51
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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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52
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Hurst V, Shimada K, Gasser SM. Nuclear Actin and Actin-Binding Proteins in DNA Repair. Trends Cell Biol 2019; 29:462-476. [PMID: 30954333 DOI: 10.1016/j.tcb.2019.02.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/27/2022]
Abstract
Nuclear actin has been implicated in a variety of DNA-related processes including chromatin remodeling, transcription, replication, and DNA repair. However, the mechanistic understanding of actin in these processes has been limited, largely due to a lack of research tools that address the roles of nuclear actin specifically, that is, distinct from its cytoplasmic functions. Recent findings support a model for homology-directed DNA double-strand break (DSB) repair in which a complex of ARP2 and ARP3 (actin-binding proteins 2 and 3) binds at the break and works with actin to promote DSB clustering and homology-directed repair. Further, it has been reported that relocalization of heterochromatic DSBs to the nuclear periphery in Drosophila is ARP2/3 dependent and actin-myosin driven. Here we provide an overview of the role of nuclear actin and actin-binding proteins in DNA repair, critically evaluating the experimental tools used and potential indirect effects.
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Affiliation(s)
- Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, CH-4056 Basel, Switzerland
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, CH-4056 Basel, Switzerland.
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53
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Ma H, Tu LC, Chung YC, Naseri A, Grunwald D, Zhang S, Pederson T. Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. J Cell Biol 2019; 218:1467-1477. [PMID: 30846483 PMCID: PMC6504907 DOI: 10.1083/jcb.201807162] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 02/08/2023] Open
Abstract
In contrast to the well-studied condensation and folding of chromosomes during mitosis, their dynamics during interphase are less understood. We deployed a CRISPR-based DNA imaging system to track the dynamics of genomic loci situated kilobases to megabases apart on a single chromosome. Two distinct modes of dynamics were resolved: local movements as well as ones that might reflect translational movements of the entire domain within the nucleoplasmic space. The magnitude of both of these modes of movements increased from early to late G1, whereas the translational movements were reduced in early S phase. The local fluctuations decreased slightly in early S and more markedly in mid-late S. These newly observed movements and their cell cycle dependence suggest the existence of a hitherto unrecognized compaction-relaxation dynamic of the interphase chromosome fiber, operating concurrently with changes in the extent of overall movements of loci in the 4D genome.
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Affiliation(s)
- Hanhui Ma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Li-Chun Tu
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA
| | - Yu-Chieh Chung
- Kavli Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwa, Japan
| | - Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, FL
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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54
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Waterman DP, Zhou F, Li K, Lee CS, Tsabar M, Eapen VV, Mazzella A, Haber JE. Live cell monitoring of double strand breaks in S. cerevisiae. PLoS Genet 2019; 15:e1008001. [PMID: 30822309 PMCID: PMC6415866 DOI: 10.1371/journal.pgen.1008001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/13/2019] [Accepted: 02/01/2019] [Indexed: 11/19/2022] Open
Abstract
We have used two different live-cell fluorescent protein markers to monitor the formation and localization of double-strand breaks (DSBs) in budding yeast. Using GFP derivatives of the Rad51 recombination protein or the Ddc2 checkpoint protein, we find that cells with three site-specific DSBs, on different chromosomes, usually display 2 or 3 foci that may coalesce and dissociate. This motion is independent of Rad52 and microtubules. Rad51-GFP, by itself, is unable to repair DSBs by homologous recombination in mitotic cells, but is able to form foci and allow repair when heterozygous with a wild type Rad51 protein. The kinetics of formation and disappearance of a Rad51-GFP focus parallels the completion of site-specific DSB repair. However, Rad51-GFP is proficient during meiosis when homozygous, similar to rad51 “site II” mutants that can bind single-stranded DNA but not complete strand exchange. Rad52-RFP and Rad51-GFP co-localize to the same DSB, but a significant minority of foci have Rad51-GFP without visible Rad52-RFP. We conclude that co-localization of foci in cells with 3 DSBs does not represent formation of a homologous recombination “repair center,” as the same distribution of Ddc2-GFP foci was found in the absence of the Rad52 protein. Double strand breaks (DSBs) pose the greatest threat to the fidelity of an organism’s genome. While much work has been done on the mechanisms of DSB repair, the arrangement and interaction of multiple DSBs within a single cell remain unclear. Using two live-cell fluorescent DSB markers, we show that cells with 3 site-specific DSBs usually form 2 or 3 foci that can may coalesce into fewer foci but also dissociate. The aggregation and mobility of DSBs into a single focus does not depend on the Rad52 recombination protein that is required for various mechanisms of homologous recombination, suggesting that merging of DSBs does not reflect formation of a homologous recombination repair center.
