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Boettiger A, Murphy S. Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends Genet 2020; 36:273-287. [PMID: 32007290 PMCID: PMC7197267 DOI: 10.1016/j.tig.2019.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022]
Abstract
It is now widely appreciated that the spatial organization of the genome is nonrandom, and its complex 3D folding has important consequences for many genome processes. Recent developments in multiplexed, super-resolution microscopy have enabled an unprecedented view of the polymeric structure of chromatin - from the loose folds of whole chromosomes to the detailed loops of cis-regulatory elements that regulate gene expression. Facilitated by the use of robotics, microfluidics, and improved approaches to super-resolution, thousands to hundreds of thousands of individual cells can now be analyzed in an individual experiment. This has led to new insights into the nature of genomic structural features identified by sequencing, such as topologically associated domains (TADs), and the nature of enhancer-promoter interactions underlying transcriptional regulation. We review these recent improvements.
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Affiliation(s)
- Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Sedona Murphy
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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52
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Heterogeneous fluid-like movements of chromatin and their implications to transcription. Biophys Rev 2020; 12:461-468. [PMID: 32206982 DOI: 10.1007/s12551-020-00675-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/02/2020] [Indexed: 01/10/2023] Open
Abstract
Eukaryotic chromatin is a complex of genome DNA and associated proteins, and its structure and dynamics play a crucial role in regulating DNA functions. Chromatin takes rather irregular structures in the nucleus and exhibits heterogeneous sub-diffusive movements as polymers fluctuating in a fluid state. Using genome-wide single-nucleosome tracking data, heterogeneity of movements was statistically analyzed, which categorized chromatin into two types: slow chromatin that moves under structurally constrained environments and fast chromatin that moves with less constraints. Interactions of chromatin to various protein factors determine the motional constraints. For example, loss of the cohesin complex that bundles the chromatin chains reduces the motional constraints and increases the population of fast chromatin. Another example is the transcriptional machinery. While it was previously thought that the transcriptional activity is associated with more open and dynamic chromatin structure, recent studies suggested a more nuanced role of transcription in chromatin dynamics: dynamic association/dissociation of active RNA polymerase II (RNAPII) and other transcription factors and Mediators (TF-Meds) transiently bridges transcriptionally active DNA regions, which forms a loose network of chromatin and constrains chromatin movement, enhancing the slow chromatin population. This new view on the dynamical effects of transcription urges a reflection on the traditional model of transcription factories and invites the more recent models of condensates/phase-separated liquid droplets of RNAPII, transcription factors, and Mediators. The combined procedure of genome-wide single-nucleosome tracking and its statistical analysis would unveil heterogeneity in the chromatin movement, which should provide a key to understanding the relations among chromatin dynamics, structure, and function.
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53
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McCord RP, Kaplan N, Giorgetti L. Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function. Mol Cell 2020; 77:688-708. [PMID: 32001106 PMCID: PMC7134573 DOI: 10.1016/j.molcel.2019.12.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapidly developing technologies have recently fueled an exciting era of discovery in the field of chromosome structure and nuclear organization. In addition to chromosome conformation capture (3C) methods, new alternative techniques have emerged to study genome architecture and biological processes in the nucleus, often in single or living cells. This sets an unprecedented stage for exploring the mechanisms that link chromosome structure and biological function. Here we review popular as well as emerging approaches to study chromosome organization, focusing on the contribution of complementary methodologies to our understanding of structures revealed by 3C methods and their biological implications, and discuss the next technical and conceptual frontiers.
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Affiliation(s)
- Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Noam Kaplan
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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54
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Oshidari R, Mekhail K, Seeber A. Mobility and Repair of Damaged DNA: Random or Directed? Trends Cell Biol 2020; 30:144-156. [DOI: 10.1016/j.tcb.2019.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/24/2022]
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55
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Babokhov M, Hibino K, Itoh Y, Maeshima K. Local Chromatin Motion and Transcription. J Mol Biol 2020; 432:694-700. [DOI: 10.1016/j.jmb.2019.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/07/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
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56
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Ashwin SS, Nozaki T, Maeshima K, Sasai M. Organization of fast and slow chromatin revealed by single-nucleosome dynamics. Proc Natl Acad Sci U S A 2019; 116:19939-19944. [PMID: 31527274 PMCID: PMC6778247 DOI: 10.1073/pnas.1907342116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Understanding chromatin organization and dynamics is important, since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bimodal nature of the mean square displacement distribution of nucleosomes allows for a natural categorization of the nucleosomes as fast and slow. Analyses of the nucleosome-nucleosome correlation functions within these categories along with the density of vibrational modes show that the nucleosomes form dynamically correlated fluid regions (i.e., dynamic domains of fast and slow nucleosomes). Perturbed nucleosome dynamics by global histone acetylation or cohesin inactivation indicate that nucleosome-nucleosome interactions along with tethering of chromatin chains organize nucleosomes into fast and slow dynamic domains. A simple polymer model is introduced, which shows the consistency of this dynamic domain picture. Statistical analyses of single-nucleosome movement provide rich information on how chromatin is dynamically organized in a fluid manner in living cells.
