 2.4 Å and 2.2 Å resolutions, respectively. The structure of the H4-tetra-acetylated NCP resembled that of the unmodified NCP, and the DNA wrapped the histone octamer as precisely as in the unmodified NCP. However, the B-factors were significantly increased for the peripheral DNAs near the N-terminal tail of the intra- or inter-nucleosomal H4. In contrast, the B-factors were negligibly affected by the H4 tetra-acetylation in histone core residues, including those composing the acidic patch, and at H4-R23, which interacts with the acidic patch of the neighboring NCP. The present study revealed that the H4 tetra-acetylation impairs NCP self-association by changing the interactions of the H4 tail with DNA, and is the first demonstration of crystallization quality NCPs reconstituted with genuine PTMs.
Collapse
Affiliation(s)
- Masatoshi Wakamori
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yoshifumi Fujii
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Noriyuki Suka
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan,
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,
| |
Collapse
|
35
|
Nalabothula N, Al-jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN. Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation. PLoS One 2015; 10:e0135410. [PMID: 26305327 PMCID: PMC4549251 DOI: 10.1371/journal.pone.0135410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/21/2015] [Indexed: 12/22/2022] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1’s role in gene regulation.
Collapse
Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Taha Al-jumaily
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Abdallah M. Eteleeb
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Robert M. Flight
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Shao Xiaorong
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Hunter Moseley
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
| | - Yvonne N. Fondufe-Mittendorf
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
| |
Collapse
|
36
|
Galvani A, Thiriet C. Nucleosome Dancing at the Tempo of Histone Tail Acetylation. Genes (Basel) 2015; 6:607-21. [PMID: 26184324 PMCID: PMC4584320 DOI: 10.3390/genes6030607] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/26/2015] [Accepted: 07/08/2015] [Indexed: 12/12/2022] Open
Abstract
The impact of histone acetylation on transcription was revealed over 50 years ago by Allfrey and colleagues. However, it took decades for an understanding of the fine mechanism by which this posttranslational modification affects chromatin structure and promotes transcription. Here, we review breakthroughs linking histone tail acetylation, histone dynamics, and transcription. We also discuss the histone exchange during transcription and highlight the important function of a pool of non-chromatinized histones in chromatin dynamics.
Collapse
Affiliation(s)
- Angélique Galvani
- UMR CNRS 6286 UFIP, Université de Nantes, Epigénétique: Proliferation et Différenciation, 2 rue de Houssinière, 44322 Nantes Cedex 03, France.
| | - Christophe Thiriet
- UMR CNRS 6286 UFIP, Université de Nantes, Epigénétique: Proliferation et Différenciation, 2 rue de Houssinière, 44322 Nantes Cedex 03, France.
| |
Collapse
|
37
|
Gansen A, Tóth K, Schwarz N, Langowski J. Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure––a FRET study. Nucleic Acids Res 2015; 43:1433-43. [PMID: 25589544 PMCID: PMC4330349 DOI: 10.1093/nar/gku1354] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Using FRET in bulk and on single molecules, we assessed the structural role of histone acetylation in nucleosomes reconstituted on the 170 bp long Widom 601 sequence. We followed salt-induced nucleosome disassembly, using donor–acceptor pairs on the ends or in the internal part of the nucleosomal DNA, and on H2B histone for measuring H2A/H2B dimer exchange. This allowed us to distinguish the influence of acetylation on salt-induced DNA unwrapping at the entry–exit site from its effect on nucleosome core dissociation. The effect of lysine acetylation is not simply cumulative, but showed distinct histone-specificity. Both H3- and H4-acetylation enhance DNA unwrapping above physiological ionic strength; however, while H3-acetylation renders the nucleosome core more sensitive to salt-induced dissociation and to dimer exchange, H4-acetylation counteracts these effects. Thus, our data suggest, that H3- and H4-acetylation have partially opposing roles in regulating nucleosome architecture and that distinct aspects of nucleosome dynamics might be independently controlled by individual histones.
Collapse
Affiliation(s)
- Alexander Gansen
- To whom correspondence should be addressed. Tel: +49 6221 423396; Fax: +49 6221 423391;
| | | | | | - Jörg Langowski
- Correspondence may also be addressed to Jörg Langowski. Tel: +49 6221 423390; Fax: +49 6221 423391;
| |
Collapse
|
38
|
Cutter AR, Hayes JJ. A brief review of nucleosome structure. FEBS Lett 2015; 589:2914-22. [PMID: 25980611 DOI: 10.1016/j.febslet.2015.05.016] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/29/2015] [Accepted: 05/05/2015] [Indexed: 12/23/2022]
Abstract
The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ∼7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.
