1
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Vidi PA, Liu J, Bonin K, Bloom K. Closing the loops: chromatin loop dynamics after DNA damage. Nucleus 2025; 16:2438633. [PMID: 39720924 DOI: 10.1080/19491034.2024.2438633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 11/29/2024] [Accepted: 11/30/2024] [Indexed: 12/26/2024] Open
Abstract
Chromatin is a dynamic polymer in constant motion. These motions are heterogeneous between cells and within individual cell nuclei and are profoundly altered in response to DNA damage. The shifts in chromatin motions following genomic insults depend on the temporal and physical scales considered. They are also distinct in damaged and undamaged regions. In this review, we emphasize the role of chromatin tethering and loop formation in chromatin dynamics, with the view that pulsing loops are key contributors to chromatin motions. Chromatin tethers likely mediate micron-scale chromatin coherence predicted by polymer models and measured experimentally, and we propose that remodeling of the tethers in response to DNA breaks enables uncoupling of damaged and undamaged chromatin regions.
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Affiliation(s)
| | - Jing Liu
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, USA
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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Delvaux de Fenffe CM, Govers J, Mattiroli F. Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes. Biochemistry 2025; 64:2138-2153. [PMID: 40312022 PMCID: PMC12096440 DOI: 10.1021/acs.biochem.5c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 04/04/2025] [Accepted: 04/08/2025] [Indexed: 05/03/2025]
Abstract
Our genome is organized into chromatin, a dynamic and modular structure made of nucleosomes. Chromatin organization controls access to the DNA sequence, playing a fundamental role in cell identity and function. How nucleosomes enable these processes is an active area of study. In this review, we provide an overview of chromatin dynamics, its properties, mechanisms, and functions. We highlight the diverse ways by which chromatin dynamics is controlled during transcription, DNA replication, and repair. Recent technological developments have promoted discoveries in this area, to which we provide an outlook on future research directions.
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Affiliation(s)
| | - Jolijn Govers
- Hubrecht Institute-KNAW & University
Medical Center Utrecht, Uppsalalaan 8, 3584 CTUtrecht, The Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute-KNAW & University
Medical Center Utrecht, Uppsalalaan 8, 3584 CTUtrecht, The Netherlands
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3
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Prakash K, Baddeley D, Eggeling C, Fiolka R, Heintzmann R, Manley S, Radenovic A, Shroff H, Smith C, Schermelleh L. Resolution in super-resolution microscopy - facts, artifacts, technological advancements and biological applications. J Cell Sci 2025; 138:jcs263567. [PMID: 40421932 DOI: 10.1242/jcs.263567] [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] [Indexed: 05/28/2025] Open
Abstract
Super-resolution microscopy (SRM) has undeniable potential for scientific discovery, yet still presents many challenges that hinder its widespread adoption, including technical trade-offs between resolution, speed and photodamage, as well as limitations in imaging live samples and larger, more complex biological structures. Furthermore, SRM often requires specialized expertise and complex instrumentation, which can deter biologists from fully embracing the technology. In this Perspective, a follow-up to our recent Q&A article, we aim to demystify these challenges by addressing common questions and misconceptions surrounding SRM. Experts offer practical insights into how biologists can maximize the benefits of SRM while navigating issues such as photobleaching, image artifacts and the limitations of existing techniques. We also highlight recent developments in SRM that continue to push the boundaries of resolution. Our goal is to equip researchers with the crucial knowledge they need to harness the full potential of SRM.
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Affiliation(s)
- Kirti Prakash
- Delft Center for Systems and Control, Faculty of Mechanical, Maritime, and Materials Engineering, Technische Universiteit Delft, Delft, 2628 CN, The Netherlands
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, 1010, New Zealand
| | - Christian Eggeling
- Institute of Applied Optics and Biophysics and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, 07745, Germany
- Leibniz Institute of Photonic Technology, Jena, 07743, Germany
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Jena, 07743, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, 07745, Germany
| | - Suliana Manley
- Laboratory of Experimental Biophysics, School of Basic Sciences, Institute of Physics Interfaculty Institute of Bioengineering, EPFL SB-LEB, Lausanne, 1015, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, School of Engineering, Institute of Bioengineering, EPFL STI IBI-STI LBEN, Lausanne, 1015, Switzerland
| | - Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA 20147, USA
| | - Carlas Smith
- Delft Center for Systems and Control, Faculty of Mechanical, Maritime, and Materials Engineering, Technische Universiteit Delft, Delft, 2628 CN, The Netherlands
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4
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Zhou H, Hutchings J, Shiozaki M, Zhao X, Doolittle LK, Yang S, Yan R, Jean N, Riggi M, Yu Z, Villa E, Rosen MK. Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography. Proc Natl Acad Sci U S A 2025; 122:e2426449122. [PMID: 40327693 PMCID: PMC12088439 DOI: 10.1073/pnas.2426449122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 03/31/2025] [Indexed: 05/08/2025] Open
Abstract
Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here, we analyzed the structure of biochemically reconstituted chromatin condensates through cryoelectron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with context-aware template matching. Our approaches were developed on chromatin condensates and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 Å resolution in reconstituted and native systems, respectively, found that nucleosomes form heterogeneous interaction networks in both cases, and gained insight into the molecular origins of surface tension in chromatin condensates. Our methods should be applicable to biomolecular condensates containing large and distinctive components in both biochemical reconstitutions and certain cellular systems.
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Affiliation(s)
- Huabin Zhou
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Joshua Hutchings
- School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | | | | | - Lynda K. Doolittle
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Shixin Yang
- Janelia Research Campus, HHMI, Ashburn, VA20147
| | - Rui Yan
- Janelia Research Campus, HHMI, Ashburn, VA20147
| | - Nikki Jean
- Janelia Research Campus, HHMI, Ashburn, VA20147
| | - Margot Riggi
- Research Department Cell and Virus Structure, Max Planck Institute for Biochemistry, Martinsried/MunichD-82152, Germany
| | - Zhiheng Yu
- Janelia Research Campus, HHMI, Ashburn, VA20147
| | - Elizabeth Villa
- School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
- HHMI, University of California, San Diego, La Jolla, CA92093
| | - Michael K. Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390
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5
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Paggi JM, Zhang B. Toward decoding the mechanisms that shape sub-megabase-scale genome organization. Curr Opin Struct Biol 2025; 92:103062. [PMID: 40344741 DOI: 10.1016/j.sbi.2025.103062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2025] [Revised: 04/15/2025] [Accepted: 04/16/2025] [Indexed: 05/11/2025]
Abstract
Understanding genome organization at the kilobase to megabase scale is critical, as it encompasses genes and regulatory elements. Improvements in the resolution of experimental techniques have revealed novel structural motifs at this scale, including micro-compartments, nucleosome clutches, microdomains, and packing domains. Here we review recent progress on developing theories to explain these observations. Key advances include elucidating the role of nucleosome positioning and epigenetic modifications, the role and mechanisms of compartmentalization in local structure, and the interplay between loop extrusion and phase separation. This work has revealed probable mechanisms by which the observed structures emerge, but it remains unclear how these factors act together in the cell. To this end, recent studies have used chromatin conformation capture data in concert with diverse genomics datasets to create native-like models of chromatin at nucleosome resolution and below. While several roadblocks remain, this strategy promises to decode how molecular forces sum to shape chromatin structure and ultimately regulate transcription.
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Affiliation(s)
- Joseph M Paggi
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA.
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6
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Chen JK, Liu T, Cai S, Ruan W, Ng CT, Shi J, Surana U, Gan L. Nanoscale analysis of human G1 and metaphase chromatin in situ. EMBO J 2025; 44:2658-2694. [PMID: 40097852 PMCID: PMC12048539 DOI: 10.1038/s44318-025-00407-2] [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: 05/26/2024] [Revised: 02/11/2025] [Accepted: 02/21/2025] [Indexed: 03/19/2025] Open
Abstract
The structure of chromatin at the nucleosome level inside cells is still incompletely understood. Here we present in situ electron cryotomography analyses of chromatin in both G1 and metaphase RPE-1 cells. G1 nucleosomes are concentrated in globular chromatin domains, and metaphase nucleosomes are concentrated in the chromatids. Classification analysis reveals that canonical mononucleosomes, and in some conditions ordered stacked dinucleosomes and mononucleosomes with a disordered gyre-proximal density, are abundant in both cell-cycle states. We do not detect class averages that have more than two stacked nucleosomes or side-by-side dinucleosomes, suggesting that groups of more than two nucleosomes are heterogeneous. Large multi-megadalton structures are abundant in G1 nucleoplasm, but not found in G1 chromatin domains and metaphase chromatin. The macromolecular phenotypes studied here represent a starting point for the comparative analysis of compaction in normal vs. unhealthy human cells, in other cell-cycle states, other organisms, and in vitro chromatin assemblies.
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Affiliation(s)
- Jon Ken Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
| | - Tingsheng Liu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Weimei Ruan
- Institute of Molecular and Cell Biology and Agency for Science Technology and Research, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology and Agency for Science Technology and Research, 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Pharmacology, National University of Singapore, Singapore, 117543, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA.