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Affiliation(s)
- David P. Waterman
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Felix Zhou
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Kevin Li
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Cheng-Sheng Lee
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael Tsabar
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Vinay V. Eapen
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Allison Mazzella
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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55
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Klein HL, Bačinskaja G, Che J, Cheblal A, Elango R, Epshtein A, Fitzgerald DM, Gómez-González B, Khan SR, Kumar S, Leland BA, Marie L, Mei Q, Miné-Hattab J, Piotrowska A, Polleys EJ, Putnam CD, Radchenko EA, Saada AA, Sakofsky CJ, Shim EY, Stracy M, Xia J, Yan Z, Yin Y, Aguilera A, Argueso JL, Freudenreich CH, Gasser SM, Gordenin DA, Haber JE, Ira G, Jinks-Robertson S, King MC, Kolodner RD, Kuzminov A, Lambert SAE, Lee SE, Miller KM, Mirkin SM, Petes TD, Rosenberg SM, Rothstein R, Symington LS, Zawadzki P, Kim N, Lisby M, Malkova A. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. MICROBIAL CELL (GRAZ, AUSTRIA) 2019; 6:1-64. [PMID: 30652105 PMCID: PMC6334234 DOI: 10.15698/mic2019.01.664] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/29/2018] [Accepted: 09/14/2018] [Indexed: 12/29/2022]
Abstract
Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L. Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Giedrė Bačinskaja
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jun Che
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Anais Cheblal
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Rajula Elango
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Anastasiya Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Devon M. Fitzgerald
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Belén Gómez-González
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Sharik R. Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Léa Marie
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Qian Mei
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Judith Miné-Hattab
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France
- Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France
| | - Alicja Piotrowska
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | | | - Christopher D. Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
| | | | - Anissia Ait Saada
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France
- University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405, Orsay, France
| | - Cynthia J. Sakofsky
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Mathew Stracy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jun Xia
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Zhenxin Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yi Yin
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA
| | - Andrés Aguilera
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Catherine H. Freudenreich
- Department of Biology, Tufts University, Medford, MA USA
- Program in Genetics, Tufts University, Boston, MA, USA
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA
| | | | - Richard D. Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sarah AE Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France
- University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405, Orsay, France
| | - Sang Eun Lee
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Kyle M. Miller
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Thomas D. Petes
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA
| | - Susan M. Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Lorraine S. Symington
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Pawel Zawadzki
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA, USA
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56
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Abstract
Recent advances in both the technologies used to measure chromatin movement and the biophysical analysis used to model them have yielded a fuller understanding of chromatin dynamics and the polymer structure that underlies it. Changes in nucleosome packing, checkpoint kinase activation, the cell cycle, chromosomal tethers, and external forces acting on nuclei in response to external and internal stimuli can alter the basal mobility of DNA in interphase nuclei of yeast or mammalian cells. Although chromatin movement is assumed to be necessary for many DNA-based processes, including gene activation by distal enhancer–promoter interaction or sequence-based homology searches during double-strand break repair, experimental evidence supporting an essential role in these activities is sparse. Nonetheless, high-resolution tracking of chromatin dynamics has led to instructive models of the higher-order folding and flexibility of the chromatin polymer. Key regulators of chromatin motion in physiological conditions or after damage induction are reviewed here.