Collapse
Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States.
| |
Collapse
|
39
|
Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 315] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
| |
Collapse
|
40
|
LeGresley SE, Wilt J, Antonik M. DNA damage may drive nucleosomal reorganization to facilitate damage detection. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:032708. [PMID: 24730875 DOI: 10.1103/physreve.89.032708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Indexed: 06/03/2023]
Abstract
One issue in genome maintenance is how DNA repair proteins find lesions at rates that seem to exceed diffusion-limited search rates. We propose a phenomenon where DNA damage induces nucleosomal rearrangements which move lesions to potential rendezvous points in the chromatin structure. These rendezvous points are the dyad and the linker DNA between histones, positions in the chromatin which are more likely to be accessible by repair proteins engaged in a random search. The feasibility of this mechanism is tested by considering the statistical mechanics of DNA containing a single lesion wrapped onto the nucleosome. We consider lesions which make the DNA either more flexible or more rigid by modeling the lesion as either a decrease or an increase in the bending energy. We include this energy in a partition function model of nucleosome breathing. Our results indicate that the steady state for a breathing nucleosome will most likely position the lesion at the dyad or in the linker, depending on the energy of the lesion. A role for DNA binding proteins and chromatin remodelers is suggested based on their ability to alter the mechanical properties of the DNA and DNA-histone binding, respectively. We speculate that these positions around the nucleosome potentially serve as rendezvous points where DNA lesions may be encountered by repair proteins which may be sterically hindered from searching the rest of the nucleosomal DNA. The strength of the repositioning is strongly dependent on the structural details of the DNA lesion and the wrapping and breathing of the nucleosome. A more sophisticated evaluation of this proposed mechanism will require detailed information about breathing dynamics, the structure of partially wrapped nucleosomes, and the structural properties of damaged DNA.
Collapse
Affiliation(s)
- Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Jamie Wilt
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Matthew Antonik
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| |
Collapse
|
41
|
Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure. Chromosoma 2013; 123:3-13. [PMID: 23996014 DOI: 10.1007/s00412-013-0435-8] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/17/2013] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
Abstract
Eukaryotic chromatin is a hierarchical collection of nucleoprotein structures that package DNA to form chromosomes. The initial levels of packaging include folding of long strings of nucleosomes into secondary structures and array-array association into higher-order tertiary chromatin structures. The core histone tail domains are required for the assembly of higher-order structures and mediate short- and long-range intra- and inter-nucleosome interactions with both DNA and protein targets to direct their assembly. However, important details of these interactions remain unclear and are a subject of much interest and recent investigations. Here, we review work defining the interactions of the histone N-terminal tails with DNA and protein targets relevant to chromatin higher-order structures, with a specific emphasis on the contributions of H3 and H4 tails to oligonucleosome folding and stabilization. We evaluate both classic and recent experiments determining tail structures, effect of tail cleavage/loss, and posttranslational modifications of the tails on nucleosomes and nucleosome arrays, as well as inter-nucleosomal and inter-array interactions of the H3 and H4 N-terminal tails.
Collapse
|
42
|
Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H. Contribution of histone N-terminal tails to the structure and stability of nucleosomes. FEBS Open Bio 2013; 3:363-9. [PMID: 24251097 PMCID: PMC3821030 DOI: 10.1016/j.fob.2013.08.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 12/17/2022] Open
Abstract
Histones are the protein components of the nucleosome, which forms the basic architecture of eukaryotic chromatin. Histones H2A, H2B, H3, and H4 are composed of two common regions, the "histone fold" and the "histone tail". Many efforts have been focused on the mechanisms by which the post-translational modifications of histone tails regulate the higher-order chromatin architecture. On the other hand, previous biochemical studies have suggested that histone tails also affect the structure and stability of the nucleosome core particle itself. However, the precise contributions of each histone tail are unclear. In the present study, we determined the crystal structures of four mutant nucleosomes, in which one of the four histones, H2A, H2B, H3, or H4, lacked the N-terminal tail. We found that the deletion of the H2B or H3 N-terminal tail affected histone-DNA interactions and substantially decreased nucleosome stability. These findings provide important information for understanding the complex roles of histone tails in regulating chromatin structure.
