Abstract
Our view of the structure and function of the interphase nucleus has changed drastically in recent years. It is now widely accepted that the nucleus is a well organized and highly compartmentalized organelle and that this organization is intimately related to nuclear function. In this context, chromatin—initially considered a randomly entangled polymer—has also been shown to be structurally organized in interphase and its organization was found to be very important to gene regulation. Relevant and not completely answered questions are how chromatin organization is achieved and what mechanisms are responsible for changes in the positions of chromatin loci in the nucleus. A significant advance in the field resulted from tagging chromosome sites with bacterial operator sequences, and visualizing these tags using green fluorescent protein fused with the appropriate repressor protein. Simultaneously, fluorescence imaging techniques evolved significantly during recent years, allowing observation of the time evolution of processes in living specimens. In this context, the motion of the tagged locus was observed and analyzed to extract quantitative information regarding its dynamics. This review focuses on recent advances in our understanding of chromatin dynamics in interphase with the emphasis placed on the information obtained from single-particle tracking (SPT) experiments. We introduce the basis of SPT methods and trajectory analysis, and summarize what has been learnt by using this new technology in the context of chromatin dynamics. Finally, we briefly describe a method of SPT in a two-photon excitation microscope that has several advantages over methods based on conventional microscopy and review the information obtained using this novel approach to study chromatin dynamics.
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References
Abramowitz M (2003) Microscope: Basics and Beyond. New York: Olympus America Inc.
Abranches R, Beven AF, Aragon-Alcaide L, Shaw PJ (1998) Transcription sites are not correlated with chromosome territories in wheat nuclei. J Cell Biol 143: 5–12.
Andrulis ED, Neiman AM, Zappulla DC, Sternglanz R (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394: 592–595.
Belmont AS, Li G, Sudlow G, Robinett C (1999) Visualization of large-scale chromatin structure and dynamics using the lac operator/lac repressor reporter system. Methods Cell Biol 58: 203–222.
Branco MR, Pombo A (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 4: e138.
Branco MR, Pombo A (2007) Chromosome organization: new facts, new models. Trends Cell Biol 17: 127–134.
Brickner JH, Walter P (2004) Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2: e342.
Chambeyron S, Da Silva NR, Lawson KA, Bickmore WA (2005) Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 132: 2215–2223.
Chaumeil J, Le Baccon P, Wutz A, Heard E (2006) A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev 20: 2223–2237.
Cheezum MK, Walker WF, Guilford WH (2001) Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys J 81: 2378–2388.
Chuang CH, Carpenter AE, Fuchsova B, Johnson T, de Lanerolle P, Belmont AS (2006) Long-range directional movement of an interphase chromosome site. Curr Biol 16: 825–831.
Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12: 439–445.
Cremer T, Cremer C (2006a) Rise, fall and resurrection of chromosome territories: a historical perspective. Part I. The rise of chromosome territories. Eur J Histochem 50: 161–176.
Cremer T, Cremer C (2006b) Rise, fall and resurrection of chromosome territories: a historical perspective. Part II. Fall and resurrection of chromosome territories during the 1950s to 1980s. Part III. Chromosome territories and the functional nuclear architecture: experiments and models from the 1990s to the present. Eur J Histochem 50: 223–272.
Cremer T, Cremer C, Schneider T, Baumann H, Hens L, Kirsch-Volders M (1982) Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments. Hum Genet 62: 201–209.
Crissman HA, Hirons GT (1994) Staining of DNA in live and fixed cells. Methods Cell Biol 41: 195–209.
Dahan M, Levi S, Luccardini C, Rostaing P, Riveau B, Triller A (2003) Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking. Science 302: 442–445.
Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295: 1306–1311.
Denk W, Strickler JH, Webb WW (1990) Two-photon laser scanning fluorescence microscopy. Science 248: 73–76.
Dundr M, Misteli T (2001) Functional architecture in the cell nucleus. Biochem J 356: 297–310.
Enderlein J (2000) Tracking of fluorescent molecules diffusing within membranes. Appl Phys B Lasers Opt 71: 773–777.
Handwerger KE, Gall JG (2006) Subnuclear organelles: new insights into form and function. Trends Cell Biol 16: 19–26.
Heard E, Bickmore W (2007) The ins and outs of gene regulation and chromosome territory organisation. Curr Opin Cell Biol 19: 311–316.
Hediger F, Taddei A, Neumann FR, Gasser SM (2004) Methods for visualizing chromatin dynamics in living yeast. Methods Enzymol 375: 345–365.
Heun P, Laroche T, Shimada K, Furrer P, Gasser SM (2001) Chromosome dynamics in the yeast interphase nucleus. Science 294: 2181–2186.
Kanda T, Sullivan KF, Wahl GM (1998) Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr Biol 8: 377–385.
Kis-Petikova K, Gratton E (2004) Distance measurement by circular scanning of the excitation beam in the two-photon microscope. Microsc Res Tech 63: 34–49.