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Affiliation(s)
- Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
- Current affiliation: Harvard Center for Advanced Imaging, Cambridge, MA 02138, USA
| | - Michael H. Hauer
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
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57
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Amitai A, Holcman D. Encounter times of chromatin loci influenced by polymer decondensation. Phys Rev E 2018; 97:032417. [PMID: 29776075 DOI: 10.1103/physreve.97.032417] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Indexed: 12/24/2022]
Abstract
The time for a DNA sequence to find its homologous counterpart depends on a long random search inside the cell nucleus. Using polymer models, we compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined locally by potential wells. We find that reducing tethering forces acting on the polymers results in local decondensation, and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude. We derive here new asymptotic formula for the MFET, confirmed by Brownian simulations. We conclude from the present modeling approach that the fast search for homology is mediated by a local chromatin decondensation due to the release of multiple chromatin tethering forces. The present scenario could explain how the homologous recombination pathway for double-stranded DNA repair is controlled by its random search step.
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Affiliation(s)
- A Amitai
- Department of Chemical Engineering and Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge 02139, Massachusetts, USA
| | - D Holcman
- Group of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, 75005 Paris, France
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58
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Smith MJ, Bryant EE, Rothstein R. Increased chromosomal mobility after DNA damage is controlled by interactions between the recombination machinery and the checkpoint. Genes Dev 2018; 32:1242-1251. [PMID: 30181361 PMCID: PMC6120718 DOI: 10.1101/gad.317966.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/02/2018] [Indexed: 12/20/2022]
Abstract
In this study, Smith et al. investigated how cells modulate chromosome mobility in response to DNA damage. They show that global chromosome mobility is regulated by the Rad51 recombinase and its mediator, Rad52, and their findings indicate that interplay between recombination factors and the checkpoint restricts increased mobility until recombination proteins are assembled at damaged sites. During homologous recombination, cells must coordinate repair, DNA damage checkpoint signaling, and movement of chromosomal loci to facilitate homology search. In Saccharomyces cerevisiae, increased movement of damaged loci (local mobility) and undamaged loci (global mobility) precedes homolog pairing in mitotic cells. How cells modulate chromosome mobility in response to DNA damage remains unclear. Here, we demonstrate that global chromosome mobility is regulated by the Rad51 recombinase and its mediator, Rad52. Surprisingly, rad51Δ rad52Δ cells display checkpoint-dependent constitutively increased mobility, indicating that a regulatory circuit exists between recombination and checkpoint machineries to govern chromosomal mobility. We found that the requirement for Rad51 in this circuit is distinct from its role in recombination and that interaction with Rad52 is necessary to alleviate inhibition imposed by mediator recruitment to ssDNA. Thus, interplay between recombination factors and the checkpoint restricts increased mobility until recombination proteins are assembled at damaged sites.
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Affiliation(s)
- Michael J Smith
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Eric E Bryant
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
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59
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Shi G, Liu L, Hyeon C, Thirumalai D. Interphase human chromosome exhibits out of equilibrium glassy dynamics. Nat Commun 2018; 9:3161. [PMID: 30089831 PMCID: PMC6082855 DOI: 10.1038/s41467-018-05606-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/05/2018] [Indexed: 01/01/2023] Open
Abstract
Fingerprints of the three-dimensional organization of genomes have emerged using advances in Hi-C and imaging techniques. However, genome dynamics is poorly understood. Here, we create the chromosome copolymer model (CCM) by representing chromosomes as a copolymer with two epigenetic loci types corresponding to euchromatin and heterochromatin. Using novel clustering techniques, we establish quantitatively that the simulated contact maps and topologically associating domains (TADs) for chromosomes 5 and 10 and those inferred from Hi-C experiments are in good agreement. Chromatin exhibits glassy dynamics with coherent motion on micron scale. The broad distribution of the diffusion exponents of the individual loci, which quantitatively agrees with experiments, is suggestive of highly heterogeneous dynamics. This is reflected in the cell-to-cell variations in the contact maps. Chromosome organization is hierarchical, involving the formation of chromosome droplets (CDs) on genomic scale, coinciding with the TAD size, followed by coalescence of the CDs, reminiscent of Ostwald ripening.
