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Investigating Chromatin Organisation Using Single Molecule Localisation Microscopy

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Chromatin Architecture

Part of the book series: Springer Theses ((Springer Theses))

Abstract

In this chapter, I discuss the technical details of single molecule localisation microscopy (SMLM) to investigate spatial and temporal organisation of DNA. The DNA is hierarchically folded at multiple levels to become more compacted and functionally organise itself inside of the nucleus. This spatial arrangement in turn affects the functionality of DNA.

My intention is not to replace one set of general rules by another such set: my intention is, rather, to convince the reader that all methodologies, even the most obvious ones, have their limits.

Paul Karl Feyerabend

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Notes

  1. 1.

    Parts of this chapter, including figures and captions, are based on the following publications: Szczurek et al. 2014; Żurek-Biesiada et al. 2015, 2016; Hagmann et al. 2014; Best et al. 2014.

References

  • Abbe E (1873) Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrmehmung. Archiv für Mikroskopische Anatomie 9:413–420. doi:10.1007/BF02956173

    Article  Google Scholar 

  • Albiez H, Cremer M, Tiberi C, Vecchio L, Schermelleh L, Dittrich S, Küpper K, Joffe B, Thormeyer T, von Hase J et al (2006) Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosom Res 14(7):707–733

    Article  CAS  Google Scholar 

  • Anton T, Bultmann S, Leonhardt H, Markaki Y (2014) Visualization of specific dna sequences in living mouse embryonic stem cells with a programmable fluorescent crispr/cas system. Nucleus 5(2):163–172

    Article  PubMed  PubMed Central  Google Scholar 

  • Baddeley D, Cannell MB, Soeller C (2010) Visualization of localization microscopy data. Microsc Microanal 16(01):64–72

    Article  CAS  PubMed  Google Scholar 

  • Baskin JM, Prescher JA, Laughlin ST, Agard NJ, Chang PV, Miller IA, Lo A, Codelli JA, Bertozzi CR (2007) Copper-free click chemistry for dynamic in vivo imaging. Proc Natl Acad Sci 104(43):16793–16797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bates M, Jones SA, Zhuang X (2013) Stochastic optical reconstruction microscopy (storm): a method for superresolution fluorescence imaging. Cold Spring Harbor Protoc 2013(6):pdb–top075143

    Google Scholar 

  • Bernas T, Zarebski M, Cook RR, Dobrucki JW (2004) Minimizing photobleaching during confocal microscopy of fluorescent probes bound to chromatin: role of anoxia and photon flux. J Microsc 215(3):281–296

    Article  CAS  PubMed  Google Scholar 

  • Best G, Prakash K, Hagmann M, Cremer C, Birk U (2014) Identify and localise: algorithms for single molecule localisation microscopy. In: Hozák P (ed) 18th international microscopy congress, number ISBN 978-80-260-6720-7

    Google Scholar 

  • Betzig E (1995) Proposed method for molecular optical imaging. Opt Lett 20(3):237–239

    Article  CAS  PubMed  Google Scholar 

  • Betzig E, Patterson GH, Sougrat R, Wolf Lindwasser O, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313(5793):1642–1645

    Article  CAS  PubMed  Google Scholar 

  • Biancardi A, Biver T, Secco F, Mennucci B (2013) An investigation of the photophysical properties of minor groove bound and intercalated dapi through quantum-mechanical and spectroscopic tools. Phys Chem Chem Phys 15(13):4596–4603

    Article  CAS  PubMed  Google Scholar 

  • Biteen JS, Thompson MA, Tselentis NK, Bowman GR, Shapiro L, Moerner WE (2008) Super-resolution imaging in live caulobacter crescentus cells using photoswitchable eyfp. Nature Methods 5(11):947–949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu C-T, Zhuang X (2016) Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529(7586):418–422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bohn M, Diesinger P, Kaufmann R, Weiland Y, Müller P, Gunkel M, Von Ketteler A, Lemmer P, Hausmann M, Heermann DW et al (2010) Localization microscopy reveals expression-dependent parameters of chromatin nanostructure. Biophys J 99(5):1358–1367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brooks Shera E, Seitzinger NK, Davis LM, Keller RA, Soper SA (1990) Detection of single fluorescent molecules. Chem Phys Lett 174(6):553–557

    Article  Google Scholar 

  • Burnette DT, Sengupta P, Dai Y, Lippincott-Schwartz J, Kachar B (2011) Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules. Proc Natl Acad Sci 108(52):21081–21086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burns DH, Callis JB, Christian GD, Davidson ER (1985) Strategies for attaining superresolution using spectroscopic data as constraints. Appl Opt 24(2):154–161

