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Presman DM, Benítez B, Lafuente AL, Vázquez Lareu A. Chromatin structure and dynamics: one nucleosome at a time. Histochem Cell Biol 2024; 162:79-90. [PMID: 38607419 DOI: 10.1007/s00418-024-02281-1] [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] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Eukaryotic genomes store information on many levels, including their linear DNA sequence, the posttranslational modifications of its constituents (epigenetic modifications), and its three-dimensional folding. Understanding how this information is stored and read requires multidisciplinary collaborations from many branches of science beyond biology, including physics, chemistry, and computer science. Concurrent recent developments in all these areas have enabled researchers to image the genome with unprecedented spatial and temporal resolution. In this review, we focus on what single-molecule imaging and tracking of individual proteins in live cells have taught us about chromatin structure and dynamics. Starting with the basics of single-molecule tracking (SMT), we describe some advantages over in situ imaging techniques and its current limitations. Next, we focus on single-nucleosome studies and what they have added to our current understanding of the relationship between chromatin dynamics and transcription. In celebration of Robert Feulgen's ground-breaking discovery that allowed us to start seeing the genome, we discuss current models of chromatin structure and future challenges ahead.
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Affiliation(s)
- Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Agustina L Lafuente
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Alejo Vázquez Lareu
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
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2
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Oses C, De Rossi MC, Bruno L, Verneri P, Diaz MC, Benítez B, Guberman A, Levi V. From the membrane to the nucleus: mechanical signals and transcription regulation. Biophys Rev 2023; 15:671-683. [PMID: 37681098 PMCID: PMC10480138 DOI: 10.1007/s12551-023-01103-3] [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: 04/06/2023] [Accepted: 07/20/2023] [Indexed: 09/09/2023] Open
Abstract
Mechanical forces drive and modulate a wide variety of processes in eukaryotic cells including those occurring in the nucleus. Relevantly, forces are fundamental during development since they guide lineage specifications of embryonic stem cells. A sophisticated macromolecular machinery transduces mechanical stimuli received at the cell surface into a biochemical output; a key component in this mechanical communication is the cytoskeleton, a complex network of biofilaments in constant remodeling that links the cell membrane to the nuclear envelope. Recent evidence highlights that forces transmitted through the cytoskeleton directly affect the organization of chromatin and the accessibility of transcription-related molecules to their targets in the DNA. Consequently, mechanical forces can directly modulate transcription and change gene expression programs. Here, we will revise the biophysical toolbox involved in the mechanical communication with the cell nucleus and discuss how mechanical forces impact on the organization of this organelle and more specifically, on transcription. We will also discuss how live-cell fluorescence imaging is producing exquisite information to understand the mechanical response of cells and to quantify the landscape of interactions of transcription factors with chromatin in embryonic stem cells. These studies are building new biophysical insights that could be fundamental to achieve the goal of manipulating forces to guide cell differentiation in culture systems.
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Affiliation(s)
- Camila Oses
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - María Cecilia De Rossi
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Luciana Bruno
- Facultad de Ciencias Exactas Y Naturales, Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Paula Verneri
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - María Candelaria Diaz
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Facultad de Ciencias Exactas Y Naturales, Departamento de Fisiología, Universidad de Buenos Aires, Biología Molecular Y Celular, C1428EGA Buenos Aires, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Facultad de Ciencias Exactas Y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
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SOX2 Modulates the Nuclear Organization and Transcriptional Activity of the Glucocorticoid Receptor. J Mol Biol 2022; 434:167869. [PMID: 36309135 DOI: 10.1016/j.jmb.2022.167869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/07/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
Steroid receptors (SRs) are ligand-dependent transcription factors (TFs) relevant to key cellular processes in both physiology and pathology, including some types of cancer. SOX2 is a master TF of pluripotency and self-renewal of embryonic stem cells, and its dysregulation is also associated with various types of human cancers. A potential crosstalk between these TFs could be relevant in malignant cells yet, to the best of our knowledge, no formal study has been performed thus far. Here we show, by quantitative live-cell imaging microscopy, that ectopic expression of SOX2 disrupts the formation of hormone-dependent intranuclear condensates of many steroid receptors (SRs), including those formed by the glucocorticoid receptor (GR). SOX2 also reduces GR's binding to specific DNA targets and modulates its transcriptional activity. SOX2-driven effects on GR condensates do not require the intrinsically disordered N-terminal domain of the receptor and, surprisingly, neither relies on GR/SOX2 interactions. SOX2 also alters the intranuclear dynamics and compartmentalization of the SR coactivator NCoA-2 and impairs GR/NCoA-2 interactions. These results suggest an indirect mechanism underlying SOX2-driven effects on SRs involving this coactivator. Together, these results highlight that the transcriptional program elicited by GR relies on its nuclear organization and is intimately linked to the distribution of other GR partners, such as the NCoA-2 coactivator. Abnormal expression of SOX2, commonly observed in many tumors, may alter the biological action of GR and, probably, other SRs as well. Understanding this crosstalk may help to improve steroid hormone-based therapies in cancers with elevated SOX2 expression.
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Goelzer M, Goelzer J, Ferguson ML, Neu CP, Uzer G. Nuclear envelope mechanobiology: linking the nuclear structure and function. Nucleus 2021; 12:90-114. [PMID: 34455929 PMCID: PMC8432354 DOI: 10.1080/19491034.2021.1962610] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and proliferation programs. In this review we will first introduce the structural elements of the nucleoskeleton and discuss the current literature on how nuclear structure and signaling are altered in relation to environmental and tissue level mechanical cues. We will focus on state-of-the-art techniques to apply mechanical force and methods to measure nuclear mechanics in conjunction with DNA, RNA, and protein visualization in living cells. Ultimately, combining real-time nuclear deformations and chromatin dynamics can be a powerful tool to study mechanisms of how forces affect the dynamics of genome function.