Collapse
Affiliation(s)
- Wakana Iwasaki
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan ; RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Nurse NP, Jimenez-Useche I, Smith IT, Yuan C. Clipping of flexible tails of histones H3 and H4 affects the structure and dynamics of the nucleosome. Biophys J 2013; 104:1081-8. [PMID: 23473491 DOI: 10.1016/j.bpj.2013.01.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/31/2012] [Accepted: 01/14/2013] [Indexed: 01/21/2023] Open
Abstract
Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to partake in intranucleosomal interactions by restricting the DNA breathing motion and compacting the nucleosome. The H3 tail effects were mostly independent of the ionic strength and valency of the ions. The H4 tail was shown to not greatly affect the nucleosome conformation, but did slightly influence the relative population of the preferred conformation. The role of the H4 tail varied depending on the valency and ionic strength, suggesting that electrostatic forces play a primary role in H4 tail interactions. Interestingly, despite the H4 tail's lack of influence, when H3 and H4 tails were simultaneously clipped, a more dramatic effect was seen than when only H3 or H4 tails were clipped. The combinatorial effect of H3 and H4 tail truncation suggests a potential mechanism by which various combinations of histone tail modifications can be used to control accessibility of DNA-binding proteins to nucleosomal DNA.
Collapse
Affiliation(s)
- Nathan P Nurse
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | | | | | | |
Collapse
|
44
|
Soliman ML, Ohm JE, Rosenberger TA. Acetate reduces PGE2 release and modulates phospholipase and cyclooxygenase levels in neuroglia stimulated with lipopolysaccharide. Lipids 2013; 48:651-62. [PMID: 23709104 DOI: 10.1007/s11745-013-3799-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/07/2013] [Indexed: 12/18/2022]
Abstract
Acetate supplementation attenuates neuroglial activation, increases histone and non-histone protein acetylation, reduces pro-inflammatory cytokine expression, and increases IL-4 transcription in rat models of neuroinflammation and Lyme's neuroborreliosis. Because eicosanoid signaling is involved in neuroinflammation, we measured the effect acetate treatment had on phospholipase, cyclooxygenase, and prostaglandin E2 (PGE2) levels in BV-2 microglia and primary astrocytes stimulated with lipopolysaccharide (LPS). In BV-2 microglia, we found that LPS increased the phosphorylation-state of cytosolic phospholipase A2 (cPLA2), reduced the levels of phospholipase C (PLC) β1, and increased the levels of cyclooxygenase (Cox)-1 and -2. Acetate treatment returned PLCβ1 and Cox-1 levels to normal, attenuated the increase in Cox-2, but had no effect on cPLA2 phosphorylation. In primary astrocytes, LPS increased the phosphorylation of cPLA2 and increased the levels of Cox-1 and Cox-2. Acetate treatment in these cells reduced secretory PLA2 IIA and PLCβ1 levels as compared to LPS-treatment groups, reversed the increase in cPLA2 phosphorylation, and returned Cox-1 levels to normal. Acetate treatment reduced PGE2 release in astrocytes stimulated with LPS to control levels, but did not alter PGE2 levels in BV-2 microglia. The amount of acetylated H3K9 bound to the promoter regions of Cox-1, Cox-2, IL-1β and NF-κB p65 genes, but not IL-4 in were increased in BV-2 microglia treated with acetate. These data suggest that acetate treatment can disrupt eicosanoid signaling in neuroglia that may, in part, be the result of altering gene expression due chromatin remodeling as a result of increasing H3K9 acetylation.
Collapse
Affiliation(s)
- Mahmoud L Soliman
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | | | | |
Collapse
|
45
|
Joshi SR, Sarpong YC, Peterson RC, Scovell WM. Nucleosome dynamics: HMGB1 relaxes canonical nucleosome structure to facilitate estrogen receptor binding. Nucleic Acids Res 2012; 40:10161-71. [PMID: 22941653 PMCID: PMC3488250 DOI: 10.1093/nar/gks815] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
High mobility group protein 1 (HMGB1) interacts with DNA and chromatin to influence the regulation of transcription, DNA repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome (N) in a nonenzymatic, ATP-independent manner. Although estrogen receptor (ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding. The isolated HMGB1-restructured nucleosomes (N′ and N″) remain stable and exhibit characteristics distinctly different from the canonical nucleosome. These findings complement previous studies that showed (i) HMGB1 stimulates in vivo transcriptional activation at estrogen response elements and (ii) knock down of HMGB1 expression by siRNA precipitously reduced transcriptional activation. The findings indicate that one aspect of the mechanism of HMGB1 action involves a restructuring of the nucleosome that appears to relax structural constraints within the nucleosome.