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7
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Wang Y, Frederick J, Medina KI, Bartom ET, Almassalha LM, Zhang Y, Wodarcyk G, Huang H, Ye IC, Gong R, Dunton CL, Duval A, Gonzalez PC, Pritchard J, Carinato J, Topchu I, Li J, Ji Z, Adli M, Backman V, Matei D. Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2407426. [PMID: 40051293 PMCID: PMC12061297 DOI: 10.1002/advs.202407426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 12/16/2024] [Indexed: 03/09/2025]
Abstract
Chromatin organization regulates transcription to influence cellular plasticity and cell fate. We explored whether chromatin nanoscale packing domains are involved in stemness and response to chemotherapy. Using an optical spectroscopic nanosensing technology we show that ovarian cancer-derived cancer stem cells (CSCs) display upregulation of nanoscale chromatin packing domains compared to non-CSCs. Cleavage under targets and tagmentation (CUT&Tag) sequencing with antibodies for repressive H3K27me3 and active H3K4me3 and H3K27ac marks mapped chromatin regions associated with differentially expressed genes. More poised genes marked by both H3K4me3 and H3K27me3 were identified in CSCs vs. non-CSCs, supporting increased transcriptional plasticity of CSCs. Pathways related to Wnt signaling and cytokine-cytokine receptor interaction were repressed in non-CSCs, while retinol metabolism and antioxidant response were activated in CSCs. Comparative transcriptomic analyses showed higher intercellular transcriptional heterogeneity at baseline in CSCs. In response to cisplatin, genes with low baseline expression levels underwent the highest upregulation in CSCs, demonstrating transcriptional plasticity under stress. Epigenome targeting drugs downregulated chromatin packing domains and promoted cellular differentiation. A disruptor of telomeric silencing 1-like (Dot1L) inhibitor blocked transcriptional plasticity, reversing stemness. These findings support that CSCs harbor upregulated chromatin packing domains, contributing to transcriptional and cell plasticity that epigenome modifiers can target.
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8
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Lin H, Seitz S, Tan Y, Lugagne JB, Wang L, Ding G, He H, Rauwolf TJ, Dunlop MJ, Connor JH, Porco JA, Tian L, Cheng JX. Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering. Nat Methods 2025; 22:1040-1050. [PMID: 39820753 PMCID: PMC12074879 DOI: 10.1038/s41592-024-02575-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 11/26/2024] [Indexed: 01/19/2025]
Abstract
Super-resolution imaging of cell metabolism is hindered by the incompatibility of small metabolites with fluorescent dyes and the limited resolution of imaging mass spectrometry. We present ultrasensitive reweighted visible stimulated Raman scattering (URV-SRS), a label-free vibrational imaging technique for multiplexed nanoscopy of intracellular metabolites. We developed a visible SRS microscope with extensive pulse chirping to improve the detection limit to ~4,000 molecules and introduced a self-supervised multi-agent denoiser to suppress non-independent noise in SRS by over 7.2 dB, resulting in a 50-fold sensitivity enhancement over near-infrared SRS. Leveraging the enhanced sensitivity, we employed Fourier reweighting to amplify sub-100-nm spatial frequencies that were previously overwhelmed by noise. Validated by Fourier ring correlation, we achieved a lateral resolution of 86 nm in cell imaging. We visualized the reprogramming of metabolic nanostructures associated with virus replication in host cells and subcellular fatty acid synthesis in engineered bacteria, demonstrating its capability towards nanoscopic spatial metabolomics.
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Affiliation(s)
- Haonan Lin
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Scott Seitz
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Yuying Tan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Jean-Baptiste Lugagne
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Le Wang
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Guangrui Ding
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Hongjian He
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Tyler J Rauwolf
- Department of Chemistry, Boston University, Boston, MA, USA
- Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - John H Connor
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - John A Porco
- Department of Chemistry, Boston University, Boston, MA, USA
- Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Photonics Center, Boston University, Boston, MA, USA.
- Department of Chemistry, Boston University, Boston, MA, USA.
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9
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Maeshima K. The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2025:pjab.101.020. [PMID: 40301047 DOI: 10.2183/pjab.101.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2025]
Abstract
The organization and dynamics of chromatin are critical for genome functions such as transcription and DNA replication/repair. Historically, chromatin was assumed to fold into the 30-nm fiber and progressively arrange into larger helical structures, as described in the textbook model. However, over the past 15 years, extensive evidence including our studies has dramatically transformed the view of chromatin from a static, regular structure to one that is more variable and dynamic. In higher eukaryotic cells, chromatin forms condensed yet liquid-like domains, which appear to be the basic unit of chromatin structure, replacing the 30-nm fiber. These domains maintain proper accessibility, ensuring the regulation of DNA reaction processes. During mitosis, these domains assemble to form more gel-like mitotic chromosomes, which are further constrained by condensins and other factors. Based on the available evidence, I discuss the physical properties of chromatin in live cells, emphasizing its viscoelastic nature-balancing local fluidity with global stability to support genome functions.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS
- Graduate Institute for Advanced Studies, SOKENDAI
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10
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Patil S, Vicidomini G, Slenders E. Open-source 3D active sample stabilization for fluorescence microscopy. BIOPHYSICAL REPORTS 2025; 5:100208. [PMID: 40254224 PMCID: PMC12124610 DOI: 10.1016/j.bpr.2025.100208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/27/2025] [Accepted: 04/09/2025] [Indexed: 04/22/2025]
Abstract
Super-resolution microscopy has enabled imaging at nanometer-scale resolution. However, achieving this level of detail without introducing artifacts that could mislead data interpretation requires maintaining sample stability throughout the entire imaging acquisition. This process can range from a few seconds to several hours, particularly when combining live-cell imaging with super-resolution techniques. Here, we present a three-dimensional active sample stabilization system based on real-time tracking of fiducial markers. To ensure broad accessibility, the system is designed using readily available off-the-shelf optical and photonic components. Additionally, the accompanying software is open source and written in Python, facilitating adoption and customization by the community. We achieve a standard deviation of the sample movement within 1 nm in both the lateral and axial directions for a duration in the range of hours. Our approach allows easy integration into existing microscopes, not only making prolonged super-resolution microscopy more accessible but also allowing confocal and widefield live-cell imaging experiments spanning hours or even days.
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Affiliation(s)
- Sanket Patil
- Molecular Microscopy and Spectroscopy (MMS), Istituto Italiano di Tecnologia, Genoa, Italy; Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy (MMS), Istituto Italiano di Tecnologia, Genoa, Italy
| | - Eli Slenders
- Molecular Microscopy and Spectroscopy (MMS), Istituto Italiano di Tecnologia, Genoa, Italy.
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11
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Fujishiro S, Sasai M, Maeshima K. Chromatin domains in the cell: Phase separation and condensation. Curr Opin Struct Biol 2025; 91:103006. [PMID: 39983411 DOI: 10.1016/j.sbi.2025.103006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 01/25/2025] [Accepted: 01/27/2025] [Indexed: 02/23/2025]
Abstract
Negatively charged genomic DNA wraps around positively charged core histone octamers to form nucleosomes, which, along with proteins and RNAs, self-organize into chromatin within the nucleus. In eukaryotic cells, chromatin forms loops that collapse into chromatin domains and serve as functional units of the genome. Chromatin domains vary in physical properties based on gene activity and are assembled into A (euchromatin) and B (heterochromatin) compartments. Since various factors-such as chromatin-binding proteins, histone modifications, transcriptional states, depletion attraction, and cations-can significantly impact chromatin organization, the formation processes of these hierarchical structures remain unclear. No single imaging, genomics, or modeling method can provide a complete picture of the process. Beautiful models can sometimes fool our thinking. In this short review, we critically discuss the formation mechanisms of the chromatin domain in the cell from a physical point of view, including phase separation and condensation.
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Affiliation(s)
- Shin Fujishiro
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan.
| | - Masaki Sasai
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan; Department of Complex Systems Science, Nagoya University, Nagoya, 464-8603, Japan.
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan; Graduate Institute for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.
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12
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Minami K, Nakazato K, Ide S, Kaizu K, Higashi K, Tamura S, Toyoda A, Takahashi K, Kurokawa K, Maeshima K. Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells. SCIENCE ADVANCES 2025; 11:eadu8400. [PMID: 40153514 PMCID: PMC11952110 DOI: 10.1126/sciadv.adu8400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2024] [Accepted: 02/25/2025] [Indexed: 03/30/2025]
Abstract
A string of nucleosomes, where genomic DNA is wrapped around histones, is organized in the cell as chromatin, ranging from euchromatin to heterochromatin, with distinct genome functions. Understanding physical differences between euchromatin and heterochromatin is crucial, yet specific labeling methods in living cells remain limited. Here, we have developed replication-dependent histone (Repli-Histo) labeling to mark nucleosomes in euchromatin and heterochromatin based on DNA replication timing. Using this approach, we investigated local nucleosome motion in the four known chromatin classes, from euchromatin to heterochromatin, of living human and mouse cells. The more euchromatic (earlier-replicated) and more heterochromatic (later-replicated) regions exhibit greater and lesser nucleosome motions, respectively. Notably, the motion profile in each chromatin class persists throughout interphase. Genome chromatin is essentially replicated from regions with greater nucleosome motions, although the replication timing is perturbed. Our findings, combined with computational modeling, suggest that earlier-replicated regions have more accessibility, and local chromatin motion can be a major determinant of genome-wide replication timing.