    Article  CAS  PubMed  Google Scholar 

  • Chandra T, Kirschner K, Thuret J-Y, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T et al (2012) Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol cell 47(2):203–214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li G-W, Park J, Blackburn EH, Weissman JS, Qi LS et al (2013) Dynamic imaging of genomic loci in living human cells by an optimized crispr/cas system. Cell 155(7):1479–1491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chenouard N, Smal I, De Chaumont F, MaÅ¡ka M, Sbalzarini IF, Gong Y, Cardinale J, Carthel C, Coraluppi S, Winter M et al (2014) Objective comparison of particle tracking methods. Nature Methods 11(3):281

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cosa G, Focsaneanu KS, McLean JRN, McNamee JP, Scaiano JC (2001) Photophysical properties of fluorescent dna-dyes bound to single-and double-stranded dna in aqueous buffered solution. Photochem Photobiol 73(6):585–599

    Article  CAS  PubMed  Google Scholar 

  • Cremer C, Cremer T (1978) Considerations on a laser-scanning-microscope with high resolution and depth of field. Microsc Acta 81:31–44

    CAS  PubMed  Google Scholar 

  • Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Rev Genet 2(4):292–301

    Article  CAS  PubMed  Google Scholar 

  • Cremer T, Küpper K, Dietzel S, Fakan S (2004) Higher order chromatin architecture in the cell nucleus: on the way from structure to function. Biol Cell 96(8):555–567

    Article  CAS  PubMed  Google Scholar 

  • Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C (2015) The 4d nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett 589:2931–2943

    Article  CAS  PubMed  Google Scholar 

  • Diana C, Carvalho PC (2010) Supramolecular biomimetic binding of the DNA-dye Hoechst 33258 by a synthetic macrocycle. Ph.D. thesis

    Google Scholar 

  • Dickson RM, Cubitt AB, Tsien RY, Moerner WE (1997) On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature 388(6640):355–358

    Article  CAS  PubMed  Google Scholar 

  • Doudna JA, Charpentier E (2014) The new frontier of genome engineering with crispr-cas9. Science 346(6213):1258096

    Article  PubMed  Google Scholar 

  • Egner A, Geisler C, Von Middendorff C, Bock H, Wenzel D, Medda R, Andresen M, Stiel AC, Jakobs S, Eggeling C et al (2007) Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters. Biophys J 93(9):3285–3290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fölling J, Bossi M, Bock H, Medda R, Wurm CA, Hein B, Jakobs S, Eggeling C, Hell SW (2008) Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nature Methods 5(11):943–945

    Article  PubMed  Google Scholar 

  • Früh SM, Schoen I, Ries J, Vogel V (2015) Molecular architecture of native fibronectin fibrils. Nature Commun 6:7275

    Article  Google Scholar 

  • Grammel M, Hang HC (2013) Chemical reporters for biological discovery. Nature Chem Biol 9(8):475–484

    Article  CAS  Google Scholar 

  • Gustafsson MGL (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198(2):82–87

    Article  CAS  PubMed  Google Scholar 

  • Hagmann M, Prakash K, Best G, Kaufmann R, Birk U, Cremer C (2014) Drift correction strategies for single molecule localisation microscopy. In: Hozák P (ed) 18th international microscopy congress, number ISBN 978-80-260-6720-7

    Google Scholar 

  • Hagmann M, Prakash K, Cremer C (2016) Visualisation enhancement for single molecule reconstructions using wigner–seitz cells (in preparation)

    Google Scholar 

  • Heilemann M, Van De Linde S, Schüttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P, Sauer M (2008) Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Edition 47(33):6172–6176

    Article  CAS  Google Scholar 

  • Heintzmann R, Cremer C (1999) Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating. In: BiOS Europe’98. International Society for Optics and Photonics, pp 185–196

    Google Scholar 

  • Hell SW, Wichmann J (1994) Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt Lett 19(11):780–782

    Article  CAS  PubMed  Google Scholar 

  • Hess ST, Girirajan TPK, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91(11):4258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hirschfeld T (1976) Optical microscopic observation of single small molecules. Appl Opt 15(12):2965–2966

    Article  CAS  PubMed  Google Scholar 

  • Hsu PD, Lander ES, Zhang F (2014) Development and applications of crispr-cas9 for genome engineering. Cell 157(6):1262–1278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hussels M, Brecht M (2011) Effect of glycerol and pva on the conformation of photosystem i. Biochemistry 50(18):3628–3637

