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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.
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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
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Ukraintsev A, Kutuzov M, Belousova E, Joyeau M, Golyshev V, Lomzov A, Lavrik O. PARP3 Affects Nucleosome Compaction Regulation. Int J Mol Sci 2023; 24:ijms24109042. [PMID: 37240388 DOI: 10.3390/ijms24109042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Genome compaction is one of the important subject areas for understanding the mechanisms regulating genes' expression and DNA replication and repair. The basic unit of DNA compaction in the eukaryotic cell is the nucleosome. The main chromatin proteins responsible for DNA compaction have already been identified, but the regulation of chromatin architecture is still extensively studied. Several authors have shown an interaction of ARTD proteins with nucleosomes and proposed that there are changes in the nucleosomes' structure as a result. In the ARTD family, only PARP1, PARP2, and PARP3 participate in the DNA damage response. Damaged DNA stimulates activation of these PARPs, which use NAD+ as a substrate. DNA repair and chromatin compaction need precise regulation with close coordination between them. In this work, we studied the interactions of these three PARPs with nucleosomes by atomic force microscopy, which is a powerful method allowing for direct measurements of geometric characteristics of single molecules. Using this method, we evaluated perturbations in the structure of single nucleosomes after the binding of a PARP. We demonstrated here that PARP3 significantly alters the geometry of nucleosomes, possibly indicating a new function of PARP3 in chromatin compaction regulation.
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Affiliation(s)
- Alexander Ukraintsev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Mikhail Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ekaterina Belousova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Marie Joyeau
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Victor Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexander Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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The Sequence Dependent Nanoscale Structure of CENP-A Nucleosomes. Int J Mol Sci 2022; 23:ijms231911385. [PMID: 36232691 PMCID: PMC9569828 DOI: 10.3390/ijms231911385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
CENP-A is a histone variant found in high abundance at the centromere in humans. At the centromere, this histone variant replaces the histone H3 found throughout the bulk chromatin. Additionally, the centromere comprises tandem repeats of α-satellite DNA, which CENP-A nucleosomes assemble upon. However, the effect of the DNA sequence on the nucleosome assembly and centromere formation remains poorly understood. Here, we investigated the structure of nucleosomes assembled with the CENP-A variant using Atomic Force Microscopy. We assembled both CENP-A nucleosomes and H3 nucleosomes on a DNA substrate containing an α-satellite motif and characterized their positioning and wrapping efficiency. We also studied CENP-A nucleosomes on the 601-positioning motif and non-specific DNA to compare their relative positioning and stability. CENP-A nucleosomes assembled on α-satellite DNA did not show any positional preference along the substrate, which is similar to both H3 nucleosomes and CENP-A nucleosomes on non-specific DNA. The range of nucleosome wrapping efficiency was narrower on α-satellite DNA compared with non-specific DNA, suggesting a more stable complex. These findings indicate that DNA sequence and histone composition may be two of many factors required for accurate centromere assembly.
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Konrad SF, Vanderlinden W, Frederickx W, Brouns T, Menze BH, De Feyter S, Lipfert J. High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes. NANOSCALE 2021; 13:5435-5447. [PMID: 33683227 DOI: 10.1039/d0nr08564b] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleosomes, the fundamental units of chromatin, regulate readout and expression of eukaryotic genomes. Single-molecule experiments have revealed force-induced nucleosome accessibility, but a high-resolution unwrapping landscape in the absence of external forces is currently lacking. Here, we introduce a high-throughput pipeline for the analysis of nucleosome conformations based on atomic force microscopy and automated, multi-parameter image analysis. Our data set of ∼10 000 nucleosomes reveals multiple unwrapping states corresponding to steps of 5 bp DNA. For canonical H3 nucleosomes, we observe that dissociation from one side impedes unwrapping from the other side, but in contrast to force-induced unwrapping, we find only a weak sequence-dependent asymmetry. Notably, centromeric CENP-A nucleosomes do not unwrap anti-cooperatively, in stark contrast to H3 nucleosomes. Finally, our results reconcile previous conflicting findings about the differences in height between H3 and CENP-A nucleosomes. We expect our approach to enable critical insights into epigenetic regulation of nucleosome structure and stability and to facilitate future high-throughput AFM studies that involve heterogeneous nucleoprotein complexes.
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Affiliation(s)
- Sebastian F Konrad
- Department of Physics and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.
| | - Willem Vanderlinden
- Department of Physics and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.
| | - Wout Frederickx
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Tine Brouns
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Björn H Menze
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Steven De Feyter
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Jan Lipfert
- Department of Physics and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.
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Stumme-Diers MP, Banerjee S, Hashemi M, Sun Z, Lyubchenko YL. Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A. Nucleic Acids Res 2019; 46:94-103. [PMID: 29040671 PMCID: PMC5758880 DOI: 10.1093/nar/gkx933] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/02/2017] [Indexed: 01/12/2023] Open
Abstract
In the absence of a functioning centromere, chromosome segregation becomes aberrant, leading to an increased rate of aneuploidy. The highly specific recognition of centromeres by kinetochores suggests that specific structural characteristics define this region, however, the structural details and mechanism underlying this recognition remains a matter of intense investigation. To address this, high-speed atomic force microscopy was used for direct visualization of the spontaneous dynamics of CENP-A nucleosomes at the sub-second time scale. We report that CENP-A nucleosomes change conformation spontaneously and reversibly, utilizing two major pathways: unwrapping, and looping of the DNA; enabling core transfer between neighboring DNA substrates. Along with these nucleosome dynamics we observed that CENP-A stabilizes the histone core against dissociating to histone subunits upon unwrapping DNA, unique from H3 cores which are only capable of such plasticity in the presence of remodeling factors. These findings have implications for the dynamics and integrity of nucleosomes at the centromere.
