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Kaur U, Muñoz EN, Narlikar GJ. Hexasomal particles: consequence or also consequential? Curr Opin Genet Dev 2024; 85:102163. [PMID: 38412564 DOI: 10.1016/j.gde.2024.102163] [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: 09/21/2023] [Revised: 12/07/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
It is long known that an RNA polymerase transcribing through a nucleosome can generate subnucleosomal particles called hexasomes. These particles lack an H2A-H2B dimer, breaking the symmetry of a nucleosome and revealing new interfaces. Whether hexasomes are simply a consequence of RNA polymerase action or they also have a regulatory impact remains an open question. Recent biochemical and structural studies of RNA polymerases and chromatin remodelers with hexasomes motivated us to revisit this question. Here, we build on previous models to discuss how formation of hexasomes can allow sophisticated regulation of transcription and also significantly impact chromatin folding. We anticipate that further cellular and biochemical analysis of these subnucleosomal particles will uncover additional regulatory roles.
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Affiliation(s)
- Upneet Kaur
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Biophysics Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Elise N Muñoz
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
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2
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Mierke CT. Extracellular Matrix Cues Regulate Mechanosensing and Mechanotransduction of Cancer Cells. Cells 2024; 13:96. [PMID: 38201302 PMCID: PMC10777970 DOI: 10.3390/cells13010096] [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: 11/12/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Extracellular biophysical properties have particular implications for a wide spectrum of cellular behaviors and functions, including growth, motility, differentiation, apoptosis, gene expression, cell-matrix and cell-cell adhesion, and signal transduction including mechanotransduction. Cells not only react to unambiguously mechanical cues from the extracellular matrix (ECM), but can occasionally manipulate the mechanical features of the matrix in parallel with biological characteristics, thus interfering with downstream matrix-based cues in both physiological and pathological processes. Bidirectional interactions between cells and (bio)materials in vitro can alter cell phenotype and mechanotransduction, as well as ECM structure, intentionally or unintentionally. Interactions between cell and matrix mechanics in vivo are of particular importance in a variety of diseases, including primarily cancer. Stiffness values between normal and cancerous tissue can range between 500 Pa (soft) and 48 kPa (stiff), respectively. Even the shear flow can increase from 0.1-1 dyn/cm2 (normal tissue) to 1-10 dyn/cm2 (cancerous tissue). There are currently many new areas of activity in tumor research on various biological length scales, which are highlighted in this review. Moreover, the complexity of interactions between ECM and cancer cells is reduced to common features of different tumors and the characteristics are highlighted to identify the main pathways of interaction. This all contributes to the standardization of mechanotransduction models and approaches, which, ultimately, increases the understanding of the complex interaction. Finally, both the in vitro and in vivo effects of this mechanics-biology pairing have key insights and implications for clinical practice in tumor treatment and, consequently, clinical translation.
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Affiliation(s)
- Claudia Tanja Mierke
- Biological Physics Division, Peter Debye Institute of Soft Matter Physics, Faculty of Physics and Earth Science, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
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3
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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4
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Thuma J, Chung YC, Tu LC. Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization. Front Mol Biosci 2023; 10:1173545. [PMID: 37065447 PMCID: PMC10102487 DOI: 10.3389/fmolb.2023.1173545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Nuclear chromosome compaction is non-random and dynamic. The spatial distance among genomic elements instantly modulates transcription. Visualization of the genome organization in the cell nucleus is essential to understand nuclear function. In addition to cell type-dependent organization, high-resolution 3D imaging shows heterogeneous compaction of chromatin organization among the same cell type. Questions remain to be answered if these structural variations were the snapshots of dynamic organization at different time points and if they are functionally different. Live-cell imaging has provided unique insights into dynamic genome organization at short (milliseconds) and long (hours) time scales. The recent development of CRISPR-based imaging opened windows for studying dynamic chromatin organization in single cells in real time. Here we highlight these CRISPR-based imaging techniques and discuss their advances and challenges as a powerful live-cell imaging method that poses high potential to generate paradigm-shifting discoveries and reveal functional implications of dynamic chromatin organization.