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Affiliation(s)
- Guang Shi
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
| | - Lei Liu
- Korea Institute for Advanced Study, Seoul, 02455, Republic of Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul, 02455, Republic of Korea
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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60
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Wong MM, Belew MD, Kwieraga A, Nhan JD, Michael WM. Programmed DNA Breaks Activate the Germline Genome in Caenorhabditis elegans. Dev Cell 2018; 46:302-315.e5. [PMID: 30086301 DOI: 10.1016/j.devcel.2018.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 06/03/2018] [Accepted: 07/01/2018] [Indexed: 12/15/2022]
Abstract
In Caenorhabditis elegans, the primordial germ cells Z2 and Z3 are born during early embryogenesis and then held in a transcriptionally quiescent state where the genome is highly compacted. When hatched L1s feed, the germline genome decompacts, and RNAPII is abruptly and globally activated. A previously documented yet unexplained feature of germline genome activation in the worm is the appearance of numerous DNA breaks coincident with RNAPII transcription. Here, we show that the DNA breaks are induced by topoisomerase II and that they function to recruit the RUVB complex to chromosomes so that RUVB can decompact the chromatin. DNA break- and RUVB-mediated decompaction is required for zygotic genome activation. This work highlights the importance of global chromatin decompaction in the rapid induction of gene expression and shows that one way cells achieve global decompaction is through programmed DNA breaks.
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Affiliation(s)
- Matthew M Wong
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Mezmur D Belew
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Amanda Kwieraga
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - James D Nhan
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - W Matthew Michael
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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61
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Caridi CP, D'Agostino C, Ryu T, Zapotoczny G, Delabaere L, Li X, Khodaverdian VY, Amaral N, Lin E, Rau AR, Chiolo I. Nuclear F-actin and myosins drive relocalization of heterochromatic breaks. Nature 2018; 559:54-60. [PMID: 29925946 PMCID: PMC6051730 DOI: 10.1038/s41586-018-0242-8] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 05/18/2018] [Indexed: 12/13/2022]
Abstract
Heterochromatin mainly comprises repeated DNA sequences that are prone to ectopic recombination. In Drosophila cells, 'safe' repair of heterochromatic double-strand breaks by homologous recombination relies on the relocalization of repair sites to the nuclear periphery before strand invasion. The mechanisms responsible for this movement were unknown. Here we show that relocalization occurs by directed motion along nuclear actin filaments assembled at repair sites by the Arp2/3 complex. Relocalization requires nuclear myosins associated with the heterochromatin repair complex Smc5/6 and the myosin activator Unc45, which is recruited to repair sites by Smc5/6. ARP2/3, actin nucleation and myosins also relocalize heterochromatic double-strand breaks in mouse cells. Defects in this pathway result in impaired heterochromatin repair and chromosome rearrangements. These findings identify de novo nuclear actin filaments and myosins as effectors of chromatin dynamics for heterochromatin repair and stability in multicellular eukaryotes.
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Affiliation(s)
- Christopher P Caridi
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Carla D'Agostino
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Taehyun Ryu
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Grzegorz Zapotoczny
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Laetitia Delabaere
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Xiao Li
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Varandt Y Khodaverdian
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Nuno Amaral
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Karolinska Institute, Stockholm, Sweden
| | - Emily Lin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Alesandra R Rau
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Irene Chiolo
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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62
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Cremer T, Cremer M, Cremer C. The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context. BIOCHEMISTRY (MOSCOW) 2018; 83:313-325. [PMID: 29626919 DOI: 10.1134/s000629791804003x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.
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Affiliation(s)
- T Cremer
- Biocenter, Department of Biology II, Ludwig Maximilian University (LMU), Munich, Germany.
