1
|
Brahmachari S, Tripathi S, Onuchic JN, Levine H. Nucleosomes play a dual role in regulating transcription dynamics. Proc Natl Acad Sci U S A 2024; 121:e2319772121. [PMID: 38968124 PMCID: PMC11252751 DOI: 10.1073/pnas.2319772121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/31/2024] [Indexed: 07/07/2024] Open
Abstract
Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a possible regulator of eukaryotic transcription, however, the modes and mechanisms of this regulation are elusive. Here, we first take a statistical mechanics approach to model the torsional response of topology-constrained chromatin. Our model recapitulates the experimentally observed weaker torsional stiffness of chromatin compared to bare DNA and proposes structural transitions of nucleosomes into chirally distinct states as the driver of the contrasting torsional mechanics. Coupling chromatin mechanics with RNAP translocation in stochastic simulations, we reveal a complex interplay of DNA supercoiling and nucleosome dynamics in governing RNAP velocity. Nucleosomes play a dual role in controlling the transcription dynamics. The steric barrier aspect of nucleosomes in the gene body counteracts transcription via hindering RNAP motion, whereas the chiral transitions facilitate RNAP motion via driving a low restoring torque upon twisting the DNA. While nucleosomes with low dissociation rates are typically transcriptionally repressive, highly dynamic nucleosomes offer less of a steric barrier and enhance the transcription elongation dynamics of weakly transcribed genes via buffering DNA twist. We use the model to predict transcription-dependent levels of DNA supercoiling in segments of the budding yeast genome that are in accord with available experimental data. The model unveils a paradigm of DNA supercoiling-mediated interaction between genes and makes testable predictions that will guide experimental design.
Collapse
Affiliation(s)
| | - Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX77005
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Physics and Astronomy, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of Biosciences, Rice University, Houston, TX77005
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
| |
Collapse
|
2
|
Ukraintsev AA, Kutuzov MM, Lavrik OI. Studying Structure and Functions of Nucleosomes with Atomic Force Microscopy. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:674-687. [PMID: 38831504 DOI: 10.1134/s0006297924040072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 06/05/2024]
Abstract
Chromatin is an epigenetic platform for implementation of DNA-dependent processes. Nucleosome, as a basic level of chromatin compaction, largely determines its properties and structure. In the study of nucleosomes structure and functions physicochemical tools are actively used, such as magnetic and optical "tweezers", "DNA curtains", nuclear magnetic resonance, X-ray crystallography, and cryogenic electron microscopy, as well as optical methods based on Förster resonance energy transfer. Despite the fact that these approaches make it possible to determine a wide range of structural and functional characteristics of chromatin and nucleosomes with high spatial and time resolution, atomic force microscopy (AFM) complements the capabilities of these methods. The results of structural studies of nucleosome focusing on the AFM method development are presented in this review. The possibilities of AFM are considered in the context of application of other physicochemical approaches.
Collapse
Affiliation(s)
- Alexander A Ukraintsev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Mikhail M Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| |
Collapse
|
3
|
Figueroa-Bossi N, Fernández-Fernández R, Kerboriou P, Bouloc P, Casadesús J, Sánchez-Romero MA, Bossi L. Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin. Nat Commun 2024; 15:2787. [PMID: 38555352 PMCID: PMC10981669 DOI: 10.1038/s41467-024-47114-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negatively-supercoiled plectoneme to "unroll" disrupting the H-NS bridges and releasing H-NS.
Collapse
Affiliation(s)
- Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Rocío Fernández-Fernández
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Patricia Kerboriou
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | | | - Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France.
| |
Collapse
|
4
|
Chen P, Li G, Li W. Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions. JACS AU 2024; 4:866-876. [PMID: 38559720 PMCID: PMC10976579 DOI: 10.1021/jacsau.3c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024]
Abstract
Nucleosome, the building block of chromatin, plays pivotal roles in all DNA-related processes. While cryogenic-electron microscopy (cryo-EM) has significantly advanced our understanding of nucleosome structures, the emerging field of single-molecule force spectroscopy is illuminating their dynamic properties. This technique is crucial for revealing how nucleosome behavior is influenced by chaperones, remodelers, histone variants, and post-translational modifications, particularly in their folding and unfolding mechanisms under tension. Such insights are vital for deciphering the complex interplay in nucleosome assembly and structural regulation, highlighting the nucleosome's versatility in response to DNA activities. In this Perspective, we aim to consolidate the latest advancements in nucleosome dynamics, with a special focus on the revelations brought forth by single-molecule manipulation. Our objective is to highlight the insights gained from studying nucleosome dynamics through this innovative approach, emphasizing the transformative impact of single-molecule manipulation techniques in the field of chromatin research.
Collapse
Affiliation(s)
- Ping Chen
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Department
of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory
for Tumor Invasion and Metastasis, Capital
Medical University, Beijing 100069, P. R. China
| | - Guohong Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wei Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| |
Collapse
|
5
|
Brouwer TB, Kaczmarczyk A, Zarguit I, Pham C, Dame RT, van Noort J. Unravelling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers. Methods Mol Biol 2024; 2819:535-572. [PMID: 39028523 DOI: 10.1007/978-1-0716-3930-6_25] [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] [Indexed: 07/20/2024]
Abstract
Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers, in particular, have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA-organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to a magnetic bead inside a flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleoprotein filaments can be extracted from the data.