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Affiliation(s)
- Micah P Stumme-Diers
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Siddhartha Banerjee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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Stumme-Diers MP, Stormberg T, Sun Z, Lyubchenko YL. Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging. J Vis Exp 2019. [PMID: 30774135 DOI: 10.3791/58820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription to take place in eukaryotic cells. The dynamics of nucleosomes provides access to the DNA by replication and transcription machineries, and critically contributes to the molecular mechanisms underlying chromatin functions. Single-molecule studies such as atomic force microscopy (AFM) imaging have contributed significantly to our current understanding of the role of nucleosome structure and dynamics. The current protocol describes the steps enabling high-resolution AFM imaging techniques to study the structural and dynamic properties of nucleosomes. The protocol is illustrated by AFM data obtained for the centromere nucleosomes in which H3 histone is replaced with its counterpart centromere protein A (CENP-A). The protocol starts with the assembly of mono-nucleosomes using a continuous dilution method. The preparation of the mica substrate functionalized with aminopropyl silatrane (APS-mica) that is used for the nucleosome imaging is critical for the AFM visualization of nucleosomes described and the procedure to prepare the substrate is provided. Nucleosomes deposited on the APS-mica surface are first imaged using static AFM, which captures a snapshot of the nucleosome population. From analyses of these images, such parameters as the size of DNA wrapped around the nucleosomes can be measured and this process is also detailed. The time-lapse AFM imaging procedure in the liquid is described for the high-speed time-lapse AFM that can capture several frames of nucleosome dynamics per second. Finally, the analysis of nucleosome dynamics enabling the quantitative characterization of the dynamic processes is described and illustrated.
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Affiliation(s)
| | - Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center;
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Stumme-Diers MP, Banerjee S, Sun Z, Lyubchenko YL. Assembly of Centromere Chromatin for Characterization by High-Speed Time-Lapse Atomic Force Microscopy. Methods Mol Biol 2018; 1814:225-242. [PMID: 29956236 DOI: 10.1007/978-1-4939-8591-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy (AFM) is an imaging technique that enables single molecule characterization of biological systems at nanometer resolution. Imaging in ambient conditions can provide details of the conformational states and interactions of a population of molecules which is well complemented by single-molecule imaging of the systems dynamics using time-lapse AFM imaging, in which images are capture at rates of 10-15 frames per second in an aqueous buffer. Here we describe the assembly and preparation of nucleosomes containing centromere protein A (CENP-A) for AFM imaging in both static and time-lapse modes. The AFM imaging and data analysis techniques described enable characterization of the extent of DNA wrapping around the histone core and time-resolved visualization of the systems intrinsic dynamic behaviors.
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Affiliation(s)
- Micah P Stumme-Diers
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Siddhartha Banerjee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
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Lyubchenko YL. Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:403001. [PMID: 30410191 PMCID: PMC6217977 DOI: 10.1088/1361-6463/aad898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly. PLoS One 2016; 11:e0165078. [PMID: 27820823 PMCID: PMC5098787 DOI: 10.1371/journal.pone.0165078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022] Open
Abstract
Centromere-specific nucleosomes are a central feature of the kinetochore complex during mitosis, in which microtubules exert pulling and pushing forces upon the centromere. CENP-A nucleosomes have been assumed to be structurally unique, thereby providing resilience under tension relative to their H3 canonical counterparts. Here, we directly test this hypothesis by subjecting CENP-A and H3 octameric nucleosomes, assembled on random or on centromeric DNA sequences, to varying amounts of applied force by using single-molecule magnetic tweezers. We monitor individual disassembly events of CENP-A and H3 nucleosomes. Regardless of the DNA sequence, the force-mediated disassembly experiments for CENP-A and H3 nucleosomes demonstrate similar rupture forces, life time residency and disassembly steps. From these experiments, we conclude that CENP-A does not, by itself, contribute unique structural features to the nucleosome that lead to a significant resistance against force-mediated disruption. The data present insights into the mechanistic basis for how CENP-A nucleosomes might contribute to the structural foundation of the centromere in vivo.
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Fang J, Liu Y, Wei Y, Deng W, Yu Z, Huang L, Teng Y, Yao T, You Q, Ruan H, Chen P, Xu RM, Li G. Structural transitions of centromeric chromatin regulate the cell cycle-dependent recruitment of CENP-N. Genes Dev 2015; 29:1058-73. [PMID: 25943375 PMCID: PMC4441053 DOI: 10.1101/gad.259432.115] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022]
Abstract
Specific recognition of centromere-specific histone variant CENP-A-containing chromatin by CENP-N is an essential process in the assembly of the kinetochore complex at centromeres prior to mammalian cell division. However, the mechanisms of CENP-N recruitment to centromeres/kinetochores remain unknown. Here, we show that a CENP-A-specific RG loop (Arg80/Gly81) plays an essential and dual regulatory role in this process. The RG loop assists the formation of a compact "ladder-like" structure of CENP-A chromatin, concealing the loop and thus impairing its role in recruiting CENP-N. Upon G1/S-phase transition, however, centromeric chromatin switches from the compact to an open state, enabling the now exposed RG loop to recruit CENP-N prior to cell division. Our results provide the first insights into the mechanisms by which the recruitment of CENP-N is regulated by the structural transitions between compaction and relaxation of centromeric chromatin during the cell cycle.
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Affiliation(s)
- Junnan Fang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqiang Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhouliang Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Teng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Yao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglong You
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ping Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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