Abstract
The cell nucleus contains many distinct subnuclear compartments, domains, and bodies that vary in their composition, structure, and function. While the cellular constituents that occupy the subnuclear regions may be well known, defining the structural details of the molecular assembly of the constituents has been more difficult. A correlative fluorescence and energy-filtering transmission electron microscopy (EFTEM) imaging method has the ability to provide these details. The correlative microscopy method described here allows the tracking of subnuclear structures from specific cells by fluorescence microscopy and then, using electron energy loss imaging in the transmission electron microscope, reveals the ultrastructural features of the nuclear components along with endogenous elemental information that relates directly to the biochemical composition of the structure. The ultrastructural features and composition of well-characterized PML bodies and interchromatin granule clusters are compared to those of ligand-activated glucocorticoid receptor (GR) foci, with GR foci containing fibrogranular nucleic acid-containing features and PML bodies being devoid of nucleic acid.
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Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645
Watanabe S, Punge A, Hollopeter G, Willig KI, Hobson RJ, Davis MW, Hell SW, Jorgensen EM (2011) Protein localization in electron micrographs using fluorescence nanoscopy. Nat Methods 8:80–84
Sosinsky GE, Giepmans BN, Deerinck TJ, Gaietta GM, Ellisman MH (2007) Markers for correlated light and electron microscopy. Methods Cell Biol 79:575–591
Giepmans BN (2008) Bridging fluorescence microscopy and electron microscopy. Histochem Cell Biol 130:211–217
Kireev I, Lakonishok M, Liu W, Joshi VN, Powell R, Belmont AS (2008) In vivo immunogold labeling confirms large-scale chromatin folding motifs. Nat Methods 5:311–313
Kukulski W, Schorb M, Welsch S, Picco A, Kaksonen M, Briggs JA (2011) Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision. J Cell Biol 192:111–119
Deerinck TJ, Giepmans BN, Smarr BL, Martone ME, Ellisman MH (2007) Light and electron microscopic localization of multiple proteins using quantum dots. Methods Mol Biol 374:43–53
Giepmans BN, Deerinck TJ, Smarr BL, Jones YZ, Ellisman MH (2005) Correlated light and electron microscopic imaging of multiple endogenous proteins using Quantum dots. Nat Methods 2:743–749
Nisman R, Dellaire G, Ren Y, Li R, Bazett-Jones DP (2004) Application of quantum dots as probes for correlative fluorescence, conventional, and energy-filtered transmission electron microscopy. J Histochem Cytochem 52:13–18
Grabenbauer M, Geerts WJ, Fernadez-Rodriguez J, Hoenger A, Koster AJ, Nilsson T (2005) Correlative microscopy and electron tomography of GFP through photooxidation. Nat Methods 2:857–862
Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY (2011) A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol 9:e1001041
Ren Y, Kruhlak MJ, Bazett-Jones DP (2003) Same serial section correlative light and energy-filtered transmission electron microscopy. J Histochem Cytochem 51:605–612
Spector DL (2001) Nuclear domains. J Cell Sci 114:2891–2893
Spector DL (2006) SnapShot: cellular bodies. Cell 127:1071
Zhao R, Bodnar MS, Spector DL (2009) Nuclear neighborhoods and gene expression. Curr Opin Genet Dev 19:172–179
Lallemand-Breitenbach V, de The H (2010) PML nuclear bodies. Cold Spring Harb Perspect Biol 2:a000661
Bazett-Jones DP, Hendzel MJ (1999) Electron spectroscopic imaging of chromatin. Methods 17:188–200
Bazett-Jones DP, Li R, Fussner E, Nisman R, Dehghani H (2008) Elucidating chromatin and nuclear domain architecture with electron spectroscopic imaging. Chromosome Res 16:397–412
Spencer CA, Kruhlak MJ, Jenkins HL, Sun X, Bazett-Jones DP (2000) Mitotic transcription repression in vivo in the absence of nucleosomal chromatin condensation. J Cell Biol 150:13–26
Kruhlak MJ, Celeste A, Dellaire G, Fernandez-Capetillo O, Muller WG, McNally JG, Bazett-Jones DP, Nussenzweig A (2006) Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J Cell Biol 172:823–834
Eskiw CH, Rapp A, Carter DR, Cook PR (2008) RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci 121:1999–2007
Eskiw CH, Fraser P (2011) Ultrastructural study of transcription factories in mouse erythroblasts. J Cell Sci 124:3676–3683
Hendzel MJ, Kruhlak MJ, Bazett-Jones DP (1998) Organization of highly acetylated chromatin around sites of heterogeneous nuclear RNA accumulation. Mol Biol Cell 9:2491–2507
Boisvert FM, Hendzel MJ, Bazett-Jones DP (2000) Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA. J Cell Biol 148:283–292
Dellaire G, Bazett-Jones DP (2004) PML nuclear bodies: dynamic sensors of DNA damage and cellular stress. Bioessays 26:963–977
Eskiw CH, Dellaire G, Mymryk JS, Bazett-Jones DP (2003) Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supramolecular trafficking and assembly. J Cell Sci 116:4455–4466
Htun H, Barsony J, Renyi I, Gould DL, Hager GL (1996) Visualization of glucocorticoid receptor translocation and intranuclear organization in living cells with a green fluorescent protein chimera. Proc Natl Acad Sci USA 93:4845–4850
Lamond AI, Spector DL (2003) Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol 4:605–612
Thiry M (1993) Differential location of nucleic acids within interchromatin granule clusters. Eur J Cell Biol 62:259–269
Pandit S, Wang D, Fu XD (2008) Functional integration of transcriptional and RNA processing machineries. Curr Opin Cell Biol 20:260–265
Spector, D. L., Lamond, A. I. (2011) Nuclear speckles. Cold Spring Harb Perspect Biol. 3.
Leapman RD, Kocsis E, Zhang G, Talbot TL, Laquerriere P (2004) Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography. Ultramicroscopy 100:115–125
Aronova MA, Kim YC, Harmon R, Sousa AA, Zhang G, Leapman RD (2007) Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST). J Struct Biol 160:35–48
Leapman RD, Aronova MA (2007) Localizing specific elements bound to macromolecules by EFTEM. Methods Cell Biol 79:593–613
Acknowledgments
The EFTEM images were collected with generous support from David Bazett-Jones. Ying Ren helped prepare the samples, and Michael Hendzel and Alioscka Sousa provided helpful critical reading of the manuscript. Maria Aronova and Richard Leapman generously provided advice, and access to multiple EFTEM microscopes. This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.
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Kruhlak, M.J. (2013). Correlative Fluorescence and EFTEM Imaging of the Organized Components of the Mammalian Nucleus. In: Sousa, A., Kruhlak, M. (eds) Nanoimaging. Methods in Molecular Biology, vol 950. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-137-0_22
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DOI: https://doi.org/10.1007/978-1-62703-137-0_22
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