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Affiliation(s)
- Jenna Thuma
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, United States
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
| | - Li-Chun Tu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
- *Correspondence: Li-Chun Tu,
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5
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Wang Y, Stormberg T, Hashemi M, Kolomeisky AB, Lyubchenko YL. Beyond Sequence: Internucleosomal Interactions Dominate Array Assembly. J Phys Chem B 2022; 126:10813-10821. [PMID: 36516875 DOI: 10.1021/acs.jpcb.2c05321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The organization of the nucleosome array is a critical component of the chromatin assembly into higher order structure as well as its function. Here, we investigated the contributions of the DNA sequence and internucleosomal interactions on the organization of the nucleosomal arrays in compact structures using atomic force microscopy. We assembled nucleosomes on DNA substrates allowing for the formation of tetranucleosomes. We found that nucleosomes are capable of close positioning with no discernible space between them, even in the case of assembled dinucleosomes. This morphology of the array is in contrast with that observed for arrays assembled with repeats of the nucleosome positioning motifs separated by uniform spacers. Simulated assembly of tetranucleosomes by random placement along the substrates revealed that nucleosome array compaction is promoted by the interaction of the nucleosomes. We developed a theoretical model to account for the role of DNA sequence and internucleosomal interactions in the formation of the nucleosome structures. These findings suggest that, in the chromatin assembly, the affinity of the nucleosomes to the DNA sequence and the strengths of the internucleosomal interactions are the two major factors defining the compactness of the chromatin.
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Affiliation(s)
- Yaqing Wang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.,Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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6
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Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin. Biochem Soc Trans 2022; 50:199-212. [PMID: 35166326 PMCID: PMC9847230 DOI: 10.1042/bst20210959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/30/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023]
Abstract
Defining the genome-wide chromatin landscape has been a goal of experimentalists for decades. Here we review highlights of these efforts, from seminal experiments showing discontinuities in chromatin structure related to gene activation to extensions of these methods elucidating general features of chromatin related to gene states by exploiting deep sequencing methods. We also review chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.
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7
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Laghmach R, Di Pierro M, Potoyan DA. The interplay of chromatin phase separation and lamina interactions in nuclear organization. Biophys J 2021; 120:5005-5017. [PMID: 34653387 DOI: 10.1016/j.bpj.2021.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
The genetic material of eukaryotes is segregated into transcriptionally active euchromatin and silent heterochromatin compartments. The spatial arrangement of chromatin compartments evolves over the course of cellular life in a process that remains poorly understood. The latest nuclear imaging experiments reveal a number of dynamical signatures of chromatin that are reminiscent of active multiphase liquids. This includes the observations of viscoelastic response, coherent motions, Ostwald ripening, and coalescence of chromatin compartments. There is also growing evidence that liquid-liquid phase separation of protein and nucleic acid components is the underlying mechanism for the dynamical behavior of chromatin. To dissect the organizational and dynamical implications of chromatin's liquid behavior, we have devised a phenomenological field-theoretic model of the nucleus as a multiphase condensate of liquid chromatin types. Employing the liquid chromatin model of the Drosophila nucleus, we have carried out an extensive set of simulations with an objective to shed light on the dynamics and chromatin patterning observed in the latest nuclear imaging experiments. Our simulations reveal the emergence of experimentally detected mesoscale chromatin channels and spheroidal droplets which arise from the dynamic interplay of chromatin type to type interactions and intermingling of chromosomal territories. We also quantitatively reproduce coherent motions of chromatin domains observed in displacement correlation spectroscopy measurements which are explained within the framework of our model by phase separation of chromatin types operating within constrained intrachromosomal and interchromosomal boundaries. Finally, we illuminate the role of heterochromatin-lamina interactions in the nuclear organization by showing that these interactions enhance the mobility of euchromatin and indirectly introduce correlated motions of heterochromatin droplets.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, Iowa.