Collapse
Affiliation(s)
- Thomas B Brouwer
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Artur Kaczmarczyk
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Ilias Zarguit
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Chi Pham
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - John van Noort
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
6
|
Mattioli R, Ilari A, Colotti B, Mosca L, Fazi F, Colotti G. Doxorubicin and other anthracyclines in cancers: Activity, chemoresistance and its overcoming. Mol Aspects Med 2023; 93:101205. [PMID: 37515939 DOI: 10.1016/j.mam.2023.101205] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023]
Abstract
Anthracyclines have been important and effective treatments against a number of cancers since their discovery. However, their use in therapy has been complicated by severe side effects and toxicity that occur during or after treatment, including cardiotoxicity. The mode of action of anthracyclines is complex, with several mechanisms proposed. It is possible that their high toxicity is due to the large set of processes involved in anthracycline action. The development of resistance is a major barrier to successful treatment when using anthracyclines. This resistance is based on a series of mechanisms that have been studied and addressed in recent years. This work provides an overview of the anthracyclines used in cancer therapy. It discusses their mechanisms of activity, toxicity, and chemoresistance, as well as the approaches used to improve their activity, decrease their toxicity, and overcome resistance.
Collapse
Affiliation(s)
- Roberto Mattioli
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, Italian National Research Council IBPM-CNR, Rome, Italy
| | - Beatrice Colotti
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Luciana Mosca
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council IBPM-CNR, Rome, Italy.
| |
Collapse
|
7
|
Marri D, Filipovic D, Kana O, Tischkau S, Bhattacharya S. Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box DNA motifs. Sci Rep 2023; 13:7742. [PMID: 37173345 PMCID: PMC10182026 DOI: 10.1038/s41598-023-34115-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The Brain and Muscle ARNTL-Like 1 protein (BMAL1) forms a heterodimer with either Circadian Locomotor Output Cycles Kaput (CLOCK) or Neuronal PAS domain protein 2 (NPAS2) to act as a master regulator of the mammalian circadian clock gene network. The dimer binds to E-box gene regulatory elements on DNA, activating downstream transcription of clock genes. Identification of transcription factor binding sites and genomic features that correlate to DNA binding by BMAL1 is a challenging problem, given that CLOCK-BMAL1 or NPAS2-BMAL1 bind to several distinct binding motifs (CANNTG) on DNA. Using three different types of tissue-specific machine learning models with features based on (1) DNA sequence, (2) DNA sequence plus DNA shape, and (3) DNA sequence and shape plus histone modifications, we developed an interpretable predictive model of genome-wide BMAL1 binding to E-box motifs and dissected the mechanisms underlying BMAL1-DNA binding. Our results indicated that histone modifications, the local shape of the DNA, and the flanking sequence of the E-box motif are sufficient predictive features for BMAL1-DNA binding. Our models also provide mechanistic insights into tissue specificity of DNA binding by BMAL1.
Collapse
Affiliation(s)
- Daniel Marri
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - David Filipovic
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Omar Kana
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Shelley Tischkau
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Sudin Bhattacharya
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA.
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA.
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
8
|
Fan H. Single‐molecule tethered particle motion to study
protein‐DNA
interaction. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
|
9
|
Asada R, Hirota K. Multi-Layered Regulations on the Chromatin Architectures: Establishing the Tight and Specific Responses of Fission Yeast fbp1 Gene Transcription. Biomolecules 2022; 12:1642. [PMID: 36358992 PMCID: PMC9687179 DOI: 10.3390/biom12111642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 04/08/2024] Open
Abstract
Transcriptional regulation is pivotal for all living organisms and is required for adequate response to environmental fluctuations and intercellular signaling molecules. For precise regulation of transcription, cells have evolved regulatory systems on the genome architecture, including the chromosome higher-order structure (e.g., chromatin loops), location of transcription factor (TF)-binding sequences, non-coding RNA (ncRNA) transcription, chromatin configuration (e.g., nucleosome positioning and histone modifications), and the topological state of the DNA double helix. To understand how these genome-chromatin architectures and their regulators establish tight and specific responses at the transcription stage, the fission yeast fbp1 gene has been analyzed as a model system for decades. The fission yeast fbp1 gene is tightly repressed in the presence of glucose, and this gene is induced by over three orders of magnitude upon glucose starvation with a cascade of multi-layered regulations on various levels of genome and chromatin architecture. In this review article, we summarize the multi-layered transcriptional regulatory systems revealed by the analysis of the fission yeast fbp1 gene as a model system.