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Affiliation(s)
- Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Kako Nakazato
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Kazunari Kaizu
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Cell Modeling and Simulation Group, The Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Koichi Higashi
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Takahashi
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Ken Kurokawa
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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13
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Oliveira RJ, Oliveira Junior AB, Contessoto VG, Onuchic JN. The synergy between compartmentalization and motorization in chromatin architecture. J Chem Phys 2025; 162:114116. [PMID: 40105139 DOI: 10.1063/5.0239634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 02/20/2025] [Indexed: 03/20/2025] Open
Abstract
High-resolution techniques capable of manipulating from single molecules to millions of cells are combined with three-dimensional modeling followed by simulation to comprehend the specific aspects of chromosomes. From the theoretical perspective, the energy landscape theory from protein folding inspired the development of the minimal chromatin model (MiChroM). In this work, two biologically relevant MiChroM energy terms were minimized under different conditions, revealing a competition between loci compartmentalization and motor-driven activity mechanisms in chromatin folding. Enhancing the motor activity energy baseline increased the lengthwise compaction and reduced the polymer entanglement. Concomitantly, decreasing compartmentalization-related interactions reduced the overall polymer collapse, although compartmentalization given by the microphase separation remained almost intact. For multiple chromosome simulations, increased motorization intensified the territory formation of the different chains and reduced compartmentalization strength lowered the probability of contact formation of different loci between multiple chains, approximating to the experimental inter-contacts of the human chromosomes. These findings have direct implications for experimental data-driven chromosome modeling, specially those involving multiple chromosomes. The interplay between phase-separation and territory formation mechanisms should be properly implemented in order to recover the genome architecture and dynamics, features that might play critical roles in regulating nuclear functions.
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Affiliation(s)
- Ronaldo J Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | | | - Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
- Department of Physics and Astronomy, Rice University, Houston, Texas 77030, USA
- Department of Chemistry, Rice University, Houston, Texas 77030, USA
- Department of Biosciences, Rice University, Houston, Texas 77030, USA
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14
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Acosta N, Gong R, Su Y, Frederick J, Medina KI, Li WS, Mohammadian K, Almassalha L, Wang G, Backman V. Three-color single-molecule localization microscopy in chromatin. LIGHT, SCIENCE & APPLICATIONS 2025; 14:123. [PMID: 40091134 PMCID: PMC11911409 DOI: 10.1038/s41377-025-01786-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 02/09/2025] [Accepted: 02/12/2025] [Indexed: 03/19/2025]
Abstract
Super-resolution microscopy has revolutionized our ability to visualize structures below the diffraction limit of conventional optical microscopy and is particularly useful for investigating complex biological targets like chromatin. Chromatin exhibits a hierarchical organization with structural compartments and domains at different length scales, from nanometers to micrometers. Single molecule localization microscopy (SMLM) methods, such as STORM, are essential for studying chromatin at the supra-nucleosome level due to their ability to target epigenetic marks that determine chromatin organization. Multi-label imaging of chromatin is necessary to unpack its structural complexity. However, these efforts are challenged by the high-density nuclear environment, which can affect antibody binding affinities, diffusivity and non-specific interactions. Optimizing buffer conditions, fluorophore stability, and antibody specificity is crucial for achieving effective antibody conjugates. Here, we demonstrate a sequential immunolabeling protocol that reliably enables three-color studies within the dense nuclear environment. This protocol couples multiplexed localization datasets with a robust analysis algorithm, which utilizes localizations from one target as seed points for distance, density and multi-label joint affinity measurements to explore complex organization of all three targets. Applying this multiplexed algorithm to analyze distance and joint density reveals that heterochromatin and euchromatin are not-distinct territories, but that localization of transcription and euchromatin couple with the periphery of heterochromatic clusters. This work is a crucial step in molecular imaging of the dense nuclear environment as multi-label capacity enables for investigation of complex multi-component systems like chromatin with enhanced accuracy.
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Affiliation(s)
- Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Ruyi Gong
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Yuanzhe Su
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Karla I Medina
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | - Wing Shun Li
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
- Applied Physics Program, Northwestern University, Evanston, IL, 60208, USA
| | - Kiana Mohammadian
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Luay Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA
| | - Geng Wang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA.
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15
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Uckelmann M, Levina V, Taveneau C, Ng XH, Pandey V, Martinez J, Mendiratta S, Houx J, Boudes M, Venugopal H, Trépout S, Fulcher AJ, Zhang Q, Flanigan S, Li M, Sierecki E, Gambin Y, Das PP, Bell O, de Marco A, Davidovich C. Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates. Nat Struct Mol Biol 2025; 32:520-530. [PMID: 39815045 PMCID: PMC11919719 DOI: 10.1038/s41594-024-01457-6] [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: 02/23/2023] [Accepted: 11/21/2024] [Indexed: 01/18/2025]
Abstract
The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organization and dynamics of chromatin compacted by gene-repressing factors are unknown. Here, using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the polycomb repressive complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilized through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provide a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.
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Affiliation(s)
- Michael Uckelmann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Vita Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Cyntia Taveneau
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Xiao Han Ng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Varun Pandey
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jasmine Martinez
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shweta Mendiratta
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin Houx
- EMBL Australia Node for Single Molecule Science and School of Biomedical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia
| | - Sylvain Trépout
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, Victoria, Australia
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Sarena Flanigan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Minrui Li
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- Faculty of Information Technology, Monash University, Clayton, Victoria, Australia
| | - Emma Sierecki
- EMBL Australia Node for Single Molecule Science and School of Biomedical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node for Single Molecule Science and School of Biomedical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia
| | - Partha Pratim Das
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Oliver Bell
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
- EMBL-Australia, Clayton, Victoria, Australia.
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16
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Lokesh NR, Pownall ME. Microscopy methods for the in vivo study of nanoscale nuclear organization. Biochem Soc Trans 2025; 53:BST20240629. [PMID: 39898979 DOI: 10.1042/bst20240629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 12/23/2024] [Accepted: 01/06/2025] [Indexed: 02/04/2025]
Abstract
Eukaryotic genomes are highly compacted within the nucleus and organized into complex 3D structures across various genomic and physical scales. Organization within the nucleus plays a key role in gene regulation, both facilitating regulatory interactions to promote transcription while also enabling the silencing of other genes. Despite the functional importance of genome organization in determining cell identity and function, investigating nuclear organization across this wide range of physical scales has been challenging. Microscopy provides the opportunity for direct visualization of nuclear structures and has pioneered key discoveries in this field. Nonetheless, visualization of nanoscale structures within the nucleus, such as nucleosomes and chromatin loops, requires super-resolution imaging to go beyond the ~220 nm diffraction limit. Here, we review recent advances in imaging technology and their promise to uncover new insights into the organization of the nucleus at the nanoscale. We discuss different imaging modalities and how they have been applied to the nucleus, with a focus on super-resolution light microscopy and its application to in vivo systems. Finally, we conclude with our perspective on how continued technical innovations in super-resolution imaging in the nucleus will advance our understanding of genome structure and function.
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Affiliation(s)
- Nidhi Rani Lokesh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, U.S.A
| | - Mark E Pownall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, U.S.A
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17
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Fillot T, Mazza D. Rethinking chromatin accessibility: from compaction to dynamic interactions. Curr Opin Genet Dev 2025; 90:102299. [PMID: 39705880 PMCID: PMC11793080 DOI: 10.1016/j.gde.2024.102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/02/2024] [Accepted: 12/03/2024] [Indexed: 12/23/2024]
Abstract
The genome is traditionally divided into condensed heterochromatin and open euchromatin. However, recent findings challenge this binary classification and the notion that chromatin condensation solely governs the accessibility of transcription factors (TFs) and, consequently, gene expression. Instead, chromatin accessibility is emerging as a factor-specific property that is influenced by multiple determinants. These include the mobility of the chromatin fiber, the capacity of TFs to engage repeatedly with it through multivalent interactions, and the four-dimensional organization of its surrounding diffusible space. Unraveling the molecular and biophysical principles that render a genomic target truly accessible remains a significant challenge, but innovative methods for locally perturbing chromatin, coupled with microscopy techniques that offer single-molecule sensitivity, provide an exciting experimental playground to test new hypotheses.
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Affiliation(s)
- Tom Fillot
- Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Davide Mazza
- Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy; IRCCS Ospedale San Raffaele, Experimental Imaging Center, Via Olgettina 58, 20132 Milan, Italy.
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18
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Pujadas Liwag EM, Acosta N, Almassalha LM, Su Y(P, Gong R, Kanemaki MT, Stephens AD, Backman V. Nuclear blebs are associated with destabilized chromatin-packing domains. J Cell Sci 2025; 138:jcs262161. [PMID: 39878045 PMCID: PMC11883274 DOI: 10.1242/jcs.262161] [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: 03/28/2024] [Accepted: 12/24/2024] [Indexed: 01/31/2025] Open
Abstract
Disrupted nuclear shape is associated with multiple pathological processes including premature aging disorders, cancer-relevant chromosomal rearrangements and DNA damage. Nuclear blebs (i.e. herniations of the nuclear envelope) can be induced by (1) nuclear compression, (2) nuclear migration (e.g. cancer metastasis), (3) actin contraction, (4) lamin mutation or depletion, and (5) heterochromatin enzyme inhibition. Recent work has shown that chromatin transformation is a hallmark of bleb formation, but the transformation of higher-order structures in blebs is not well understood. As higher-order chromatin has been shown to assemble into nanoscopic packing domains, we investigated whether (1) packing domain organization is altered within nuclear blebs and (2) whether alteration in packing domain structure contributed to bleb formation. Using dual-partial wave spectroscopic microscopy, we show that chromatin-packing domains within blebs are transformed both by B-type lamin depletion and the inhibition of heterochromatin enzymes compared to what is seen in the nuclear body. Pairing these results with single-molecule localization microscopy of constitutive heterochromatin, we show fragmentation of nanoscopic heterochromatin domains within bleb domains. Overall, these findings indicate that chromatin within blebs is associated with a fragmented higher-order chromatin structure.