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, Iowa; Department of Biochemistry and Molecular Biology, Ames, Iowa; Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa.
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8
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Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA. Engineering nucleosomes for generating diverse chromatin assemblies. Nucleic Acids Res 2021; 49:e52. [PMID: 33590100 PMCID: PMC8136823 DOI: 10.1093/nar/gkab070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/09/2021] [Accepted: 02/04/2021] [Indexed: 01/01/2023] Open
Abstract
Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.
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Affiliation(s)
- Zenita Adhireksan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Deepti Sharma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Phoi Leng Lee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Qiuye Bao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sivaraman Padavattan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Wayne K Shum
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Gabriela E Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Curt A Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
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9
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Sartsanga C, Phengchat R, Fukui K, Wako T, Ohmido N. Surface structures consisting of chromatin fibers in isolated barley (Hordeum vulgare) chromosomes revealed by helium ion microscopy. Chromosome Res 2021; 29:81-94. [PMID: 33615407 DOI: 10.1007/s10577-021-09649-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
The chromosome compaction of chromatin fibers results in the formation of the nucleosome, which consists of a DNA unit coiled around a core of histone molecules associated with linker histone. The compaction of chromatin fibers has been a topic of controversy since the discovery of chromosomes in the 19th century. Although chromatin fibers were first identified using electron microscopy, the chromatin fibers on the surface of chromosome structures in plants remain unclear due to shrinking and breaking caused by prior chromosome isolation or preparation with alcohol and acid fixation, and critical point drying occurred into dehydration and denatured chromosomal proteins. This study aimed to develop a high-quality procedure for the isolation and preparation of plant chromosomes, maintaining the native chromosome structure, to elucidate the organization of chromatin fibers on the surface of plant chromosomes by electron microscopy. A simple technique to isolate intact barley (Hordeum vulgare) chromosomes with a high yield was developed, allowing chromosomes to be observed with a high-resolution scanning ion microscopy and helium ion microscopy (HIM) imaging technology, based on a scanning helium ion beam. HIM images from the surface chromatin fibers were analyzed to determine the size and alignment of the chromatin fibers. The unit size of the chromatin fibers was 11.6 ± 3.5 nm and was closely aligned to the chromatin network model. Our findings indicate that compacting the surface structure of barley via a chromatin network and observation via HIM are powerful tools for investigating the structure of chromatin.
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Affiliation(s)
- Channarong Sartsanga
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Rinyaporn Phengchat
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshiyuki Wako
- Institute of Crop Sciences, National Agriculture and Food Research Organization, 2-1-1 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan.
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10
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Zidovska A. The rich inner life of the cell nucleus: dynamic organization, active flows, and emergent rheology. Biophys Rev 2020; 12:1093-1106. [PMID: 33064286 PMCID: PMC7575674 DOI: 10.1007/s12551-020-00761-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
The cell nucleus stores the genetic material essential for life, and provides the environment for transcription, maintenance, and replication of the genome. Moreover, the nucleoplasm is filled with subnuclear bodies such as nucleoli that are responsible for other vital functions. Overall, the nucleus presents a highly heterogeneous and dynamic environment with diverse functionality. Here, we propose that its biophysical complexity can be organized around three inter-related and interactive facets: heterogeneity, activity, and rheology. Most nuclear constituents are sites of active, ATP-dependent processes and are thus inherently dynamic: The genome undergoes constant rearrangement, the nuclear envelope flickers and fluctuates, nucleoli migrate and coalesce, and many of these events are mediated by nucleoplasmic flows and interactions. And yet there is spatiotemporal organization in terms of hierarchical structure of the genome, its coherently moving regions and membrane-less compartmentalization via phase-separated nucleoplasmic constituents. Moreover, the non-equilibrium or activity-driven nature of the nucleus gives rise to emergent rheology and material properties that impact all cellular processes via the central dogma of molecular biology. New biophysical insights into the cell nucleus can come from appreciating this rich inner life.
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Affiliation(s)
- Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, USA.
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