Collapse
Affiliation(s)
- Ryuta Asada
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
| |
Collapse
|
10
|
Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products. Proc Natl Acad Sci U S A 2022; 119:e2206513119. [PMID: 35939666 PMCID: PMC9388122 DOI: 10.1073/pnas.2206513119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleosomes, the fundamental structural unit of chromatin, consists of ∼147 DNA base pairs wrapped around a histone protein octamer. To characterize the strength of the nucleosomal barrier and its contribution as a mechanism of control of gene expression, it is essential to determine the forces required to unwrap the DNA from the core particle and the stepwise transitions involved. In this study, we performed combined optical tweezers and single-molecule fluorescence measurements to identify the specific DNA segments unwrapped during the force transitions observed in mechanical stretching of nucleosomes. Furthermore, we characterize the mechanical signatures of subnucleosomal hexasomes and tetrasomes. The characterization performed in this work is essential for the interpretation of ongoing studies of chromatin remodelers, polymerases, and histone chaperones. Nucleosome DNA unwrapping and its disassembly into hexasomes and tetrasomes is necessary for genomic access and plays an important role in transcription regulation. Previous single-molecule mechanical nucleosome unwrapping revealed a low- and a high-force transitions, and force-FRET pulling experiments showed that DNA unwrapping is asymmetric, occurring always first from one side before the other. However, the assignment of DNA segments involved in these transitions remains controversial. Here, using high-resolution optical tweezers with simultaneous single-molecule FRET detection, we show that the low-force transition corresponds to the undoing of the outer wrap of one side of the nucleosome (∼27 bp), a process that can occur either cooperatively or noncooperatively, whereas the high-force transition corresponds to the simultaneous unwrapping of ∼76 bp from both sides. This process may give rise stochastically to the disassembly of nucleosomes into hexasomes and tetrasomes whose unwrapping/rewrapping trajectories we establish. In contrast, nucleosome rewrapping does not exhibit asymmetry. To rationalize all previous nucleosome unwrapping experiments, it is necessary to invoke that mechanical unwrapping involves two nucleosome reorientations: one that contributes to the change in extension at the low-force transition and another that coincides but does not contribute to the high-force transition.
Collapse
|
11
|
Abstract
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic modification of the 3D-genome organization. It is generally accepted that protein–protein and protein–DNA interactions form the basis of 3D-genome organization. However, the constant generation of mechanical forces, torques, and other stresses produced by various proteins translocating along DNA could be playing a larger role in genome organization than currently appreciated. Clearly, a thorough understanding of the mechanical determinants imposed by DNA transactions on the 3D organization of the genome is required. We provide here an overview of our current knowledge and highlight the importance of DNA and chromatin mechanics in gene expression.
Collapse
Affiliation(s)
- Rajiv Kumar Jha
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - Fedor Kouzine
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| |
Collapse
|
12
|
Li S, Peng Y, Landsman D, Panchenko AR. DNA methylation cues in nucleosome geometry, stability and unwrapping. Nucleic Acids Res 2022; 50:1864-1874. [PMID: 35166834 DOI: 10.1093/nar/gkac097] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 01/04/2023] Open
Abstract
Cytosine methylation at the 5-carbon position is an essential DNA epigenetic mark in many eukaryotic organisms. Although countless structural and functional studies of cytosine methylation have been reported, our understanding of how it influences the nucleosome assembly, structure, and dynamics remains obscure. Here, we investigate the effects of cytosine methylation at CpG sites on nucleosome dynamics and stability. By applying long molecular dynamics simulations on several microsecond time scale, we generate extensive atomistic conformational ensembles of full nucleosomes. Our results reveal that methylation induces pronounced changes in geometry for both linker and nucleosomal DNA, leading to a more curved, under-twisted DNA, narrowing the adjacent minor grooves, and shifting the population equilibrium of sugar-phosphate backbone geometry. These DNA conformational changes are associated with a considerable enhancement of interactions between methylated DNA and the histone octamer, doubling the number of contacts at some key arginines. H2A and H3 tails play important roles in these interactions, especially for DNA methylated nucleosomes. This, in turn, prevents a spontaneous DNA unwrapping of 3-4 helical turns for the methylated nucleosome with truncated histone tails, otherwise observed in the unmethylated system on several microseconds time scale.
Collapse
Affiliation(s)
- Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| |
Collapse
|
13
|
Basu A, Bobrovnikov DG, Ha T. DNA mechanics and its biological impact. J Mol Biol 2021; 433:166861. [PMID: 33539885 DOI: 10.1016/j.jmb.2021.166861] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Almost all nucleoprotein interactions and DNA manipulation events involve mechanical deformations of DNA. Extraordinary progresses in single-molecule, structural, and computational methods have characterized the average mechanical properties of DNA, such as bendability and torsional rigidity, in high resolution. Further, the advent of sequencing technology has permitted measuring, in high-throughput, how such mechanical properties vary with sequence and epigenetic modifications along genomes. We review these recent technological advancements, and discuss how they have contributed to the emerging idea that variations in the mechanical properties of DNA play a fundamental role in regulating, genome-wide, diverse processes involved in chromatin organization.
Collapse
Affiliation(s)
- Aakash Basu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| |
Collapse
|
14
|
Winogradoff D, Li P, Joshi H, Quednau L, Maffeo C, Aksimentiev A. Chiral Systems Made from DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003113. [PMID: 33717850 PMCID: PMC7927625 DOI: 10.1002/advs.202003113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA's chirality, from plasmonics and spintronics to biosensing.