    Article  CAS  PubMed  Google Scholar 

  • Jianzhuang L, Wenqing L, Yupeng T (1991) Automatic thresholding of gray-level pictures using two-dimension otsu method. In: 1991 international conference on circuits and systems, 1991. Conference proceedings, China, pp 325–327. IEEE

    Google Scholar 

  • Kaufmann R, Piontek J, Grüll F, Kirchgessner M, Rossa J, Wolburg H, Blasig IE, Cremer C (2012) Visualization and quantitative analysis of reconstituted tight junctions using localization microscopy. PloS One 7(2):e31128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Klein T, Löschberger A, Proppert S, Wolter S, van de Linde S, Sauer M (2011) Live-cell dstorm with snap-tag fusion proteins. Nature Methods 8(1):7–9

    Article  CAS  PubMed  Google Scholar 

  • Lemmer P, Gunkel M, Baddeley D, Kaufmann R, Urich A, Weiland Y, Reymann J, Müller P, Hausmann M, Cremer C (2008) Spdm: light microscopy with single-molecule resolution at the nanoscale. Appl Phys B 93(1):1–12

    Article  CAS  Google Scholar 

  • Lemmer P, Gunkel M, Weiland Y, Müller P, Baddeley D, Rainer Kaufmann A, Urich HE, Amberger R, Hausmann M et al (2009) Using conventional fluorescent markers for far-field fluorescence localization nanoscopy allows resolution in the 10-nm range. J Microsc 235(2):163–171

    Article  CAS  PubMed  Google Scholar 

  • Lidke K, Rieger B, Jovin T, Heintzmann R (2005) Superresolution by localization of quantum dots using blinking statistics. Opt Express 13(18):7052–7062

    Article  PubMed  Google Scholar 

  • Manley S, Gillette JM, Patterson GH, Shroff H, Hess HF, Betzig E, Lippincott-Schwartz J (2008) High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nature Methods 5(2):155–157

    Article  CAS  PubMed  Google Scholar 

  • Miyanari Y, Ziegler-Birling C, Torres-Padilla M-E (2013) Live visualization of chromatin dynamics with fluorescent tales. Nature Struct Mol Biol 20(11):1321–1324

    Article  CAS  Google Scholar 

  • Moerner WE, Kador L (1989) Optical detection and spectroscopy of single molecules in a solid. Phys Rev Lett 62(21):2535

    Article  CAS  PubMed  Google Scholar 

  • Müller P, Schmitt E, Jacob A, Hoheisel J, Kaufmann R, Cremer C, Hausmann M (2010) Combo-fish enables high precision localization microscopy as a prerequisite for nanostructure analysis of genome loci. Int J Mol Sci 11(10):4094–4105

    Article  PubMed  PubMed Central  Google Scholar 

  • Neice A (2010) Chapter 3 - methods and limitations of subwavelength imaging. In: Hawkes PW (ed) Advances in imaging and electron physics, vol 163. Elsevier, pp 117–140. doi:10.1016/S1076-5670(10)63003-0

  • Nieuwenhuizen RPJ, Lidke KA, Bates M, Puig DL, Grünwald D, Stallinga S, Rieger B (2013) Measuring image resolution in optical nanoscopy. Nature Methods 10(6):557–562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Piterburg M, Panet H, Weiss A (2012) Photoconversion of dapi following uv or violet excitation can cause dapi to fluoresce with blue or cyan excitation. J Microsc 246(1):89–95

    Article  CAS  PubMed  Google Scholar 

  • Prakash K, Fournier D, Redl S, Best G, Borsos M, Tiwari VK, Tachibana-Konwalski K, Ketting RF, Parekh SH, Cremer C et al (2015) Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes. Proc Natl Acad Sci 112(47):14635–14640

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES et al (2014) A 3d map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7):1665–1680

    Article  CAS  PubMed  Google Scholar 

  • Rayleigh L (1896) Xv. on the theory of optical images, with special reference to the microscope. Lond Edinb Dublin Philos Mag J Sci 42(255):167–195

    Google Scholar 

  • Rust MJ, Bates M, Zhuang X (2006) Stochastic optical reconstruction microscopy (storm) provides sub-diffraction-limit image resolution. Nature Methods 3(10):793

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ricci MA, Manzo C, García-Parajo MF, Lakadamyali M, Cosma MP (2015) Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160(6):1145–1158

    Article  CAS  PubMed  Google Scholar 

  • Schoen I, Ries J, Klotzsch E, Ewers H, Vogel V (2011) Binding-activated localization microscopy of dna structures. Nano Lett 11(9):4008–4011