Collapse
Affiliation(s)
- Sachindra R Joshi
- Department of Chemistry and Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | | | | | | |
Collapse
|
46
|
Kulaeva OI, Zheng G, Polikanov YS, Colasanti AV, Clauvelin N, Mukhopadhyay S, Sengupta AM, Studitsky VM, Olson WK. Internucleosomal interactions mediated by histone tails allow distant communication in chromatin. J Biol Chem 2012; 287:20248-57. [PMID: 22518845 DOI: 10.1074/jbc.m111.333104] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Action across long distances on chromatin is a hallmark of eukaryotic transcriptional regulation. Although chromatin structure per se can support long-range interactions, the mechanisms of efficient communication between widely spaced DNA modules in chromatin remain a mystery. The molecular simulations described herein suggest that transient binary internucleosomal interactions can mediate distant communication in chromatin. Electrostatic interactions between the N-terminal tails of the core histones and DNA enhance the computed probability of juxtaposition of sites that lie far apart along the DNA sequence. Experimental analysis of the rates of communication in chromatin constructs confirms that long-distance communication occurs efficiently and independently of distance on tail-containing, but not on tailless, chromatin. Taken together, our data suggest that internucleosomal interactions involving the histone tails are essential for highly efficient, long-range communication between regulatory elements and their targets in eukaryotic genomes.
Collapse
Affiliation(s)
- Olga I Kulaeva
- Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Davis WB, Bjorklund CC, Deline M. Probing the effects of DNA-protein interactions on DNA hole transport: the N-terminal histone tails modulate the distribution of oxidative damage and chemical lesions in the nucleosome core particle. Biochemistry 2012; 51:3129-42. [PMID: 22409399 DOI: 10.1021/bi201734c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability of DNA to transport positive charges, or holes, over long distances is well-established, but the mechanistic details of how this process is influenced by packaging into DNA-protein complexes have not been fully delineated. In eukaryotes, genomic DNA is packaged into chromatin through its association with the core histone octamer to form the nucleosome core particle (NCP), a complex whose structure can be modulated through changes in the local environment and the histone proteins. Because (i) varying the salt concentration and removing the histone tails influence the structure of the NCP in known ways and (ii) previous studies have shown that DNA hole transport (HT) occurs in the nucleosome, we have used our previously described 601 sequence NCPs to test the hypothesis that DNA HT dynamics can be modulated by structural changes in a DNA-protein complex. We show that at low salt concentrations there is a sharp increase in long-range DNA HT efficiency in the NCP as compared to naked DNA. This enhancement of HT can be negated by either removal of the histone tails at low salt concentrations or disruption of the interaction of the packaged DNA and the histone tails by increasing the buffer's ionic strength. Association of the histone tails with 601 DNA at low salt concentrations shifts the guanine damage spectrum to favor lesions like 8-oxoguanine in the NCP, most likely through modulation of the rate of the reaction of the guanine radical cation with oxygen. These experimental results indicate that for most genomic DNA, the influence of DNA-protein interactions on DNA HT will depend strongly on the level of protection of the DNA nucleobases from oxygen. Further, these results suggest that the oxidative damage arising from DNA HT may vary in different genomic regions depending on the presence of either euchromatin or heterochromatin.
Collapse
Affiliation(s)
- William B Davis
- School of Molecular Biosciences, Biotechnology/Life Sciences 135, Washington State University, Pullman, Washington 99164-7520, USA.