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Affiliation(s)
- Emily M. Pujadas Liwag
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Luay Matthew Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Yuanzhe (Patrick) Su
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Ruyi Gong
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Masato T. Kanemaki
- Department of Chromosome Science, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
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19
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Li WS, Carter LM, Almassalha LM, Gong R, Pujadas-Liwag EM, Kuo T, MacQuarrie KL, Carignano M, Dunton C, Dravid V, Kanemaki MT, Szleifer I, Backman V. Mature chromatin packing domains persist after RAD21 depletion in 3D. SCIENCE ADVANCES 2025; 11:eadp0855. [PMID: 39854464 PMCID: PMC11759041 DOI: 10.1126/sciadv.adp0855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 12/20/2024] [Indexed: 01/26/2025]
Abstract
Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for TAD and loop connectivity features in Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with multiomic analysis and single-molecule localization microscopy, we study the role of cohesin in regulating the conformationally defined chromatin nanoscopic packing domains. Our results indicate that packing domains are not physical manifestation of TADs. Using electron microscopy, we found that only 20% of packing domains are lost upon RAD21 depletion. The effect of RAD21 depletion is restricted to small, poorly packed (nascent) packing domains. In addition, we present evidence that cohesin-mediated loop extrusion generates nascent domains that undergo maturation through nucleosome posttranslational modifications. Our results demonstrate that a 3D genomic structure, composed of packing domains, is generated through cohesin activity and nucleosome modifications.
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Affiliation(s)
- Wing Shun Li
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Lucas M. Carter
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Luay Matthew Almassalha
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Ruyi Gong
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Emily M. Pujadas-Liwag
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Tiffany Kuo
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Kyle L. MacQuarrie
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marcelo Carignano
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Cody Dunton
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Vinayak Dravid
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
- Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology (IIN), Northwestern University, Evanston, IL 60208, USA
| | - Masato T. Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
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20
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Wagh K, Stavreva DA, Hager GL. Transcription dynamics and genome organization in the mammalian nucleus: Recent advances. Mol Cell 2025; 85:208-224. [PMID: 39413793 PMCID: PMC11741928 DOI: 10.1016/j.molcel.2024.09.022] [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: 05/17/2024] [Revised: 07/31/2024] [Accepted: 09/19/2024] [Indexed: 10/18/2024]
Abstract
Single-molecule tracking (SMT) has emerged as the dominant technology to investigate the dynamics of chromatin-transcription factor (TF) interactions. How long a TF needs to bind to a regulatory site to elicit a transcriptional response is a fundamentally important question. However, highly divergent estimates of TF binding have been presented in the literature, stemming from differences in photobleaching correction and data analysis. TF movement is often interpreted as specific or non-specific association with chromatin, yet the dynamic nature of the chromatin polymer is often overlooked. In this perspective, we highlight how recent SMT studies have reshaped our understanding of TF dynamics, chromatin mobility, and genome organization in the mammalian nucleus, focusing on the technical details and biological implications of these approaches. In a remarkable convergence of fixed and live-cell imaging, we show how super-resolution and SMT studies of chromatin have dovetailed to provide a convincing nanoscale view of genome organization.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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21
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Almassalha LM, Carignano M, Liwag EP, Li WS, Gong R, Acosta N, Dunton CL, Gonzalez PC, Carter LM, Kakkaramadam R, Kröger M, MacQuarrie KL, Frederick J, Ye IC, Su P, Kuo T, Medina KI, Pritchard JA, Skol A, Nap R, Kanemaki M, Dravid V, Szleifer I, Backman V. Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system. SCIENCE ADVANCES 2025; 11:eadq6652. [PMID: 39792661 PMCID: PMC11721585 DOI: 10.1126/sciadv.adq6652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 12/04/2024] [Indexed: 01/12/2025]
Abstract
In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate that the human genome is an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion. We show that packing domains are not topologically associated domains. Instead, packing domains exist across a structure-function life cycle that couples heterochromatin and transcription in situ, explaining how heterochromatin enzyme inhibition can produce a paradoxical decrease in transcription by destabilizing domain cores. Applied to development and aging, we show the pairing of heterochromatin and transcription at myogenic genes that could be disrupted by nuclear swelling. In sum, packing domains represent a foundation to explore the interactions of chromatin and transcription at the single-cell level in human health.
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Affiliation(s)
- Luay M. Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Marcelo Carignano
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Emily Pujadas Liwag
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Wing Shun Li
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
| | - Ruyi Gong
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Nicolas Acosta
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Cody L. Dunton
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Paola Carrillo Gonzalez
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Lucas M. Carter
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Rivaan Kakkaramadam
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Martin Kröger
- Magnetism and Interface Physics and Computational Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Kyle L. MacQuarrie
- Stanley Manne Children’s Research Institute, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jane Frederick
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - I Chae Ye
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Patrick Su
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Tiffany Kuo
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Karla I. Medina
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Josh A Pritchard
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Andrew Skol
- Stanley Manne Children’s Research Institute, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
| | - Rikkert Nap
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Masato Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Vinayak Dravid
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
- Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology (IIN), Northwestern University, Evanston, IL 60208, USA
| | - Igal Szleifer
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
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22
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Shaban HA, Gasser SM. Dynamic 3D genome reorganization during senescence: defining cell states through chromatin. Cell Death Differ 2025; 32:9-15. [PMID: 37596440 PMCID: PMC11748698 DOI: 10.1038/s41418-023-01197-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023] Open
Abstract
Cellular senescence, a cell state characterized by growth arrest and insensitivity to growth stimulatory hormones, is accompanied by a massive change in chromatin organization. Senescence can be induced by a range of physiological signals and pathological stresses and was originally thought to be an irreversible state, implicated in normal development, wound healing, tumor suppression and aging. Recently cellular senescence was shown to be reversible in some cases, with exit being triggered by the modulation of the cell's transcriptional program by the four Yamanaka factors, the suppression of p53 or H3K9me3, PDK1, and/or depletion of AP-1. Coincident with senescence reversal are changes in chromatin organization, most notably the loss of senescence-associated heterochromatin foci (SAHF) found in oncogene-induced senescence. In addition to fixed-cell imaging, chromatin conformation capture and multi-omics have been used to examine chromatin reorganization at different spatial resolutions during senescence. They identify determinants of SAHF formation and other key features that differentiate distinct types of senescence. Not surprisingly, multiple factors, including the time of induction, the type of stress experienced, and the type of cell involved, influence the global reorganization of chromatin in senescence. Here we discuss how changes in the three-dimensional organization of the genome contribute to the regulation of transcription at different stages of senescence. In particular, the distinct contributions of heterochromatin- and lamina-mediated interactions, changes in gene expression, and other cellular control mechanisms are discussed. We propose that high-resolution temporal and spatial analyses of the chromatin landscape during senescence will identify early markers of the different senescence states to help guide clinical diagnosis.
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Affiliation(s)
- Haitham A Shaban
- Precision Oncology Center, Department of Oncology, Lausanne University Hospital, 1005, Lausanne, Switzerland.
- Agora Cancer Research Center Lausanne, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.
- Spectroscopy Department, Institute of Physics Research National Research Centre, Cairo, 33 El-Behouth St., Dokki, Giza, 12311, Egypt.
| | - Susan M Gasser
- Fondation ISREC, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
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23
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Valades-Cruz CA, Barth R, Abdellah M, Shaban HA. Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D. Nat Protoc 2025; 20:163-179. [PMID: 39198619 DOI: 10.1038/s41596-024-01038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/22/2024] [Indexed: 09/01/2024]
Abstract
To understand the dynamic nature of the genome, the localization and rearrangement of DNA and DNA-binding proteins must be analyzed across the entire nucleus of single living cells. Recently, we developed a computational light microscopy technique, called high-resolution diffusion (Hi-D) mapping, which can accurately detect, classify and map diffusion dynamics and biophysical parameters such as the diffusion constant, the anomalous exponent, drift velocity and model physical diffusion from the data at a high spatial resolution across the genome in living cells. Hi-D combines dense optical flow to detect and track local chromatin and nuclear protein motion genome-wide and Bayesian inference to characterize this local movement at nanoscale resolution. Here we present the Python implementation of Hi-D, with an option for parallelizing the calculations to run on multicore central processing units (CPUs). The functionality of Hi-D is presented to the users via user-friendly documented Python notebooks. Hi-D reduces the analysis time to less than 1 h using a multicore CPU with a single compute node. We also present different applications of Hi-D for live-imaging of DNA, histone H2B and RNA polymerase II sequences acquired with spinning disk confocal and super-resolution structured illumination microscopy.
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Affiliation(s)
- Cesar Augusto Valades-Cruz
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Roman Barth
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Marwan Abdellah
- Ecole polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Haitham A Shaban
- Spectroscopy Department, Institute of Physics Research National Research Centre, Cairo, Egypt.
- Agora Cancer Research Center, Lausanne, Switzerland.
- Precision Oncology Center, Department of Oncology Lausanne University Hospital, Lausanne, Switzerland.
- Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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24
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Wang Z, Wang B, Niu D, Yin C, Bi Y, Cattoglio C, Loh KM, Lavis LD, Ge H, Deng W. Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells. Nat Struct Mol Biol 2025; 32:125-136. [PMID: 39367253 DOI: 10.1038/s41594-024-01385-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/07/2024] [Indexed: 10/06/2024]
Abstract
Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable 'confined target search' mechanism. PTFs such as FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-PTF MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domains, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested that transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation.