    Article  CAS  PubMed  Google Scholar 

  • Sengupta P, van Engelenburg SB, Lippincott-Schwartz J (2014) Superresolution imaging of biological systems using photoactivated localization microscopy. Chem Rev 114(6):3189–3202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sheppard CJR, Wilson T (1981) Effects of high angles of convergence on v (z) in the scanning acoustic microscope. Appl Phys Lett 38(11):858–859

    Article  Google Scholar 

  • Shroff H, Galbraith CG, Galbraith JA, Betzig E (2008) Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nature Methods 5(5):417–423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Small AR, Parthasarathy R (2014) Superresolution localization methods. Ann Rev Phys Chem 65:107–125

    Article  CAS  Google Scholar 

  • Small A, Stahlheber S (2014) Fluorophore localization algorithms for super-resolution microscopy. Nature Methods 11(3):267–279

    Article  CAS  PubMed  Google Scholar 

  • Sunney Xie X, Dunn RC et al (1994) Probing single molecule dynamics. Science 265:361

    Article  Google Scholar 

  • Szczurek AT, Prakash K, Lee H-K, Å»urek-Biesiada DJ, Best G, Hagmann M, Dobrucki JW, Cremer C, Birk U (2014) Single molecule localization microscopy of the distribution of chromatin using hoechst and dapi fluorescent probes. Nucleus 5(4):331–340

    Article  PubMed  PubMed Central  Google Scholar 

  • Thanisch K, Schneider K, Morbitzer R, Solovei I, Lahaye T, Bultmann S, Leonhardt H (2013) Targeting and tracing of specific dna sequences with dtales in living cells. Nucleic Acids Res, gkt1348

    Google Scholar 

  • Thompson RE, Larson DR, Webb WW (2002) Precise nanometer localization analysis for individual fluorescent probes. Biophys J 82(5):2775–2783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uno SN, Kamiya M, Yoshihara T, Sugawara K, Okabe K, Tarhan MC, Fujita H, Funatsu T, Okada Y, Tobita S et al (2014) A spontaneously blinking fluorophore based on intramolecular spirocyclization for live-cell super-resolution imaging. Nature Chem 6(8):681–689

    CAS  Google Scholar 

  • Van Oijen AM, Köhler J, Schmidt J, Müller M, Brakenhoff GJ (1998) 3-dimensional super-resolution by spectrally selective imaging. Chem Phys Lett 292(1):183–187

    Article  Google Scholar 

  • Weiland Y, Lemmer P, Cremer C (2011) Combining fish with localisation microscopy: super-resolution imaging of nuclear genome nanostructures. Chromosom Res 19(1):5–23

    Article  CAS  Google Scholar 

  • Whelan DR, Bell TDM (2015) Image artifacts in single molecule localization microscopy: why optimization of sample preparation protocols matters. Sci Rep 5:7924

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wood AJ, Lo T-W, Zeitler B, Pickle CS, Ralston EJ, Lee AH, Amora R, Miller JC, Leung E, Meng X et al (2011) Targeted genome editing across species using zfns and talens. Science 333(6040):307–307

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu K, Zhong G, Zhuang X (2013) Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339(6118):452–456

    Article  CAS  PubMed  Google Scholar 

  • Zessin PJM, Finan K, Heilemann M (2012) Super-resolution fluorescence imaging of chromosomal dna. J Struct Biol 177(2):344–348

    Article  CAS  PubMed  Google Scholar 

  • Zhimulëv IF (1996) Morphology and structure of polytene chromosomes. Academic Press, New York

    Book  Google Scholar 

  • Zipfel WR, Williams RM, Webb WW (2003) Nonlinear magic: multiphoton microscopy in the biosciences. Nature Biotechnol 21(11):1369–1377

    Article  CAS  Google Scholar 

  • Å»urek-Biesiada D, Szczurek AT, Prakash K, Mohana GK, Lee H-K, Roignant J-Y, Birk U, Dobrucki JW, Cremer C (2015) Localization microscopy of dna in situ using vybrant dyecycle violet fluorescent probe: a new approach to study nuclear nanostructure at single molecule resolution. Exp Cell Res 343:97–106

    Article  PubMed  Google Scholar 

  • Å»urek-Biesiada D, Szczurek AT, Prakash K, Best G, Mohana GK, Lee H-K, Roignant J-Y, Dobrucki JW, Cremer C, Birk U (2016) Quantitative super-resolution localization microscopy of dna in situ using vybrant dyecycle violet fluorescent probe. Data Brief 7:157–171

    Article  PubMed  PubMed Central  Google Scholar 

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Prakash, K. (2017). Investigating Chromatin Organisation Using Single Molecule Localisation Microscopy. In: Chromatin Architecture. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-319-52183-1_2

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