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Affiliation(s)
- S S Ashwin
- Department of Applied Physics, Nagoya University, Nagoya 464-8603, Japan
| | - Tadasu Nozaki
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI, Shizuoka 411-8540, Japan
| | - Masaki Sasai
- Department of Applied Physics, Nagoya University, Nagoya 464-8603, Japan;
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57
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Maeshima K, Ide S, Babokhov M. Dynamic chromatin organization without the 30-nm fiber. Curr Opin Cell Biol 2019; 58:95-104. [DOI: 10.1016/j.ceb.2019.02.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 12/24/2022]
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58
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Polymer coil-globule phase transition is a universal folding principle of Drosophila epigenetic domains. Epigenetics Chromatin 2019; 12:28. [PMID: 31084607 PMCID: PMC6515630 DOI: 10.1186/s13072-019-0269-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/06/2019] [Indexed: 01/02/2023] Open
Abstract
Background Localized functional domains within chromosomes, known as topologically associating domains (TADs), have been recently highlighted. In Drosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the “missing link” between epigenetics and gene activity. Recent observations (Boettiger et al. in Nature 529(7586):418–422, 2016) provide access to structural features of these domains with unprecedented resolution thanks to super-resolution experiments. In particular, they give access to the distribution of the radii of gyration for domains of different linear length and associated with different transcriptional activity states: active, inactive or repressed. Intriguingly, the observed scaling laws lack consistent interpretation in polymer physics. Results We develop a new methodology conceived to extract the best information from such super-resolution data by exploiting the whole distribution of gyration radii, and to place these experimental results on a theoretical framework. We show that the experimental data are compatible with the finite-size behavior of a self-attracting polymer. The same generic polymer model leads to quantitative differences between active, inactive and repressed domains. Active domains behave as pure polymer coils, while inactive and repressed domains both lie at the coil–globule crossover. For the first time, the “color-specificity” of both the persistence length and the mean interaction energy are estimated, leading to important differences between epigenetic states. Conclusion These results point toward a crucial role of criticality to enhance the system responsivity, resulting in both energy transitions and structural rearrangements. We get strong indications that epigenetically induced changes in nucleosome–nucleosome interaction can cause chromatin to shift between different activity states. Electronic supplementary material The online version of this article (10.1186/s13072-019-0269-6) contains supplementary material, which is available to authorized users.
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59
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Wright RHG, Le Dily F, Beato M. ATP, Mg 2+, Nuclear Phase Separation, and Genome Accessibility. Trends Biochem Sci 2019; 44:565-574. [PMID: 31072688 DOI: 10.1016/j.tibs.2019.03.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/13/2019] [Accepted: 03/07/2019] [Indexed: 12/23/2022]
Abstract
Misregulation of the processes controlling eukaryotic gene expression can result in disease. Gene expression is influenced by the surrounding chromatin; hence the nuclear environment is also of vital importance. Recently, understanding of chromatin hierarchical folding has increased together with the discovery of membrane-less organelles which are distinct, dynamic liquid droplets that merge and expand within the nucleus. These 'sieve'-like regions may compartmentalize and separate functionally distinct regions of chromatin. This article aims to discuss recent studies on nuclear phase within the context of poly(ADP-ribose), ATP, and Mg2+ levels, and we propose a combinatorial complex role for these molecules in phase separation and genome regulation. We also discuss the implications of this process for gene regulation and discuss possible strategies to test this.
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Affiliation(s)
- Roni H G Wright
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Francois Le Dily
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
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60
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Nagashima R, Hibino K, Ashwin SS, Babokhov M, Fujishiro S, Imai R, Nozaki T, Tamura S, Tani T, Kimura H, Shribak M, Kanemaki MT, Sasai M, Maeshima K. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J Cell Biol 2019; 218:1511-1530. [PMID: 30824489 PMCID: PMC6504897 DOI: 10.1083/jcb.201811090] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
When a gene is activated, chromatin in the transcribed region is thought to be more open and dynamic. However, Nagashima et al. found that this is not necessarily the case—inhibition of transcription globally increases chromatin motion, revealing the existence of loose genome chromatin networks via transcriptional machinery. Although chromatin organization and dynamics play a critical role in gene transcription, how they interplay remains unclear. To approach this issue, we investigated genome-wide chromatin behavior under various transcriptional conditions in living human cells using single-nucleosome imaging. While transcription by RNA polymerase II (RNAPII) is generally thought to need more open and dynamic chromatin, surprisingly, we found that active RNAPII globally constrains chromatin movements. RNAPII inhibition or its rapid depletion released the chromatin constraints and increased chromatin dynamics. Perturbation experiments of P-TEFb clusters, which are associated with active RNAPII, had similar results. Furthermore, chromatin mobility also increased in resting G0 cells and UV-irradiated cells, which are transcriptionally less active. Our results demonstrated that chromatin is globally stabilized by loose connections through active RNAPII, which is compatible with models of classical transcription factories or liquid droplet formation of transcription-related factors. Together with our computational modeling, we propose the existence of loose chromatin domain networks for various intra-/interchromosomal contacts via active RNAPII clusters/droplets.