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Affiliation(s)
- Zuhui Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bo Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences (CLS), Peking University, Beijing, China
| | - Di Niu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences (CLS), Peking University, Beijing, China
| | - Chao Yin
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences (CLS), Peking University, Beijing, China
| | - Ying Bi
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing, China
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Kyle M Loh
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Hao Ge
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
- Beijing International Center for Mathematical Research, Peking University, Beijing, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences (CLS), Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.
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25
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Chen L, Maristany MJ, Farr SE, Luo J, Gibson BA, Doolittle LK, Espinosa JR, Huertas J, Redding S, Collepardo-Guevara R, Rosen MK. Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.23.627571. [PMID: 39763792 PMCID: PMC11703229 DOI: 10.1101/2024.12.23.627571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2025]
Abstract
Cellular chromatin displays heterogeneous structure and dynamics, properties that control diverse nuclear processes. Models invoke phase separation of conformational ensembles of chromatin fibers as a mechanism regulating chromatin organization in vivo. Here we combine biochemistry and molecular dynamics simulations to examine, at single base-pair resolution, how nucleosome spacing controls chromatin phase separation. We show that as DNA linkers extend from 25 bp to 30 bp, as examplars of 10N+5 and 10N (integer N) bp lengths, chromatin condensates become less thermodynamically stable and nucleosome mobility increases. Simulations reveal that this is due to trade-offs between inter- and intramolecular nucleosome stacking, favored by rigid 10N+5 and 10N bp linkers, respectively. A remodeler can induce or inhibit phase separation by moving nucleosomes, changing the balance between intra- and intermolecular stacking. The intrinsic phase separation capacity of chromatin enables fine tuning of compaction and dynamics, likely contributing to heterogeneous chromatin organization in vivo.
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Affiliation(s)
- Lifeng Chen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - M. Julia Maristany
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Equal contributions
| | - Stephen E. Farr
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
- Equal contributions
| | - Jinyue Luo
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bryan A. Gibson
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Current address: Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN. 38105-3678, USA
| | - Lynda K. Doolittle
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jorge R. Espinosa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Jan Huertas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sy Redding
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Michael K. Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Marine Biological Laboratory Chromatin Collaborative, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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26
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Bairamukov VY, Ankudinov AV, Kovalev RA, Pantina RA, Grigoriev SV, Varfolomeeva EY. Chromatin condensed domains revealed by AFM, and their transformation in mechanically deformed normal and malignant cell nuclei. Biochem Biophys Res Commun 2024; 736:150861. [PMID: 39461009 DOI: 10.1016/j.bbrc.2024.150861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024]
Abstract
It has been generally accepted that heterochromatin is represented by a regular, dense and closed structure, while euchromatin is open and sparse. Recent evidence indicates that chromatin is comprised of irregular nucleosome clutches compacted within the nucleus. Transcriptional events transform the chromatin architecture, resulting in appearance of 100-300 nm nucleosomal aggregates. Meanwhile, the current paradigm of chromatin architecture is largely fragmented. In this communication, we unraveled chromatin ultrastructure of normal and malignant cell nuclei through mechanical deformation of the nuclei and Atomic Force Microscopy (AFM) analysis of the resulting landscape. In human skin fibroblasts cell nuclei, nanodomains of about 16.5-33.5 nm were revealed. Hierarchical folding of the chromatin of normal nuclei was observed: the nanodomains formed irregular fiber-like structures that coalesced into the macroscale chromatin compartments. In fibrosarcoma cell nuclei DNA supercoiling domains (SDs) of about 66.3-113.0 nm, uniformly distributed within the nuclei, were revealed. Transformation of the morphology of the condensed chromatin domains through up- and downregulation of supercoiling was demonstrated.
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Affiliation(s)
- V Yu Bairamukov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300, Gatchina, Russia; Alferov Saint Petersburg National Research Academic University of the Russian Academy of Sciences, 8/3, Khlopina St., 194021, Saint Petersburg, Russia.
| | - A V Ankudinov
- The Ioffe Physical-Technical Institute of the Russian Academy of Sciences, 26, Politekhnicheskaya, 194021, Saint Petersburg, Russia
| | - R A Kovalev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300, Gatchina, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300, Gatchina, Russia
| | - S V Grigoriev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300, Gatchina, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300, Gatchina, Russia
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27
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Frederick J, Virk RKA, Ye IC, Almassalha LM, Wodarcyk GM, VanDerway D, Gonzalez PC, Nap RJ, Agrawal V, Anthony NM, Carinato J, Li WS, Dunton CL, Medina KI, Kakkaramadam R, Jain S, Shahabi S, Ameer G, Szleifer IG, Backman V. Leveraging chromatin packing domains to target chemoevasion in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.14.623612. [PMID: 39605341 PMCID: PMC11601449 DOI: 10.1101/2024.11.14.623612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains (TADs). However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based mechanistic model that connects chromatin organization to cell fate decisions, specifically survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional efficiency through macromolecular crowding. The model accurately predicts chemoevasion in vitro, suggesting that changes in packing domains affect the likelihood of survival. Consistent results across diverse cancer types indicate that the model captures fundamental principles of chromatin-mediated adaptation, independent of the specific cancer or chemotherapy mechanisms involved. Based on these insights, we hypothesized that compounds capable of modulating packing domains, termed Transcriptional Plasticity Regulators (TPRs), could prevent cellular adaptation to chemotherapy. Using live-cell chromatin imaging, we conducted a compound screen that identified several TPRs which synergistically enhanced chemotherapy-induced cell death. The most effective TPR significantly improved therapeutic outcomes in a patient-derived xenograft (PDX) model of ovarian cancer. These findings underscore the central role of chromatin in cellular adaptation to cytotoxic stress and present a novel framework for enhancing cancer therapies, with broad potential across multiple cancer types.
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Affiliation(s)
- Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Ranya K A Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - I Chae Ye
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Luay M Almassalha
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Gastroenterology and Hepatology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Greta M Wodarcyk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - David VanDerway
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Paola Carrillo Gonzalez
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Rikkert J Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Nicholas M Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - John Carinato
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Wing Shun Li
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Cody L Dunton
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Karla I Medina
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Rivaan Kakkaramadam
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Shohreh Shahabi
- Department of Obstetrics and Gynecology, Prentice Women's Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Guillermo Ameer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Igal G Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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28
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Gupta R, Goswami Y, Yuan L, Roy B, Pereiro E, Shivashankar GV. Correlative light and soft X-ray tomography of in situ mesoscale heterochromatin structure in intact cells. Sci Rep 2024; 14:27706. [PMID: 39532928 PMCID: PMC11557596 DOI: 10.1038/s41598-024-77361-2] [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: 01/29/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024] Open
Abstract
Heterochromatin organization is critical to many genome-related programs including transcriptional silencing and DNA repair. While super-resolution imaging, electron microscopy, and multiomics methods have provided indirect insights into the heterochromatin organization, a direct measurement of mesoscale heterochromatin ultrastructure is still missing. We use a combination of correlative light microscopy and cryo-soft X-ray tomography (CLXT) to analyze heterochromatin organization in the intact hydrated state of human mammary fibroblast cells. Our analysis reveals that the heterochromatin ultra-structure has a typical mean domain size of approximately 80 nm and a mean separation of approximately 120 nm between domains. Functional perturbations yield further insights into the molecular density and alterations in the mesoscale organization of the heterochromatin regions. Furthermore, our polymer simulations provide a mechanistic basis for the experimentally observed size and separation distributions of the mesoscale chromatin domains. Collectively, our results provide direct, label-free observation of heterochromatin organization in the intact hydrated state of cells.
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Affiliation(s)
- Rajshikhar Gupta
- Laboratory of Nanoscale Biology, Paul Scherrer Institut, Villigen, Aargau, Switzerland
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Yagyik Goswami
- Laboratory of Nanoscale Biology, Paul Scherrer Institut, Villigen, Aargau, Switzerland
| | - Luezhen Yuan
- Laboratory of Nanoscale Biology, Paul Scherrer Institut, Villigen, Aargau, Switzerland
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Bibhas Roy
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Secunderabad, India
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Cerdanyola del Vallés, Barcelona, Spain
| | - G V Shivashankar
- Laboratory of Nanoscale Biology, Paul Scherrer Institut, Villigen, Aargau, Switzerland.
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.