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63
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Zimmer C, Fabre E. Chromatin mobility upon DNA damage: state of the art and remaining questions. Curr Genet 2018; 65:1-9. [DOI: 10.1007/s00294-018-0852-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022]
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64
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Poli J, Gasser SM, Papamichos-Chronakis M. The INO80 remodeller in transcription, replication and repair. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0290. [PMID: 28847827 DOI: 10.1098/rstb.2016.0290] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Montpellier and Centre de Recherche en Biologie Cellulaire (CRBM), UMR5237, CNRS, Montpellier 34095, Cedex 5, France
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland .,Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Manolis Papamichos-Chronakis
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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65
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Caridi CP, Delabaere L, Tjong H, Hopp H, Das D, Alber F, Chiolo I. Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. Methods Enzymol 2018. [PMID: 29523239 DOI: 10.1016/bs.mie.2017.11.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Heterochromatin is mostly composed of long stretches of repeated DNA sequences prone to ectopic recombination during double-strand break (DSB) repair. In Drosophila, "safe" homologous recombination (HR) repair of heterochromatic DSBs relies on a striking relocalization of repair sites to the nuclear periphery. Central to understanding heterochromatin repair is the ability to investigate the 4D dynamics (movement in space and time) of repair sites. A specific challenge of these studies is preventing phototoxicity and photobleaching effects while imaging the sample over long periods of time, and with sufficient time points and Z-stacks to track repair foci over time. Here we describe an optimized approach for high-resolution live imaging of heterochromatic DSBs in Drosophila cells, with a specific emphasis on the fluorescent markers and imaging setup used to capture the motion of repair foci over long-time periods. We detail approaches that minimize photobleaching and phototoxicity with a DeltaVision widefield deconvolution microscope, and image processing techniques for signal recovery postimaging using SoftWorX and Imaris software. We present a method to derive mean square displacement curves revealing some of the biophysical properties of the motion. Finally, we describe a method in R to identify tracts of directed motions (DMs) in mixed trajectories. These approaches enable a deeper understanding of the mechanisms of heterochromatin dynamics and genome stability in the three-dimensional context of the nucleus and have broad applicability in the field of nuclear dynamics.
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Affiliation(s)
| | | | - Harianto Tjong
- University of Southern California, Los Angeles, CA, United States
| | - Hannah Hopp
- University of Southern California, Los Angeles, CA, United States
| | - Devika Das
- University of Southern California, Los Angeles, CA, United States
| | - Frank Alber
- University of Southern California, Los Angeles, CA, United States
| | - Irene Chiolo
- University of Southern California, Los Angeles, CA, United States.
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66
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Abstract
Chromatin is organized into higher-order structures that form subcompartments in interphase nuclei. Different categories of specialized enzymes act on chromatin and regulate its compaction and biophysical characteristics in response to physiological conditions. We present an overview of the function of chromatin structure and its dynamic changes in response to genotoxic stress, focusing on both subnuclear organization and the physical mobility of DNA. We review the requirements and mechanisms that cause chromatin relocation, enhanced mobility, and chromatin unfolding as a consequence of genotoxic lesions. An intriguing link has been established recently between enhanced chromatin dynamics and histone loss.
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Affiliation(s)
- Michael H Hauer
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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67
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Amitai A. Chromatin Configuration Affects the Dynamics and Distribution of a Transiently Interacting Protein. Biophys J 2018; 114:766-771. [PMID: 29395046 DOI: 10.1016/j.bpj.2017.12.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/13/2017] [Accepted: 12/27/2017] [Indexed: 01/20/2023] Open
Affiliation(s)
- Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts; Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts.
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68
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Shukron O, Hauer M, Holcman D. Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration. Sci Rep 2017; 7:10346. [PMID: 28871173 PMCID: PMC5583259 DOI: 10.1038/s41598-017-10842-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/15/2017] [Indexed: 11/16/2022] Open
Abstract
Stochastic single particle trajectories are used to explore the local chromatin organization. We present here a statistical analysis of the first contact time distributions between two tagged loci recorded experimentally. First, we extract the association and dissociation times from data for various genomic distances between loci, and we show that the looping time occurs in confined nanometer regions. Second, we characterize the looping time distribution for two loci in the presence of multiple DNA damages. Finally, we construct a polymer model, that accounts for the local chromatin organization before and after a double-stranded DNA break (DSB), to estimate the level of chromatin decompaction. This novel passage time statistics method allows extracting transient dynamic at scales varying from one to few hundreds of nanometers, it predicts the local changes in the number of binding molecules following DSB and can be used to characterize the local dynamic of the chromatin.