Collapse
Affiliation(s)
- David Winogradoff
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Pin‐Yi Li
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Himanshu Joshi
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Lauren Quednau
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Christopher Maffeo
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Aleksei Aksimentiev
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| |
Collapse
|
15
|
Topoisomerase activity is linked to altered nucleosome positioning and transcriptional regulation in the fission yeast fbp1 gene. PLoS One 2020; 15:e0242348. [PMID: 33180846 PMCID: PMC7660550 DOI: 10.1371/journal.pone.0242348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/01/2020] [Indexed: 01/26/2023] Open
Abstract
Chromatin structure, including nucleosome positioning, has a fundamental role in transcriptional regulation through influencing protein-DNA interactions. DNA topology is known to influence chromatin structure, and in doing so, can also alter transcription. However, detailed mechanism(s) linking transcriptional regulation events to chromatin structure that is regulated by changes in DNA topology remain to be well defined. Here we demonstrate that nucleosome positioning and transcriptional output from the fission yeast fbp1 and prp3 genes are altered by excess topoisomerase activity. Given that lncRNAs (long noncoding RNAs) are transcribed from the fbp1 upstream region and are important for fbp1 gene expression, we hypothesized that local changes in DNA topological state caused by topoisomerase activity could alter lncRNA and fbp1 transcription. In support of this, we found that topoisomerase overexpression caused destabilization of positioned nucleosomes within the fbp1 promoter region, which was accompanied by aberrant fbp1 transcription. Similarly, the direct recruitment of topoisomerase, but not a catalytically inactive form, to the promoter region of fbp1 caused local changes in nucleosome positioning that was also accompanied by altered fbp1 transcription. These data indicate that changes in DNA topological state induced by topoisomerase activity could lead to altered fbp1 transcription through modulating nucleosome positioning.
Collapse
|
16
|
Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint. PLoS One 2019; 14:e0224936. [PMID: 31747397 PMCID: PMC6867626 DOI: 10.1371/journal.pone.0224936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/30/2019] [Indexed: 12/22/2022] Open
Abstract
The restricted access of regulatory factors to their binding sites on DNA wrapped around the nucleosomes is generally interpreted in terms of molecular shielding exerted by nucleosomal structure and internucleosomal interactions. Binding of proteins to DNA often includes intercalation of hydrophobic amino acids into the DNA. To assess the role of constrained superhelicity in limiting these interactions, we studied the binding of small molecule intercalators to chromatin in close to native conditions by laser scanning cytometry. We demonstrate that the nucleosome-constrained superhelical configuration of DNA is the main barrier to intercalation. As a result, intercalating compounds are virtually excluded from the nucleosome-occupied regions of the chromatin. Binding of intercalators to extranucleosomal regions is limited to a smaller degree, in line with the existence of net supercoiling in the regions comprising linker and nucleosome free DNA. Its relaxation by inducing as few as a single nick per ~50 kb increases intercalation in the entire chromatin loop, demonstrating the possibility for long-distance effects of regulatory potential.
Collapse
|
17
|
Juhász S, Elbakry A, Mathes A, Löbrich M. ATRX Promotes DNA Repair Synthesis and Sister Chromatid Exchange during Homologous Recombination. Mol Cell 2018; 71:11-24.e7. [PMID: 29937341 DOI: 10.1016/j.molcel.2018.05.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/20/2018] [Accepted: 05/10/2018] [Indexed: 01/15/2023]
Abstract
ATRX is a chromatin remodeler that, together with its chaperone DAXX, deposits the histone variant H3.3 in pericentromeric and telomeric regions. Notably, ATRX is frequently mutated in tumors that maintain telomere length by a specific form of homologous recombination (HR). Surprisingly, in this context, we demonstrate that ATRX-deficient cells exhibit a defect in repairing exogenously induced DNA double-strand breaks (DSBs) by HR. ATRX operates downstream of the Rad51 removal step and interacts with PCNA and RFC-1, which are collectively required for DNA repair synthesis during HR. ATRX depletion abolishes DNA repair synthesis and prevents the formation of sister chromatid exchanges at exogenously induced DSBs. DAXX- and H3.3-depleted cells exhibit identical HR defects as ATRX-depleted cells, and both ATRX and DAXX function to deposit H3.3 during DNA repair synthesis. This suggests that ATRX facilitates the chromatin reconstitution required for extended DNA repair synthesis and sister chromatid exchange during HR.