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29
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Popenko V, Spirin P, Prassolov V, Leonova O. Chromomeres, Topologically Associating Domains and Structural Organization of Chromatin Bodies in Somatic Nuclei (Macronuclei) of Ciliates. FRONT BIOSCI-LANDMRK 2024; 29:378. [PMID: 39614448 DOI: 10.31083/j.fbl2911378] [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: 06/25/2024] [Revised: 09/25/2024] [Accepted: 10/09/2024] [Indexed: 12/01/2024]
Abstract
BACKGROUND In the twentieth century, the textbook idea of packaging genomic material in the cell nucleus and metaphase chromosomes was the presence of a hierarchy of structural levels of chromatin organization: nucleosomes - nucleosomal fibrils -30 nm fibrils - chromomeres - chromonemata - mitotic chromosomes. Chromomeres were observed in partially decondensed chromosomes and interphase chromatin as ~100 nm globular structures. They were thought to consist of loops of chromatin fibres attached at their bases to a central protein core. However, Hi-C and other related methods led to a new concept of chromatin organization in the nuclei of higher eukaryotes, according to which nucleosomal fibrils themselves determine the spatial configuration of chromatin in the form of topologically associating domains (TADs), which are formed by a loop extrusion process and are regions whose DNA sequences preferentially contact each other. Somatic macronuclei of ciliates are transcriptionally active, highly polyploid nuclei. A feature of macronuclei is that their genome is represented by a large number of "gene-sized" (~1-25 kb) or of "subchromosomal" (~50-1700 kb) size minichromosomes. The inactive macronuclear chromatin of "subchromosomal" ciliates usually looks like bodies 100-200 nm in size. The aim of this work was to find out which of the models (chromomeres or TADs) is more consistent with the confocal and electron microscopic data on structural organization of chromatin bodies. METHODS Macronuclear chromatin of four "subchromosomal" ciliate species (Bursaria truncatella, Paramecium multimicronucleatum, Didinium nasutum, Climacostomum virens) was examined using electron microscopy and confocal microscopy during regular growth, starvation and encystment. RESULTS Chromatin bodies ~70-200 nm in size observed in the interphase macronuclei consisted of tightly packed nucleosomes. Some of them were interconnected by one or more chromatin fibrils. Under hypotonic conditions in vitro, chromatin bodies decompacted, forming rosette-shaped structures of chromatin fibrils around an electron-dense centre. When the activity of the macronucleus decreased during starvation or encystment, chromatin bodies assembled into chromonema-like fibrils 100-300 nm thick. This data allows us to consider chromatin bodies as analogues of chromomeres. On the other hand, most likely, the formation of DNA loops in chromatin bodies occurs by the loop extrusion as in TADs. CONCLUSIONS The data obtained is well explained by the model, according to which the chromatin bodies of ciliate macronuclei combine features inherent in both chromomeres and TADs; that is, they can be considered as chromomeres with loops packed in the same way as the loops in TADs.
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Affiliation(s)
- Vladimir Popenko
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Precision Genome Editing and General Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Precision Genome Editing and General Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga Leonova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Maarouf A, Iqbal F, Sanaullah S, Locatelli M, Atanasiu AT, Kolbin D, Hommais C, Mühlemann JK, Bonin K, Bloom K, Liu J, Vidi PA. RAD51 regulates eukaryotic chromatin motions in the absence of DNA damage. Mol Biol Cell 2024; 35:ar136. [PMID: 39292916 PMCID: PMC11617103 DOI: 10.1091/mbc.e24-04-0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/12/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024] Open
Abstract
In yeasts and higher eukaryotes, chromatin motions may be tuned to genomic functions, with transcriptional activation and the DNA damage response both leading to profound changes in chromatin dynamics. The RAD51 recombinase is a key mediator of chromatin mobility following DNA damage. As functions of RAD51 beyond DNA repair are being discovered, we asked whether RAD51 modulates chromatin dynamics in the absence of DNA damage and found that inhibition or depletion of RAD51 alters chromatin motions in undamaged cells. Inhibition of RAD51 increased nucleosome clustering. Predictions from polymer models are that chromatin clusters reduce chain mobility and, indeed, we measured reduced motion of individual chromatin loci in cells treated with a RAD51 inhibitor. This effect was conserved in mammalian cells, yeasts, and plant cells. In contrast, RAD51 depletion or inhibition increased global chromatin motions at the microscale. The results uncover a role for RAD51 in regulating local and global chromatin dynamics independently from DNA damage and highlight the importance of considering different physical scales when studying chromatin dynamics.
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Affiliation(s)
- Amine Maarouf
- Institut de Cancérologie de l'Ouest, Angers F-49055, France
| | - Fadil Iqbal
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202
| | - Sarvath Sanaullah
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Maëlle Locatelli
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrew T. Atanasiu
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Chloé Hommais
- Institut de Cancérologie de l'Ouest, Angers F-49055, France
| | - Joëlle K. Mühlemann
- Climate Resilient Crop Production Laboratory, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit (KU) Leuven, Leuven 3000, Belgium
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jing Liu
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Pierre-Alexandre Vidi
- Institut de Cancérologie de l'Ouest, Angers F-49055, France
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
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31
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Cremer C, Schock F, Failla AV, Birk U. Modulated illumination microscopy: Application perspectives in nuclear nanostructure analysis. J Microsc 2024; 296:121-128. [PMID: 38618985 DOI: 10.1111/jmi.13297] [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: 07/04/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
The structure of the cell nucleus of higher organisms has become a major topic of advanced light microscopy. So far, a variety of methods have been applied, including confocal laser scanning fluorescence microscopy, 4Pi, STED and localisation microscopy approaches, as well as different types of patterned illumination microscopy, modulated either laterally (in the object plane) or axially (along the optical axis). Based on our experience, we discuss here some application perspectives of Modulated Illumination Microscopy (MIM) and its combination with single-molecule localisation microscopy (SMLM). For example, spatially modulated illumination microscopy/SMI (illumination modulation along the optical axis) has been used to determine the axial extension (size) of small, optically isolated fluorescent objects between ≤ 200 nm and ≥ 40 nm diameter with a precision down to the few nm range; it also allows the axial positioning of such structures down to the 1 nm scale; combined with laterally structured illumination/SIM, a 3D localisation precision of ≤1 nm is expected using fluorescence yields typical for SMLM applications. Together with the nanosizing capability of SMI, this can be used to analyse macromolecular nuclear complexes with a resolution approaching that of cryoelectron microscopy.
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Affiliation(s)
- Christoph Cremer
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
- Interdisciplinary Centre for Scientific Computing (IWR), University of Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Florian Schock
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - Udo Birk
- Institute for Photonics and Robotics (IPR), Department of Applied Future Technologies, University of Applied Sciences of the Grisons (FH Graubünden), Chur, Switzerland
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32
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Lacen A, Lee HT. Tracing the Chromatin: From 3C to Live-Cell Imaging. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:659-682. [PMID: 39483638 PMCID: PMC11523001 DOI: 10.1021/cbmi.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 11/03/2024]
Abstract
Chromatin organization plays a key role in gene regulation throughout the cell cycle. Understanding the dynamics governing the accessibility of chromatin is crucial for insight into mechanisms of gene regulation, DNA replication, and cell division. Extensive research has been done to track chromatin dynamics to explain how cells function and how diseases develop, in the hope of this knowledge leading to future therapeutics utilizing proteins or drugs that modify the accessibility or expression of disease-related genes. Traditional methods for studying the movement of chromatin throughout the cell relied on cross-linking spatially adjacent sections or hybridizing fluorescent probes to chromosomal loci and then constructing dynamic models from the static data collected at different time points. While these traditional methods are fruitful in understanding fundamental aspects of chromatin organization, they are limited by their invasive sample preparation protocols and diffraction-limited microscope resolution. These limitations have been challenged by modern methods based on high- or super-resolution microscopy and specific labeling techniques derived from gene targeting tools. These modern methods are more sensitive and less invasive than traditional methods, therefore allowing researchers to track chromosomal organization, compactness, and even the distance or rate of chromatin domain movement in detail and real time. This review highlights a selection of recently developed methods of chromatin tracking and their applications in fixed and live cells.
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Affiliation(s)
- Arianna
N. Lacen
- Department of Chemistry, The
University of Alabama at Birmingham, 901 14th Street South, CHEM 274, Birmingham, Alabama 35294-1240, United States
| | - Hui-Ting Lee
- Department of Chemistry, The
University of Alabama at Birmingham, 901 14th Street South, CHEM 274, Birmingham, Alabama 35294-1240, United States
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33
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Dasgupta N, Arnold R, Equey A, Gandhi A, Adams PD. The role of the dynamic epigenetic landscape in senescence: orchestrating SASP expression. NPJ AGING 2024; 10:48. [PMID: 39448585 PMCID: PMC11502686 DOI: 10.1038/s41514-024-00172-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/24/2024] [Indexed: 10/26/2024]
Abstract
Senescence and epigenetic alterations stand out as two well-characterized hallmarks of aging. When cells become senescent, they cease proliferation and release inflammatory molecules collectively termed the Senescence-Associated Secretory Phenotype (SASP). Senescence and SASP are implicated in numerous age-related diseases. Senescent cell nuclei undergo epigenetic reprogramming, which intricately regulates SASP expression. This review outlines the current understanding of how senescent cells undergo epigenetic changes and how these alterations govern SASP expression.
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Affiliation(s)
- Nirmalya Dasgupta
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
| | - Rouven Arnold
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anais Equey
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Armin Gandhi
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Peter D Adams
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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Chu FY, Clavijo AS, Lee S, Zidovska A. Transcription-dependent mobility of single genes and genome-wide motions in live human cells. Nat Commun 2024; 15:8879. [PMID: 39438437 PMCID: PMC11496510 DOI: 10.1038/s41467-024-51149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/31/2024] [Indexed: 10/25/2024] Open
Abstract
The human genome is highly dynamic across all scales. At the gene level, chromatin is persistently remodeled and rearranged during active processes such as transcription, replication and DNA repair. At the genome level, chromatin moves in micron-scale domains that break up and re-form over seconds, but the origin of these coherent motions is unknown. Here, we investigate the connection between genomic motions and gene-level activity. Simultaneous mapping of single-gene and genome-wide motions shows that the coupling of gene transcriptional activity to flows of the nearby genome is modulated by chromatin compaction. A motion correlation analysis suggests that a single active gene drives larger-scale motions in low-compaction regions, but high-compaction chromatin drives gene motion regardless of its activity state. By revealing unexpected connections among gene activity, spatial heterogeneities of chromatin and its emergent genome-wide motions, these findings uncover aspects of the genome's spatiotemporal organization that directly impact gene regulation and expression.