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Affiliation(s)
- Ofir Shukron
- Applied Mathematics and Computational Biology, Ecole Normale Supérieure, IBENS, 46 rue d'Ulm, 75005, Paris, France
| | - Michael Hauer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - David Holcman
- Applied Mathematics and Computational Biology, Ecole Normale Supérieure, IBENS, 46 rue d'Ulm, 75005, Paris, France. .,Mathematical Institute, University of Oxford, Oxford, OX2 6GG, United Kingdom.
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69
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Miné-Hattab J, Recamier V, Izeddin I, Rothstein R, Darzacq X. Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage. Mol Biol Cell 2017; 28:mbc.E17-05-0317. [PMID: 28794266 PMCID: PMC5687033 DOI: 10.1091/mbc.e17-05-0317] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/21/2017] [Accepted: 08/02/2017] [Indexed: 12/19/2022] Open
Abstract
The dynamic organization of genes inside the nucleus is an important determinant for their function. Using fast DNA tracking microscopy in S. cerevisiae cells and improved analysis of mean square displacements, we quantified DNA motion at time scales ranging from 10 milliseconds to minute and found that following DNA damage, DNA exhibits distinct sub-diffusive regimes. In response to double-strand breaks, chromatin is more mobile at large time scales but, surprisingly, its mobility is reduced at short time scales. This effect is even more pronounced at the site of damage. Such a pattern of dynamics is consistent with a global increase in chromatin persistence length in response to DNA damage. Scale-dependent nuclear exploration is regulated by the Rad51 repair protein, both at the break and throughout the genome. We propose a model in which stiffening of the damaged ends by the repair complex, combined with global increased stiffness, act like a "needle in a ball of yarn", enhancing the ability of the break to traverse the chromatin meshwork.
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Affiliation(s)
- Judith Miné-Hattab
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
- Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA
- Nuclear Dynamics, CNRS UMR 3664, Institut Curie, Paris 75005, France
| | - Vincent Recamier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
| | - Ignacio Izeddin
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
- Institut Langevin, CNRS, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xavier Darzacq
- Division of Genetics, Genomics & Development, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
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70
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Shukron O, Holcman D. Statistics of randomly cross-linked polymer models to interpret chromatin conformation capture data. Phys Rev E 2017; 96:012503. [PMID: 29347098 DOI: 10.1103/physreve.96.012503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Indexed: 06/07/2023]
Abstract
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a statistical analysis of the randomly cross-linked (RCL) polymer model, where monomer pairs are connected randomly, generating a heterogeneous ensemble of chromatin conformations. We obtain asymptotic formulas for the steady-state variance, encounter probability, the radius of gyration, instantaneous displacement, and the mean first encounter time between any two monomers. The analytical results are confirmed by Brownian simulations. Finally, the present results are used to extract the mean number of cross links in a chromatin region from conformation capture data.
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Affiliation(s)
- O Shukron
- Group of Applied Mathematics and Computational Biology, IBENS, Ecole Normale Supérieure, 46 rue d'Ulm 75005 Paris, France
| | - D Holcman
- Group of Applied Mathematics and Computational Biology, IBENS, Ecole Normale Supérieure, 46 rue d'Ulm 75005 Paris, France
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71
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Shinkai S, Nozaki T, Maeshima K, Togashi Y. Bridging the dynamics and organization of chromatin domains by mathematical modeling. Nucleus 2017; 8:353-359. [PMID: 28406741 PMCID: PMC5597300 DOI: 10.1080/19491034.2017.1313937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The genome is 3-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling. Our mathematical analysis suggested that as the chromatin domain becomes smaller and more compact, nucleosome movement becomes increasingly restricted. Here, we show the implication of these results for bridging the gap between chromatin dynamics and organization, and provide physical insight into chromatin domains as efficient units to conduct genome functions in the thermal noisy environment of the cell.
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Affiliation(s)
- Soya Shinkai
- a Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD) , Hiroshima University , Kagamiyama , Higashi-Hiroshima , Japan
| | - Tadasu Nozaki
- b Structural Biology Center , National Institute of Genetics , Yata, Mishima , Japan
| | - Kazuhiro Maeshima
- b Structural Biology Center , National Institute of Genetics , Yata, Mishima , Japan
| | - Yuichi Togashi
- a Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD) , Hiroshima University , Kagamiyama , Higashi-Hiroshima , Japan
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