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Affiliation(s)
- Matthew Goelzer
- Materials Science and Engineering, Boise State University, Boise, ID, US
| | | | - Matthew L. Ferguson
- Biomolecular Science, Boise State University, Boise, ID, US
- Physics, Boise State University, Boise, ID, US
| | - Corey P. Neu
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, US
| | - Gunes Uzer
- Mechanical and Biomedical Engineering, Boise State University, Boise, ID, US
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Dong S, Chen X, Yang H, Tang X, Chen J, Lin X, Peng Y. Visualization photofragmentation-induced rhodamine B release from gold nanorod delivery system by combination two-photon luminescence imaging with correlation spectroscopy. JOURNAL OF BIOPHOTONICS 2020; 13:e201960103. [PMID: 31919964 DOI: 10.1002/jbio.201960103] [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: 09/06/2019] [Revised: 11/25/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Plasmon-enhanced gold nanorod (AuNR) with high photothermal conversion efficiency is a promising light-controllable nanodrug delivery system for cancer therapy. Understanding the mechanism for the light-controllable drug release of AuNR delivery systems is important for the development of nanomedicine. In this study, the rhodamine B (RB) released from AuNR-RB nanodelivery system was quantitated and visualized by using two-photon luminescence (TPL) imaging combined with correlation spectroscopy. The photofragmentation of AuNR induced by femtosecond pulsed laser was revealed by TPL correlation spectroscopy when the laser energy was above the thermal damage threshold of AuNR, and the RB released from this nanodrug delivery system was visualized by TPL imaging. Furthermore, the photofragmentation-induced release of RB from AuNR-RB nanodelivery system was visualized in living MCF-7 breast cancer cells by TPL imaging combined with correlation spectroscopy. These results provided a novel optical approach to quantify the release of drugs from gold nanocarriers in complex biological media.
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Affiliation(s)
- Shiqing Dong
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Xiuqin Chen
- Fujian Provincial Key Laboratory of Polymer Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou, China
| | - Hongqin Yang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Xiaoqiong Tang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Jianling Chen
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Xiu Lin
- Fujian Provincial Key Laboratory of Quantum Manipulation and New Energy Materials, College of Physics and Energy, Fujian Normal University, Fuzhou, China
| | - Yiru Peng
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory of Polymer Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou, China
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Fluorescence correlation spectroscopy reveals the dynamics of kinesins interacting with organelles during microtubule-dependent transport in cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118572. [DOI: 10.1016/j.bbamcr.2019.118572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 01/26/2023]
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Murade CU, Shubeita GT. A Molecular Sensor Reveals Differences in Macromolecular Crowding between the Cytoplasm and Nucleoplasm. ACS Sens 2019; 4:1835-1843. [PMID: 31250628 DOI: 10.1021/acssensors.9b00569] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We describe a molecular sensor that reports, using fluorescence resonance energy transfer (FRET), on the degree of macromolecular crowding in different cellular compartments. The oligonucleotide-based sensor is sensitive to changes in the volume fraction of macromolecules over a wide range in vitro and, when introduced in cells, rapidly distributes and shows a striking contrast between the cytosol and the nucleus. This contrast can be modulated by osmotic stress or by using a number of drugs that alter chromatin organization within the nucleus. These findings suggest that the sensor can be used as a tool to probe chromosome organization. Further, our finding that the cell maintains different degrees of macromolecular crowding in the cytoplasm and nucleoplasm has implications on molecular mechanisms since crowding can alter protein conformations, binding rates, reaction kinetics, and therefore protein function.
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Affiliation(s)
- Chandrashekhar U. Murade
- Physics Program, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - George T. Shubeita
- Physics Program, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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Fluorescence fluctuation spectroscopy: an invaluable microscopy tool for uncovering the biophysical rules for navigating the nuclear landscape. Biochem Soc Trans 2019; 47:1117-1129. [DOI: 10.1042/bst20180604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Nuclear architecture is fundamental to the manner by which molecules traverse the nucleus. The nucleoplasm is a crowded environment where dynamic rearrangements in local chromatin compaction locally redefine the space accessible toward nuclear protein diffusion. Here, we review a suite of methods based on fluorescence fluctuation spectroscopy (FFS) and how they have been employed to interrogate chromatin organization, as well as the impact this structural framework has on nuclear protein target search. From first focusing on a set of studies that apply FFS to an inert fluorescent tracer diffusing inside the nucleus of a living cell, we demonstrate the capacity of this technology to measure the accessibility of the nucleoplasm. Then with a baseline understanding of the exploration volume available to nuclear proteins during target search, we review direct applications of FFS to fluorescently labeled transcription factors (TFs). FFS can detect changes in TF mobility due to DNA binding, as well as the formation of TF complexes via changes in brightness due to oligomerization. Collectively, we find that FFS-based methods can uncover how nuclear proteins in general navigate the nuclear landscape.
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Affiliation(s)
- Christian Eggeling
- Institute of Applied Optics, Faculty of Physics and Astronomy, Friedrich-Schiller-University Jena; Max-Wien-Platz, 1, 07743 Jena, Germany // Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany // MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Christian Hellriegel
- Carl Zeiss Microscopy GmbH, Carl-Zeiss-Promenade, 10, 07745 Jena, Germany // Harvard Center for Biological Imaging, Room 2052 Biological Laboratories, 16 Divinity Ave., Cambridge, MA 02138, USA
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