| | | | | |
Collapse
|
48
|
Voltz K, Trylska J, Calimet N, Smith JC, Langowski J. Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J 2012; 102:849-58. [PMID: 22385856 DOI: 10.1016/j.bpj.2011.11.4028] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 11/10/2011] [Accepted: 11/28/2011] [Indexed: 11/25/2022] Open
Abstract
To permit access to DNA-binding proteins involved in the control and expression of the genome, the nucleosome undergoes structural remodeling including unwrapping of nucleosomal DNA segments from the nucleosome core. Here we examine the mechanism of DNA dissociation from the nucleosome using microsecond timescale coarse-grained molecular dynamics simulations. The simulations exhibit short-lived, reversible DNA detachments from the nucleosome and long-lived DNA detachments not reversible on the timescale of the simulation. During the short-lived DNA detachments, 9 bp dissociate at one extremity of the nucleosome core and the H3 tail occupies the space freed by the detached DNA. The long-lived DNA detachments are characterized by structural rearrangements of the H3 tail including the formation of a turn-like structure at the base of the tail that sterically impedes the rewrapping of DNA on the nucleosome surface. Removal of the H3 tails causes the long-lived detachments to disappear. The physical consistency of the CG long-lived open state was verified by mapping a CG structure representative of this state back to atomic resolution and performing molecular dynamics as well as by comparing conformation-dependent free energies. Our results suggest that the H3 tail may stabilize the nucleosome in the open state during the initial stages of the nucleosome remodeling process.
Collapse
Affiliation(s)
- Karine Voltz
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | |
Collapse
|
49
|
Ettig R, Kepper N, Stehr R, Wedemann G, Rippe K. Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping. Biophys J 2012; 101:1999-2008. [PMID: 22004754 DOI: 10.1016/j.bpj.2011.07.057] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 07/17/2011] [Accepted: 07/27/2011] [Indexed: 11/25/2022] Open
Abstract
The nucleosome complex of DNA wrapped around a histone protein octamer organizes the genome of eukaryotes and regulates the access of protein factors to the DNA. We performed molecular dynamics simulations of the nucleosome in explicit water to study the dynamics of its histone-DNA interactions. A high-resolution histone-DNA interaction map was derived that revealed a five-nucleotide periodicity, in which the two DNA strands of the double helix made alternating contacts. On the 100-ns timescale, the histone tails mostly maintained their initial positions relative to the DNA, and the spontaneous unwrapping of DNA was limited to 1-2 basepairs. In steered molecular dynamics simulations, external forces were applied to the linker DNA to investigate the unwrapping pathway of the nucleosomal DNA. In comparison with a nucleosome without the unstructured N-terminal histone tails, the following findings were obtained: 1), Two main barriers during unwrapping were identified at DNA position ±70 and ±45 basepairs relative to the central DNA basepair at the dyad axis. 2), DNA interactions of the histone H3 N-terminus and the histone H2A C-terminus opposed the initiation of unwrapping. 3), The N-terminal tails of H2A, H2B, and H4 counteracted the unwrapping process at later stages and were essential determinants of nucleosome dynamics. Our detailed analysis of DNA-histone interactions revealed molecular mechanisms for modulating access to nucleosomal DNA via conformational rearrangements of its structure.
Collapse
Affiliation(s)
- Ramona Ettig
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | | | | | | | | |
Collapse
|
50
|
Yang Z, Hayes JJ. The divalent cations Ca2+ and Mg2+ play specific roles in stabilizing histone-DNA interactions within nucleosomes that are partially redundant with the core histone tail domains. Biochemistry 2011; 50:9973-81. [PMID: 22007636 DOI: 10.1021/bi201377x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We previously reported that reconstituted nucleosomes undergo sequence-dependent translational repositioning upon removal of the core histone tail domains under physiological conditions, indicating that the tails influence the choice of position. We report here that removal of the core histone tail domains increases the exposure of the DNA backbone in nucleosomes to hydroxyl radicals, a nonbiased chemical cleavage reagent, indicative of an increase in the motility of the DNA on the histone surface. Moreover, we demonstrate that the divalent cations Mg(2+) and Ca(2+) can replace the role of the tail domains with regard to stabilization of histone-DNA interactions within the nucleosome core and restrict repositioning of nucleosomes upon tail removal. However, when nucleosomes were incubated with Mg(2+) after tail removal, the original distribution of translational positions was not re-established, indicating that divalent cations increase the energy barrier between translational positions rather than altering the free energy differences between positions. Interestingly, other divalent cations such as Zn(2+), Fe(2+), Co(2+), and Mn(2+) had little or no effect on the stability of histone-DNA interactions within tailless nucleosomes. These results support the idea that specific binding sites for Mg(2+) and Ca(2+) ions exist within the nucleosome and play a critical role in nucleosome stability that is partially redundant with the core histone tail domains.
Collapse
Affiliation(s)
- Zungyoon Yang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | | |
Collapse
|