Collapse
Affiliation(s)
- Szilvia Juhász
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Amira Elbakry
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Arthur Mathes
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany.
| |
Collapse
|
18
|
Xin B, Rohs R. Relationship between histone modifications and transcription factor binding is protein family specific. Genome Res 2018; 28:321-333. [PMID: 29326300 PMCID: PMC5848611 DOI: 10.1101/gr.220079.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/10/2018] [Indexed: 12/20/2022]
Abstract
The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies focusing on BSs within DNA regulatory regions found correlations between HM patterns and TF binding specificities. However, a mechanistic understanding of TF-DNA binding specificity determinants is still not available. The ability to predict in vivo TF binding on a genome-wide scale requires the identification of features that determine TF binding based on evolutionary relationships of DNA binding proteins. To reveal protein family-dependent mechanisms of TF binding, we conducted comprehensive comparisons of HM patterns surrounding BSs and non-BSs with exactly matched core motifs for TFs in three cell lines: 33 TFs in GM12878, 37 TFs in K562, and 18 TFs in H1-hESC. These TFs displayed protein family-specific preferences for HM patterns surrounding BSs, with high agreement among cell lines. Moreover, compared to models based on DNA sequence and shape at flanking regions of BSs, HM-augmented quantitative machine-learning methods resulted in increased performance in a TF family-specific manner. Analysis of the relative importance of features in these models indicated that TFs, displaying larger HM pattern differences between BSs and non-BSs, bound DNA in an HM-specific manner on a protein family-specific basis. We propose that TF family-specific HM preferences reveal distinct mechanisms that assist in guiding TFs to their cognate BSs by altering chromatin structure and accessibility.
Collapse
Affiliation(s)
- Beibei Xin
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Remo Rohs
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| |
Collapse
|
19
|
Brouwer TB, Kaczmarczyk A, Pham C, van Noort J. Unraveling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers. Methods Mol Biol 2018; 1837:317-349. [PMID: 30109618 DOI: 10.1007/978-1-4939-8675-0_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers in particular have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to magnetics bead inside flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleo-protein filaments can be extracted from the data.
Collapse
Affiliation(s)
- Thomas B Brouwer
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - Chi Pham
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands.
| |
Collapse
|
20
|
Chen X, Zhao E, Fu YV. Using single-molecule approach to visualize the nucleosome assembly in yeast nucleoplasmic extracts. Sci Bull (Beijing) 2017; 62:399-404. [PMID: 36659283 DOI: 10.1016/j.scib.2017.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In eukaryotic cells, the smallest subunit of chromatin is the nucleosome, which consists of a segment of DNA wound on histone protein cores. Despite many years of effort, the process of nucleosome assembly and disassembly is still not very clear. Here, we present a convenient method to investigate the process of nucleosome assembly at the single molecule level. We invented a novel system derived from the yeast nucleoplasmic extracts (YNPE), and demonstrated that the YNPE supports the nucleosome assembly under physiological condition. By combining the total internal reflection fluorescence microscopy with microfluidic flow-cell technique, the dynamic process of nucleosome assembly in YNPE was visualized at single-molecule level. Our system provides a novel in vitro single-molecule tool to investigate the dynamics of nucleosome assembly under physiological conditions.
Collapse
Affiliation(s)
- Xiuqiang Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ershuang Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu V Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
21
|
Alabert C, Jasencakova Z, Groth A. Chromatin Replication and Histone Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:311-333. [PMID: 29357065 DOI: 10.1007/978-981-10-6955-0_15] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure to reassemble nucleosomes at replication forks blocks DNA replication progression in higher eukaryotes and leads to genomic instability, we further underline the importance of the mechanistic link between DNA replication and chromatin duplication.
Collapse
Affiliation(s)
- Constance Alabert
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zuzana Jasencakova
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
22
|
Abstract
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo.
Collapse
|
23
|
Jiang C, Lionberger TA, Wiener DM, Meyhofer E. Electromagnetic tweezers with independent force and torque control. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:084304. [PMID: 27587135 DOI: 10.1063/1.4960811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Magnetic tweezers are powerful tools to manipulate and study the mechanical properties of biological molecules and living cells. In this paper we present a novel, bona fide electromagnetic tweezer (EMT) setup that allows independent control of the force and torque applied via micrometer-sized magnetic beads to a molecule under study. We implemented this EMT by combining a single solenoid that generates force (f-EMT) with a set of four solenoids arranged into a symmetric quadrupole to generate torque (τ-EMT). To demonstrate the capability of the tweezers, we attached optically asymmetric Janus beads to single, tethered DNA molecules. We show that tension in the piconewton force range can be applied to single DNA molecules and the molecule can simultaneously be twisted with torques in the piconewton-nanometer range. Furthermore, the EMT allows the two components to be independently controlled. At various force levels applied to the Janus bead, the trap torsional stiffness can be continuously changed simply by varying the current magnitude applied to the τ-EMT. The flexible and independent control of force and torque by the EMT makes it an ideal tool for a range of measurements where tensional and torsional properties need to be studied simultaneously on a molecular or cellular level.
Collapse
Affiliation(s)
- Chang Jiang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Troy A Lionberger
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Diane M Wiener
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Edgar Meyhofer
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
24
|
Corless S, Gilbert N. Effects of DNA supercoiling on chromatin architecture. Biophys Rev 2016; 8:245-258. [PMID: 27738453 PMCID: PMC5039215 DOI: 10.1007/s12551-016-0210-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022] Open
Abstract
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo.
Collapse
Affiliation(s)
- Samuel Corless
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH42XU UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH42XU UK
| |
Collapse
|
25
|
Gerasimova NS, Pestov NA, Kulaeva OI, Clark DJ, Studitsky VM. Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription. Transcription 2016; 7:91-5. [PMID: 27115204 DOI: 10.1080/21541264.2016.1182240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.