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Affiliation(s)
- Fang-Yi Chu
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexis S Clavijo
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Suho Lee
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA.
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35
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Carignano MA, Kroeger M, Almassalha LM, Agrawal V, Li WS, Pujadas-Liwag EM, Nap RJ, Backman V, Szleifer I. Local volume concentration, packing domains, and scaling properties of chromatin. eLife 2024; 13:RP97604. [PMID: 39331520 PMCID: PMC11434620 DOI: 10.7554/elife.97604] [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] [Indexed: 09/29/2024] Open
Abstract
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally defined domains observed by single-cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as RAD21 degradation.
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Affiliation(s)
- Marcelo A Carignano
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Martin Kroeger
- Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH ZurichZurichSwitzerland
| | - Luay M Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial HospitalEvanstonUnited States
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Wing Shun Li
- Applied Physics Program, Northwestern UniversityChicagoUnited States
| | | | - Rikkert J Nap
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
- Department of Chemistry, Northwestern UniversityEvanstonUnited States
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36
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Labade AS, Chiang ZD, Comenho C, Reginato PL, Payne AC, Earl AS, Shrestha R, Duarte FM, Habibi E, Zhang R, Church GM, Boyden ES, Chen F, Buenrostro JD. Expansion in situ genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614614. [PMID: 39386718 PMCID: PMC11463693 DOI: 10.1101/2024.09.24.614614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Microscopy and genomics are both used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. While emerging multiplexed imaging methods can simultaneously localize genomic regions and nuclear proteins, their ability to accurately measure DNA-protein interactions is constrained by the diffraction limit of optical microscopy. Here, we describe expansion in situ genome sequencing (ExIGS), a technology that enables sequencing of genomic DNA and superresolution localization of nuclear proteins in single cells. We applied ExIGS to fibroblast cells derived from an individual with Hutchinson-Gilford progeria syndrome to characterize how variation in nuclear morphology affects spatial chromatin organization. Using this data, we discovered that lamin abnormalities are linked to hotspots of aberrant euchromatin repression that may erode cell identity. Further, we show that lamin abnormalities heterogeneously increase the repressive environment of the nucleus in tissues and aged cells. These results demonstrate that ExIGS may serve as a generalizable platform for connecting nuclear abnormalities to changes in gene regulation across disease contexts.
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37
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Naas J, Nies G, Li H, Stoldt S, Schmitzer B, Jakobs S, Munk A. MultiMatch: geometry-informed colocalization in multi-color super-resolution microscopy. Commun Biol 2024; 7:1139. [PMID: 39271907 PMCID: PMC11399439 DOI: 10.1038/s42003-024-06772-8] [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: 02/28/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
With recent advances in multi-color super-resolution light microscopy, it is possible to simultaneously visualize multiple subunits within biological structures at nanometer resolution. To optimally evaluate and interpret spatial proximity of stainings on such an image, colocalization analysis tools have to be able to integrate prior knowledge on the local geometry of the recorded biological complex. We present MultiMatch to analyze the abundance and location of chain-like particle arrangements in multi-color microscopy based on multi-marginal optimal unbalanced transport methodology. Our object-based colocalization model statistically addresses the effect of incomplete labeling efficiencies enabling inference on existent, but not fully observable particle chains. We showcase that MultiMatch is able to consistently recover existing chain structures in three-color STED images of DNA origami nanorulers and outperforms geometry-uninformed triplet colocalization methods in this task. MultiMatch generalizes to an arbitrary number of color channels and is provided as a user-friendly Python package comprising colocalization visualizations.
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Affiliation(s)
- Julia Naas
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Giacomo Nies
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Housen Li
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Stefan Stoldt
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Bernhard Schmitzer
- Institute for Computer Science, University of Göttingen, Göttingen, Germany
| | - Stefan Jakobs
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy TNM, Göttingen, Germany
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
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Iida S, Ide S, Tamura S, Sasai M, Tani T, Goto T, Shribak M, Maeshima K. Orientation-independent-DIC imaging reveals that a transient rise in depletion attraction contributes to mitotic chromosome condensation. Proc Natl Acad Sci U S A 2024; 121:e2403153121. [PMID: 39190347 PMCID: PMC11388287 DOI: 10.1073/pnas.2403153121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/19/2024] [Indexed: 08/28/2024] Open
Abstract
Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion attraction/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using an orientation-independent-differential interference contrast module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prophase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like. These results suggest that a transient rise in depletion attraction, likely triggered by the relocation of macromolecules (proteins, RNAs, and others) via nuclear envelope breakdown and by a subsequent decrease in cell volumes, contributes to mitotic chromosome condensation, shedding light on a different aspect of the condensation mechanism in living human cells.
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Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka411-8540, Japan
- Graduate Institute for Advanced Studies (SOKENDAI), Mishima, Shizuoka411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka411-8540, Japan
- Graduate Institute for Advanced Studies (SOKENDAI), Mishima, Shizuoka411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka411-8540, Japan
| | - Masaki Sasai
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto606-8103, Japan
- Department of Complex Systems Science, Nagoya University, Nagoya464-8603, Japan
| | - Tomomi Tani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka563-8577, Japan
| | - Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido080-8555, Japan
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido080-8555, Japan
| | | | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka411-8540, Japan
- Graduate Institute for Advanced Studies (SOKENDAI), Mishima, Shizuoka411-8540, Japan
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Yang SH, Zeng YZ, Jia XZ, Gu YW, Wood C, Yang RS, Yang JS, Yang WJ. Activated dormant stem cells recover spermatogenesis in chemoradiotherapy-induced infertility. Cell Rep 2024; 43:114582. [PMID: 39096488 DOI: 10.1016/j.celrep.2024.114582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/23/2024] [Accepted: 07/18/2024] [Indexed: 08/05/2024] Open
Abstract
Male infertility is a recognized side effect of chemoradiotherapy. Extant spermatogonial stem cells (SSCs) may act as originators for any subsequent recovery. However, which type of SSCs, the mechanism by which they survive and resist toxicity, and how they act to restart spermatogenesis remain largely unknown. Here, we identify a small population of Set domain-containing protein 4 (Setd4)-expressing SSCs that occur in a relatively dormant state in the mouse seminiferous tubule. Extant beyond high-dose chemoradiotherapy, these cells then activate to recover spermatogenesis. Recovery fails when Setd4+ SSCs are deleted. Confirmed to be of fetal origin, these Setd4+ SSCs are shown to facilitate early testicular development and also contribute to steady-state spermatogenesis in adulthood. Upon activation, chromatin remodeling increases their genome-wide accessibility, enabling Notch1 and Aurora activation with corresponding silencing of p21 and p53. Here, Setd4+ SSCs are presented as the originators of both testicular development and spermatogenesis recovery in chemoradiotherapy-induced infertility.
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Affiliation(s)
- Shu-Hua Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi-Zhe Zeng
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xi-Zheng Jia
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Gu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Christopher Wood
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ri-Sheng Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jin-Shu Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei-Jun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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40
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Hibino K, Sakai Y, Tamura S, Takagi M, Minami K, Natsume T, Shimazoe MA, Kanemaki MT, Imamoto N, Maeshima K. Single-nucleosome imaging unveils that condensins and nucleosome-nucleosome interactions differentially constrain chromatin to organize mitotic chromosomes. Nat Commun 2024; 15:7152. [PMID: 39169041 PMCID: PMC11339268 DOI: 10.1038/s41467-024-51454-y] [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: 07/05/2023] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
For accurate mitotic cell division, replicated chromatin must be assembled into chromosomes and faithfully segregated into daughter cells. While protein factors like condensin play key roles in this process, it is unclear how chromosome assembly proceeds as molecular events of nucleosomes in living cells and how condensins act on nucleosomes to organize chromosomes. To approach these questions, we investigate nucleosome behavior during mitosis of living human cells using single-nucleosome tracking, combined with rapid-protein depletion technology and computational modeling. Our results show that local nucleosome motion becomes increasingly constrained during mitotic chromosome assembly, which is functionally distinct from condensed apoptotic chromatin. Condensins act as molecular crosslinkers, locally constraining nucleosomes to organize chromosomes. Additionally, nucleosome-nucleosome interactions via histone tails constrain and compact whole chromosomes. Our findings elucidate the physical nature of the chromosome assembly process during mitosis.
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Affiliation(s)
- Kayo Hibino
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Yuji Sakai
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Toyoaki Natsume
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Masato T Kanemaki
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
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41
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Rahman F, Augoustides V, Tyler E, Daugird TA, Arthur C, Legant WR. Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.27.605159. [PMID: 39211261 PMCID: PMC11360932 DOI: 10.1101/2024.07.27.605159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The nucleus coordinates many different processes. Visualizing how these are spatially organized requires imaging protein complexes, epigenetic marks, and DNA across scales from single molecules to the whole nucleus. To accomplish this, we developed a multiplexed imaging protocol to localize 13 different nuclear targets with nanometer precision in single cells. We show that nuclear specification into active and repressive states exists along a spectrum of length scales, emerging below one micron and becoming strengthened at the nanoscale with unique organizational principles in both heterochromatin and euchromatin. HP1-α was positively correlated with DNA at the microscale but uncorrelated at the nanoscale. RNA Polymerase II, p300, and CDK9 were positively correlated at the microscale but became partitioned below 300 nm. Perturbing histone acetylation or transcription disrupted nanoscale organization but had less effect at the microscale. We envision that our imaging and analysis pipeline will be useful to reveal the organizational principles not only of the cell nucleus but also other cellular compartments.