Kurz A, Lampel S, Nickolenko JE et al. (1996) Active and inactive genes localize preferentially in the periphery of chromosome territories. J Cell Biol 135: 1195–1205.
Lakadamyali M, Rust MJ, Babcock HP, Zhuang X (2003) Visualizing infection of individual influenza viruses. Proc Natl Acad Sci U S A 100: 9280–9285.
Larson DR, Zipfel WR, Williams RM et al. (2003) Water-soluble quantum dots for multiphoton fluorescence imaging in vivo. Science 300: 1434–1436.
Levi V, Gratton E (2007) Exploring dynamics in living cells by tracking single particles. Cell Biochem Biophys 48: 1–15.
Levi V, Ruan Q, Gratton E (2005a) 3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells. Biophys J 88: 2919–2928.
Levi V, Ruan Q, Plutz M, Belmont AS, Gratton E (2005b) Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope. Biophys J 89: 4275–4285.
Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80: 224–234.
Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157: 579–589.
Marshall WF, Straight A, Marko JF et al. (1997) Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7: 930–939.
Menon BB, Sarma NJ, Pasula S et al. (2005) Reverse recruitment: the Nup84 nuclear pore subcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation. Proc Natl Acad Sci U S A 102: 5749–5754.
Qian H, Sheetz MP, Elson EL (1991) Single particle tracking. Analysis of diffusion and flow in two-dimensional systems. Biophys J 60: 910–921.
Robinett CC, Straight A, Li G et al. (1996) In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J Cell Biol 135: 1685–1700.
Rosa A, Maddocks JH, Neumann FR, Gasser SM, Stasiak A (2006) Measuring limits of telomere movement on nuclear envelope. Biophys J 90: L24–26.
Saxton MJ (1993) Lateral diffusion in an archipelago. Single-particle diffusion. Biophys J 64: 1766–1780.
Saxton MJ (1994a) Anomalous diffusion due to obstacles: a Monte Carlo study. Biophys J 66: 394–401.
Saxton MJ (1994b) Single-particle tracking: models of directed transport. Biophys J 67: 2110–2119.
Saxton MJ (1995) Single-particle tracking: effects of corrals. Biophys J 69: 389–398.
Saxton MJ (1996) Anomalous diffusion due to binding: a Monte Carlo study. Biophys J 70: 1250–1262.
Saxton MJ (1997) Single-particle tracking: the distribution of diffusion coefficients. Biophys J 72: 1744–1753.
Saxton MJ, Jacobson K (1997) Single-particle tracking: applications to membrane dynamics. Annu Rev Biophys Biomol Struct 26: 373–399.
Schmid M, Arib G, Laemmli C, Nishikawa J, Durussel T, Laemmli UK (2006) Nup-PI: the nucleopore-promoter interaction of genes in yeast. Mol Cell 21: 379–391.
Simonis M, Klous P, Splinter E et al. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38: 1348–1354.
So PT, Dong CY, Masters BR, Berland KM (2000) Two-photon excitation fluorescence microscopy. Annu Rev Biomed Eng 2: 399–429.
Svoboda K, Yasuda R (2006) Principles of two-photon excitation microscopy and its applications to neuroscience. Neuron 50: 823–839.
Thompson RE, Larson DR, Webb WW (2002) Precise nanometer localization analysis for individual fluorescent probes. Biophys J 82: 2775–2783.
Tumbar T, Belmont AS (2001) Interphase movements of a DNA chromosome region modulated by VP16 transcriptional activator. Nat Cell Biol 3: 134–139.
Vazquez J, Belmont AS, Sedat JW (2001) Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr Biol 11: 1227–1239.
Verschure PJ, van Der Kraan I, Manders EM, van Driel R (1999) Spatial relationship between transcription sites and chromosome territories. J Cell Biol 147: 13–24.
Volpi EV, Chevret E, Jones T et al. (2000) Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 113(Pt 9): 1565–1576.
Wokosin DL, Loughrey CM, Smith GL (2004) Characterization of a range of fura dyes with two-photon excitation. Biophys J 86: 1726–1738.
Xu C, Webb WW (1996) Measurement of two-photon excitaton cross sections of molecular fluorophores with data from 690 nm to 1050 nm. J Opt Soc B 13: 481–491.
Xu C, Zipfel W, Shear JB, Williams RM, Webb WW (1996) Multiphoton fluorescence excitation: new spectral windows for biological nonlinear microscopy. Proc Natl Acad Sci U S A 93: 10763–10768.
Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR (2003) Myosin V walks hand-over-hand: single fluorophore imaging with 1.5–nm localization. Science 300: 2061–2065.
Zink D, Cremer T, Saffrich R et al. (1998) Structure and dynamics of human interphase chromosome territories in vivo. Hum Genet 102: 241–251.
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Levi, V., Gratton, E. Chromatin dynamics during interphase explored by single-particle tracking. Chromosome Res 16, 439–449 (2008). https://doi.org/10.1007/s10577-008-1240-8
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DOI: https://doi.org/10.1007/s10577-008-1240-8