Collapse
Affiliation(s)
- N S Gerasimova
- a Biology Faculty, Lomonosov Moscow State University , Moscow , Russia
| | - N A Pestov
- b Department of Pharmacology , Rutgers-Robert Wood Johnson Medical School , Piscataway , NJ , USA
| | - O I Kulaeva
- a Biology Faculty, Lomonosov Moscow State University , Moscow , Russia.,c Cancer Epigenetics Program, Fox Chase Cancer Center , Philadelphia , PA , USA
| | - D J Clark
- d Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - V M Studitsky
- a Biology Faculty, Lomonosov Moscow State University , Moscow , Russia.,b Department of Pharmacology , Rutgers-Robert Wood Johnson Medical School , Piscataway , NJ , USA.,c Cancer Epigenetics Program, Fox Chase Cancer Center , Philadelphia , PA , USA
| |
Collapse
|
26
|
Abstract
A huge amount of information is stored in genomic DNA and this stored information resides inside the nucleus with the aid of chromosomal condensation factors. It has been reported that the repeat nucleosome core particle (NCP) consists of 147-bp of DNA and two copies of H2A, H2B, H3 and H4. Regulation of chromosomal structure is important to many processes inside the cell. In vivo, a group of histone chaperones facilitate and regulate nucleosome assembly. How NCPs are constructed with the aid of histone chaperones remains unclear. In this study, the histone chaperone-mediated nucleosome assembly process was investigated using single-molecule tethered particle motion (TPM) experiments. It was found that Asf1 is able to exert more influence than Nap1 and poly glutamate acid (PGA) on the nucleosome formation process, which highlights Asf1’s specific role in tetrasome formation. Thermodynamic parameters supported a model whereby energetically favored nucleosomal complexes compete with non-nucleosomal complexes. In addition, our kinetic findings propose the model that histone chaperones mediate nucleosome assembly along a path that leads to enthalpy-favored products with free histones as reaction substrates.
Collapse
|
27
|
Transcribing through the nucleosome. Trends Biochem Sci 2014; 39:577-86. [DOI: 10.1016/j.tibs.2014.10.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/20/2022]
|
28
|
Abstract
The widespread adoption of short-read DNA sequencing as a digital epigenomic readout platform has motivated the development of genome-wide tools that achieve base-pair resolution. New methods for footprinting and affinity purification of nucleosomes, RNA polymerases, chromatin remodellers and transcription factors have increased the resolution of epigenomic profiling by two orders of magnitude, leading to new insights into how the chromatin landscape affects gene regulation. These digital epigenomic tools have also been applied to directly profile both turnover kinetics and transcription in situ. In this Review, we describe how these new genome-wide tools allow interrogation of diverse aspects of the epigenome.
Collapse
|
29
|
Nam GM, Arya G. Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes. Nucleic Acids Res 2014; 42:9691-9. [PMID: 25100871 PMCID: PMC4150795 DOI: 10.1093/nar/gku694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Torsionally stressed DNA plays a critical role in genome organization and regulation. While the effects of torsional stresses on naked DNA have been well studied, little is known about how these stresses propagate within chromatin and affect its organization. Here we investigate the torsional behavior of nucleosome arrays by means of Brownian dynamics simulations of a coarse-grained model of chromatin. Our simulations reveal a strong dependence of the torsional response on the rotational phase angle Ψ0 between adjacent nucleosomes. Extreme values of Ψ0 lead to asymmetric, bell-shaped extension-rotation profiles with sharp maxima shifted toward positive or negative rotations, depending on the sign of Ψ0, and to fast, irregular propagation of DNA twist. In contrast, moderate Ψ0 yield more symmetric profiles with broad maxima and slow, uniform propagation of twist. The observed behavior is shown to arise from an interplay between nucleosomal transitions into states with crossed and open linker DNAs and global supercoiling of arrays into left- and right-handed coils, where Ψ0 serves to modulate the energy landscape of nucleosomal states. Our results also explain the torsional resilience of chromatin, reconcile differences between experimentally measured extension-rotation profiles, and suggest a role of torsional stresses in regulating chromatin assembly and organization.
Collapse
Affiliation(s)
- Gi-Moon Nam
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0448, USA
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0448, USA
| |
Collapse
|
30
|
Abstract
The double helical structure of DNA lends itself to topological constraints. Many DNA-based processes alter the topological state of DNA, generating torsional stress, which is efficiently relieved by topoisomerases. Maintaining this topological balance is crucial to cell survival, as excessive torsional strain risks DNA damage. Here, we review the mechanisms that generate and modulate DNA torsion within the cell. In particular, we discuss how transcription-generated torsional stress affects Pol II kinetics and chromatin dynamics, highlighting an emerging role of DNA torsion as a feedback mediator of torsion-generating processes.
Collapse
Affiliation(s)
- Sheila S Teves
- Molecular and Cell Biology; University of California, Berkeley; Berkeley, CA USA
| | - Steven Henikoff
- Basic Sciences Division; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Howard Hughes Medical Institute; Seattle, WA USA
| |
Collapse
|
31
|
Abstract
Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions.