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42
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Uckelmann M, Levina V, Taveneau C, Ng XH, Pandey V, Martinez J, Mendiratta S, Houx J, Boudes M, Venugopal H, Trépout S, Zhang Q, Flanigan S, Li M, Sierecki E, Gambin Y, Das PP, Bell O, de Marco A, Davidovich C. Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.08.539931. [PMID: 38405976 PMCID: PMC10888862 DOI: 10.1101/2023.05.08.539931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions (IDRs) of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.
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43
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Pabba MK, Meyer J, Celikay K, Schermelleh L, Rohr K, Cardoso MC. DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes. Histochem Cell Biol 2024; 162:109-131. [PMID: 38758428 PMCID: PMC11227476 DOI: 10.1007/s00418-024-02285-x] [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: 03/27/2024] [Indexed: 05/18/2024]
Abstract
The dynamics of DNA in the cell nucleus plays a role in cellular processes and fates but the interplay of DNA mobility with the hierarchical levels of DNA organization is still underexplored. Here, we made use of DNA replication to directly label genomic DNA in an unbiased genome-wide manner. This was followed by live-cell time-lapse microscopy of the labeled DNA combining imaging at different resolutions levels simultaneously and allowing one to trace DNA motion across organization levels within the same cells. Quantification of the labeled DNA segments at different microscopic resolution levels revealed sizes comparable to the ones reported for DNA loops using 3D super-resolution microscopy, topologically associated domains (TAD) using 3D widefield microscopy, and also entire chromosomes. By employing advanced chromatin tracking and image registration, we discovered that DNA exhibited higher mobility at the individual loop level compared to the TAD level and even less at the chromosome level. Additionally, our findings indicate that chromatin movement, regardless of the resolution, slowed down during the S phase of the cell cycle compared to the G1/G2 phases. Furthermore, we found that a fraction of DNA loops and TADs exhibited directed movement with the majority depicting constrained movement. Our data also indicated spatial mobility differences with DNA loops and TADs at the nuclear periphery and the nuclear interior exhibiting lower velocity and radius of gyration than the intermediate locations. On the basis of these insights, we propose that there is a link between DNA mobility and its organizational structure including spatial distribution, which impacts cellular processes.
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Affiliation(s)
- Maruthi K Pabba
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Janis Meyer
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany
| | - Kerem Celikay
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany
| | | | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany.
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
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44
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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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45
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Semeigazin A, Iida S, Minami K, Tamura S, Ide S, Higashi K, Toyoda A, Kurokawa K, Maeshima K. Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells. Histochem Cell Biol 2024; 162:23-40. [PMID: 38743310 DOI: 10.1007/s00418-024-02293-x] [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: 04/21/2024] [Indexed: 05/16/2024]
Abstract
Since Robert Feulgen first stained DNA in the cell, visualizing genome chromatin has been a central issue in cell biology to uncover how chromatin is organized and behaves in the cell. To approach this issue, we have developed single-molecule imaging of nucleosomes, a basic unit of chromatin, to unveil local nucleosome behavior in living cells. In this study, we investigated behaviors of nucleosomes with various histone H4 mutants in living HeLa cells to address the role of H4 tail acetylation, including H4K16Ac and others, which are generally associated with more transcriptionally active chromatin regions. We ectopically expressed wild-type (wt) or mutated H4s (H4K16 point; H4K5,8,12,16 quadruple; and H4 tail deletion) fused with HaloTag in HeLa cells. Cells that expressed wtH4-Halo, H4K16-Halo mutants, and multiple H4-Halo mutants had euchromatin-concentrated distribution. Consistently, the genomic regions of the wtH4-Halo nucleosomes corresponded to Hi-C contact domains (or topologically associating domains, TADs) with active chromatin marks (A-compartment). Utilizing single-nucleosome imaging, we found that none of the H4 deacetylation or acetylation mimicked H4 mutants altered the overall local nucleosome motion. This finding suggests that H4 mutant nucleosomes embedded in the condensed euchromatic domains with excess endogenous H4 nucleosomes cannot cause an observable change in the local motion. Interestingly, H4 with four lysine-to-arginine mutations displayed a substantial freely diffusing fraction in the nucleoplasm, whereas H4 with a truncated N-terminal tail was incorporated in heterochromatic regions as well as euchromatin. Our study indicates the power of single-nucleosome imaging to understand individual histone/nucleosome behavior reflecting chromatin environments in living cells.
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Affiliation(s)
- Adilgazy Semeigazin
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Koichi Higashi
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ken Kurokawa
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
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46
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Salari H, Fourel G, Jost D. Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization. Nat Commun 2024; 15:5393. [PMID: 38918438 PMCID: PMC11199603 DOI: 10.1038/s41467-024-49727-7] [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: 07/24/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
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Affiliation(s)
- Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007, Lyon, France.
| | - Geneviève Fourel
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
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47
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Hsiao YT, Liao IH, Wu BK, Chu HPC, Hsieh CL. Probing chromatin condensation dynamics in live cells using interferometric scattering correlation spectroscopy. Commun Biol 2024; 7:763. [PMID: 38914653 PMCID: PMC11196589 DOI: 10.1038/s42003-024-06457-2] [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: 11/24/2023] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
Chromatin organization and dynamics play important roles in governing the regulation of nuclear processes of biological cells. However, due to the constant diffusive motion of chromatin, examining chromatin nanostructures in living cells has been challenging. In this study, we introduce interferometric scattering correlation spectroscopy (iSCORS) to spatially map nanoscopic chromatin configurations within unlabeled live cell nuclei. This label-free technique captures time-varying linear scattering signals generated by the motion of native chromatin on a millisecond timescale, allowing us to deduce chromatin condensation states. Using iSCORS imaging, we quantitatively examine chromatin dynamics over extended periods, revealing spontaneous fluctuations in chromatin condensation and heterogeneous compaction levels in interphase cells, independent of cell phases. Moreover, we observe changes in iSCORS signals of chromatin upon transcription inhibition, indicating that iSCORS can probe nanoscopic chromatin structures and dynamics associated with transcriptional activities. Our scattering-based optical microscopy, which does not require labeling, serves as a powerful tool for visualizing dynamic chromatin nano-arrangements in live cells. This advancement holds promise for studying chromatin remodeling in various crucial cellular processes, such as stem cell differentiation, mechanotransduction, and DNA repair.
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Affiliation(s)
- Yi-Teng Hsiao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - I-Hsin Liao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Bo-Kuan Wu
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | | | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan.
- Department of Physics, National Taiwan University, Taipei, Taiwan.
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48
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Carignano M, Kröger M, Almassalha LM, Agrawal V, Li WS, Pujadas-Liwag EM, Nap RJ, Backman V, Szleifer I. Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin. ARXIV 2024:arXiv:2310.02257v3. [PMID: 38495560 PMCID: PMC10942481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally-defined domains observed by single cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as Rad21 degradation.
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Affiliation(s)
- Marcelo Carignano
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Martin Kröger
- Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Luay Matthew Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago IL 60611, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Wing Shun Li
- Applied Physics Program, Northwestern, University, Evanston, IL 60208, USA
| | | | - Rikkert J. Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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49
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Shim AR, Frederick J, Pujadas EM, Kuo T, Ye IC, Pritchard JA, Dunton CL, Gonzalez PC, Acosta N, Jain S, Anthony NM, Almassalha LM, Szleifer I, Backman V. Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure. PLoS One 2024; 19:e0301000. [PMID: 38805476 PMCID: PMC11132451 DOI: 10.1371/journal.pone.0301000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/10/2024] [Indexed: 05/30/2024] Open
Abstract
As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.
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Affiliation(s)
- Anne R. Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Emily M. Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Tiffany Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - I. Chae Ye
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Joshua A. Pritchard
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Cody L. Dunton
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Paola Carrillo Gonzalez
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicholas M. Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, United States of America
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Chemistry, Northwestern University, Evanston, Illinois, United States of America
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
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50
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Kant A, Guo Z, Vinayak V, Neguembor MV, Li WS, Agrawal V, Pujadas E, Almassalha L, Backman V, Lakadamyali M, Cosma MP, Shenoy VB. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nat Commun 2024; 15:4338. [PMID: 38773126 PMCID: PMC11109243 DOI: 10.1038/s41467-024-48698-z] [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: 04/24/2023] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, histone modifications, and chromatin extrusion. We predict that the size of heterochromatic domains is governed by a balance among the diffusive flux of methylated histones sustaining them and the acetylation reactions in the domains and the process of loop extrusion via supercoiling by RNAPII at their periphery, which contributes to size reduction. Super-resolution and nano-imaging of five distinct cell lines confirm the predictions indicating that the absence of transcription leads to larger heterochromatin domains. Furthermore, the model accurately reproduces the findings regarding how transcription-mediated supercoiling loss can mitigate the impacts of excessive cohesin loading. Our findings shed light on the role of transcription in genome organization, offering insights into chromatin dynamics and potential therapeutic targets.
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Affiliation(s)
- Aayush Kant
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zixian Guo
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vinayak Vinayak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Wing Shun Li
- Department of Applied Physics, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Vasundhara Agrawal
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Emily Pujadas
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Luay Almassalha
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA
| | - Vadim Backman
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- ICREA, Barcelona, 08010, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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