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Affiliation(s)
- Ryosuke Nagashima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - Kayo Hibino
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - S S Ashwin
- Department of Applied Physics, Nagoya University, Nagoya, Japan.,Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan
| | - Michael Babokhov
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Shin Fujishiro
- Department of Applied Physics, Nagoya University, Nagoya, Japan.,Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan
| | - Ryosuke Imai
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - Tadasu Nozaki
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Tomomi Tani
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Michael Shribak
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA
| | - Masato T Kanemaki
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan.,Molecular Cell Engineering Laboratory, National Institute of Genetics, ROIS, Mishima, Japan
| | - Masaki Sasai
- Department of Applied Physics, Nagoya University, Nagoya, Japan.,Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan .,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
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61
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Put S, Sakaue T, Vanderzande C. Active dynamics and spatially coherent motion in chromosomes subject to enzymatic force dipoles. Phys Rev E 2019; 99:032421. [PMID: 30999440 DOI: 10.1103/physreve.99.032421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motorlike enzymes. The enzymes can bind and unbind to specific sites of the polymer and produce a dipolar force on two neighboring monomers when bound. We study the resulting nonequilibrium dynamics of the polymer and find that the motion of the monomers has several properties that were observed experimentally for chromosomal loci: a subdiffusive mean-square displacement and the appearance of regions of correlated motion. We also determine the velocity autocorrelation of the monomers and find that the underlying stochastic process is not fractional Brownian motion. Finally, we show that the active forces swell the polymer by an amount that becomes constant for large polymers.
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Affiliation(s)
- Stefanie Put
- Faculty of Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Takahiro Sakaue
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Carlo Vanderzande
- Faculty of Sciences, Hasselt University, 3590 Diepenbeek, Belgium
- Institute for Theoretical Physics, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
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62
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Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes. Proc Natl Acad Sci U S A 2018; 115:7753-7758. [PMID: 29987017 PMCID: PMC6065008 DOI: 10.1073/pnas.1806297115] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleus of a eukaryotic cell is a nonequilibrium system where chromatin is subjected to active processes that continuously rearrange it over the cell's life cycle. Tracking the motion of chromosomal loci provides information about the organization of the genome and the physical processes shaping that organization. Optical experiments report that loci move with subdiffusive dynamics and that there is spatially coherent motion of the chromatin. We recently showed that it is possible to predict the 3D architecture of genomes through a physical model for chromosomes that accounts for the biochemical interactions mediated by proteins and regulated by epigenetic markers through a transferable energy landscape. Here, we study the temporal dynamics generated by this quasi-equilibrium energy landscape assuming Langevin dynamics at an effective temperature. Using molecular dynamics simulations of two interacting human chromosomes, we show that the very same interactions that account for genome architecture naturally reproduce the spatial coherence, viscoelasticity, and the subdiffusive behavior of the motion in interphase chromosomes as observed in numerous experiments. The agreement between theory and experiments suggests that even if active processes are involved, an effective quasi-equilibrium landscape model can largely mimic their dynamical effects.
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63
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Sen O, Saurin AT, Higgins JMG. The live cell DNA stain SiR-Hoechst induces DNA damage responses and impairs cell cycle progression. Sci Rep 2018; 8:7898. [PMID: 29785044 PMCID: PMC5962532 DOI: 10.1038/s41598-018-26307-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022] Open
Abstract
SiR-Hoechst (SiR-DNA) is a far-red fluorescent DNA probe being used widely for time-lapse imaging of living cells that is reported to be minimally toxic at concentrations as high as 10-25 µM. However, measuring nuclear import of Cyclin B1, inhibition of mitotic entry, and the induction of γH2AX foci in cultured human cells reveals that SiR-Hoechst induces DNA damage responses and G2 arrest at concentrations well below 1 µM. SiR-Hoechst is useful for live cell imaging, but it should be used with caution and at the lowest practicable concentration.
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Affiliation(s)
- Onur Sen
- Cell Division Biology Group, Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Adrian T Saurin
- Division of Cancer Research, School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Jonathan M G Higgins
- Cell Division Biology Group, Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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