Collapse
Affiliation(s)
- Fedor Kouzine
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - David Levens
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - Laura Baranello
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| |
Collapse
|
32
|
Doxorubicin, DNA torsion, and chromatin dynamics. Biochim Biophys Acta Rev Cancer 2013; 1845:84-9. [PMID: 24361676 DOI: 10.1016/j.bbcan.2013.12.002] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/16/2013] [Accepted: 12/10/2013] [Indexed: 11/23/2022]
Abstract
Doxorubicin is one of the most important anti-cancer chemotherapeutic drugs, being widely used for the treatment of solid tumors and acute leukemias. The action of doxorubicin and other anthracycline drugs has been intensively investigated during the last several decades, but the mechanisms that have been proposed for cell killing remain disparate and controversial. In this review, we examine the proposed models for doxorubicin action from the perspective of the chromatin landscape, which is altered in many types of cancer due to recurrent mutations in chromatin modifiers. We highlight recent evidence for effects of anthracyclines on DNA torsion and chromatin dynamics that may underlie basic mechanisms of doxorubicin-mediated cell death and suggest new therapeutic strategies for cancer treatment.
Collapse
|
33
|
Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol 2013; 21:88-94. [PMID: 24317489 PMCID: PMC3947361 DOI: 10.1038/nsmb.2723] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/30/2013] [Indexed: 01/03/2023]
Abstract
As RNA polymerase II (Pol II) transcribes a gene, it encounters an array of well-ordered nucleosomes. How it traverses through this array in vivo remains unresolved. One model proposes that torsional stress generated during transcription destabilizes nucleosomes ahead of Pol II. Here, we describe a method for high-resolution mapping of underwound DNA, using next-generation sequencing, and show that torsion is correlated with gene expression in Drosophila melanogaster cells. Accumulation of torsional stress, through topoisomerase inhibition, results in increased Pol II at transcription start sites. Whereas topoisomerase I inhibition results in increased nascent RNA transcripts, topoisomerase II inhibition causes little change. Despite the different effects on Pol II elongation, topoisomerase inhibition results in increased nucleosome turnover and salt solubility within gene bodies, thus suggesting that the elongation-independent effects of torsional stress on nucleosome dynamics contributes to the destabilization of nucleosomes.
Collapse
|
34
|
Matsuoka T, Choul Kim B, Moraes C, Han M, Takayama S. Micro- and nanofluidic technologies for epigenetic profiling. BIOMICROFLUIDICS 2013; 7:41301. [PMID: 23964309 PMCID: PMC3739826 DOI: 10.1063/1.4816835] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/26/2013] [Indexed: 05/10/2023]
Abstract
This short review provides an overview of the impact micro- and nanotechnologies can make in studying epigenetic structures. The importance of mapping histone modifications on chromatin prompts us to highlight the complexities and challenges associated with histone mapping, as compared to DNA sequencing. First, the histone code comprised over 30 variations, compared to 4 nucleotides for DNA. Second, whereas DNA can be amplified using polymerase chain reaction, chromatin cannot be amplified, creating challenges in obtaining sufficient material for analysis. Third, while every person has only a single genome, there exist multiple epigenomes in cells of different types and origins. Finally, we summarize existing technologies for performing these types of analyses. Although there are still relatively few examples of micro- and nanofluidic technologies for chromatin analysis, the unique advantages of using such technologies to address inherent challenges in epigenetic studies, such as limited sample material, complex readouts, and the need for high-content screens, make this an area of significant growth and opportunity.
Collapse
Affiliation(s)
- Toshiki Matsuoka
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | | | |
Collapse
|
35
|
Teves SS, Henikoff S. The heat shock response: A case study of chromatin dynamics in gene regulation. Biochem Cell Biol 2013; 91:42-8. [DOI: 10.1139/bcb-2012-0075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent studies in transcriptional regulation using the Drosophila heat shock response system have elucidated many of the dynamic regulatory processes that govern transcriptional activation and repression. The classic view that the control of gene expression occurs at the point of RNA polymerase II (Pol II) recruitment is now giving way to a more complex outlook of gene regulation. Promoter chromatin dynamics coordinate with transcription factor binding to maintain the promoters of active genes accessible. For a large number of genes, the rate-limiting step in Pol II progression occurs during its initial elongation, where Pol II transcribes 30–50 bp and pauses for further signals. These paused genes have unique genic chromatin architecture and dynamics compared with genes where Pol II recruitment is rate limiting for expression. Further elongation of Pol II along the gene causes nucleosome turnover, a continuous process of eviction and replacement, which suggests a potential mechanism for Pol II transit along a nucleosomal template. In this review, we highlight recent insights into transcription regulation of the heat shock response and discuss how the dynamic regulatory processes involved at each transcriptional stage help to generate faithful yet highly responsive gene expression.
Collapse
Affiliation(s)
- Sheila S. Teves
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| |
Collapse
|
36
|
Vlijm R, Smitshuijzen JSJ, Lusser A, Dekker C. NAP1-assisted nucleosome assembly on DNA measured in real time by single-molecule magnetic tweezers. PLoS One 2012; 7:e46306. [PMID: 23050009 PMCID: PMC3457989 DOI: 10.1371/journal.pone.0046306] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/30/2012] [Indexed: 11/19/2022] Open
Abstract
While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood. We study NAP1 (nucleosome assembly protein 1) assisted nucleosome formation at the single-molecule level using magnetic tweezers. This method allows to apply a well-defined stretching force and supercoiling density to a single DNA molecule, and to study in real time the change in linking number, stiffness and length of the DNA during nucleosome formation. We observe a decrease in end-to-end length when NAP1 and core histones (CH) are added to the dsDNA. We characterize the formation of complete nucleosomes by measuring the change in linking number of DNA, which is induced by the NAP1-assisted nucleosome assembly, and which does not occur for non-nucleosomal bound histones H3 and H4. By rotating the magnets, the supercoils formed upon nucleosome assembly are removed and the number of assembled nucleosomes can be counted. We find that the compaction of DNA at low force is about 56 nm per assembled nucleosome. The number of compaction steps and associated change in linking number indicate that NAP1-assisted nucleosome assembly is a two-step process.
Collapse
Affiliation(s)
- Rifka Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | | | | |
Collapse
|
37
|
Potoyan DA, Savelyev A, Papoian GA. Recent successes in coarse-grained modeling of DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1114] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
38
|
Dobrovolskaia IV, Kenward M, Arya G. Twist propagation in dinucleosome arrays. Biophys J 2011; 99:3355-64. [PMID: 21081084 DOI: 10.1016/j.bpj.2010.09.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 09/13/2010] [Accepted: 09/28/2010] [Indexed: 12/01/2022] Open
Abstract
We present a Monte Carlo simulation study of the distribution and propagation of twist from one DNA linker to another for a two-nucleosome array subjected to externally applied twist. A mesoscopic model of the array that incorporates nucleosome geometry along with the bending and twisting mechanics of the linkers is employed and external twist is applied in stepwise increments to mimic quasistatic twisting of chromatin fibers. Simulation results reveal that the magnitude and sign of the imposed and induced twist on contiguous linkers depend strongly on their relative orientation. Remarkably, the relative direction of the induced and applied twist can become inverted for a subset of linker orientations-a phenomenon we refer to as "twist inversion". We characterize the twist inversion, as a function of relative linker orientation, in a phase diagram and explain its key features using a simple model based on the geometry of the nucleosome/linker complex. In addition to twist inversion, our simulations reveal "nucleosome flipping", whereby nucleosomes may undergo sudden flipping in response to applied twist, causing a rapid bending of the linker and a significant change in the overall twist and writhe of the array. Our findings shed light on the underlying mechanisms by which torsional stresses impact chromatin organization.
Collapse
Affiliation(s)
- Irina V Dobrovolskaia
- Department of NanoEngineering, University of California at San Diego, La Jolla, CA, USA
| | | | | |
Collapse
|
39
|
Abstract
DNA supercoiling plays essential role in maintaining proper chromosome structure, as well as the equilibrium between genome dynamics and stability under specific physicochemical and physiological conditions. In mesophilic organisms, DNA is negatively supercoiled and, until recently, positive supercoiling was considered a peculiar mark of (hyper)thermophilic archaea needed to survive high temperatures. However, several lines of evidence suggest that negative and positive supercoiling might coexist in both (hyper)thermophilic and mesophilic organisms, raising the possibility that positive supercoiling might serve as a regulator of various cellular events, such as chromosome condensation, gene expression, mitosis, sister chromatid cohesion, centromere identity and telomere homoeostasis.
Collapse
|
40
|
Abstract
Coarse-grained (CG) modeling approaches are widely used to simulate many important biological processes involving DNA, including chromatin folding and genomic packaging. The bending propensity of a semiflexible DNA molecule critically influences these processes. However, existing CG DNA models do not retain a sufficient fidelity of the important local chain motions, whose propagation at larger length scales would generate correct DNA persistent lengths, in particular when the solution's ionic strength is widely varied. Here we report on a development of an accurate CG model for the double-stranded DNA chain, with explicit treatment of mobile ions, derived systematically from all-atom molecular dynamics simulations. Our model generates complex local motions of the DNA chain, similar to fully atomistic dynamics, leading also to a quantitative agreement of our simulation results with the experimental data on the dependence of the DNA persistence length on the solution ionic strength. We also predict a structural transition in a torsionally stressed DNA nanocircle as the buffer ionic strength is increased beyond a threshold value.
Collapse
Affiliation(s)
- Alexey Savelyev
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Garegin A. Papoian
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| |
Collapse
|
41
|
Chromatin fiber dynamics under tension and torsion. Int J Mol Sci 2010; 11:1557-79. [PMID: 20480035 PMCID: PMC2871131 DOI: 10.3390/ijms11041557] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/20/2010] [Accepted: 03/19/2010] [Indexed: 01/22/2023] Open
Abstract
Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome and chromatin structural changes. Indeed, magnetic and optical tweezers have allowed opportunities to handle single nucleosomal particles or nucleosomal arrays and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors acting on the DNA. These challenging technical approaches provide us with deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of cellular metabolism.
Collapse
|