Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy

Methods in Molecular Biology

Volumn 950, Issue , 2013, Pages 43-64

  Markaki, Yolanda ^a   Smeets, Daniel ^a   Cremer, Marion ^a   Schermelleh, Lothar ^b  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

3D FISH; Click chemistry; DNA replication labeling; Fluorescence in situ hybridization; Immuno FISH; RNA FISH; Structured illumination microscopy; Super resolution imaging

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; DNA; INDOLE DERIVATIVE; URIDINE;

ANIMAL; ARTICLE; DNA DENATURATION; FLUORESCENCE IN SITU HYBRIDIZATION; FLUORESCENT ANTIBODY TECHNIQUE; ILLUMINATION; METABOLISM; METHODOLOGY; MICROSCOPY; MOUSE; NUCLEAR SHAPE; STAINING; THREE DIMENSIONAL IMAGING; TISSUE FIXATION;

ANIMALS; CELL NUCLEUS SHAPE; DNA; FLUORESCENT ANTIBODY TECHNIQUE; IMAGING, THREE-DIMENSIONAL; IN SITU HYBRIDIZATION, FLUORESCENCE; INDOLES; LIGHTING; MICE; MICROSCOPY; NUCLEIC ACID DENATURATION; STAINING AND LABELING; TISSUE FIXATION; URIDINE;

MAMMALIA;

EID: 84870564868     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-137-0_4     Document Type: Article

References (34)

1. Cremer T, Cremer M (2010) Chromosome territories. Cold Spring Harb Perspect Biol 2: a003889
2. Cremer M, Grasser F, Lanctôt C et al (2008) Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. Methods Mol Biol 463:205-239
3. Foster HA, Bridger JM (2005) The genome and the nucleus: a marriage made by evolution. Genome organisation and nuclear architecture. Chromosoma 114:212-229
4. Misteli T (2010) Higher-order genome organization in human disease. Cold Spring Harb Perspect Biol 2:a000794
5. Volpi EV, Bridger JM (2008) FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques 45:385-386, 385-6, 388, 390 passim
6. Speicher MR, Gwyn BS, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12: 368-375
7. Bolzer A, Kreth G, Solovei I et al (2005) Threedimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3:e157
8. Silverman AP, Kool ET (2007) Oligonucleotide probes for RNA-targeted fluorescence in situ hybridization. Adv Clin Chem 43:79-115
9. Blanco AM, Artero R (2010) A practical approach to FRET-based PNA fluorescence in situ hybridization. Methods 52:343-351
10. Pawley JB (2006) Handbook of biological confocal microscopy. Springer, New York, p 985
11. Schermelleh L, Heintzmann R, Leonhardt H (2010) A guide to super-resolution fluorescence microscopy. J Cell Biol 190:165-175
12. Huang B, Babcock H, Zhuang X (2010) Breaking the diffraction barrier: super-resolution imaging of cells. Cell 143:1047-1058
13. Toomre D, Bewersdorf J (2010) A new wave of cellular imaging. Annu Rev Cell Dev Biol 26:285-314
14. Hell SW (2009) Microscopy and its focal switch. Nat Methods 6:24-32
15. Gustafsson MGL, Shao L, Carlton PM et al (2008) Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J 94:4957-4970
16. Gustafsson MG (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198:82-87
17. Schermelleh L, Carlton PM, Haase S et al (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320:1332-1336
18. Baddeley D, Chagin VO, Schermelleh L et al (2010) Measurement of replication structures at the nanometer scale using super-resolution light microscopy. Nucleic Acids Res 38:e8
19. Brown ACN, Oddos S, Dobbie IM et al (2011) Remodelling of cortical actin where lytic granules dock at natural killer cell immune synapses revealed by super-resolution microscopy. PLoS Biol 9:e1001152
20. Guizetti J, Schermelleh L, Mantler J et al (2011) Cortical constriction during abscission involves helices of ESCRT-III-dependent fi laments. Science 331:1616-1620
21. Markaki Y, Gunkel M, Schermelleh L et al (2010) Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment. Cold Spring Harb Symp Quant Biol 75:475-492
22. Elia N, Sougrat R, Spurlin TA, Hurley JH, Lippincott-Schwartz J (2011) Dynamics of endosomal sorting complex required for transport (ESCRT) machinery during cytokinesis and its role in abscission. Proc Natl Acad Sci USA 108:4846-4851
23. Bennett BT, Bewersdorf J, Knight KL (2009) Immuno fluorescence imaging of DNA damage response proteins: optimizing protocols for super-resolution microscopy. Methods 48: 63-71
24. Markaki Y, Smeets D, Fiedler S, Schmid VJ, Cremer T, Cremer M (2012) The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture. Bioessays 34(5):412-426
25. Solovei I, Cavallo A, Schermelleh L et al (2002) Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp Cell Res 276:10-23
26. Wallace W, Schaefer LH, Swedlow JR (2001) A workingperson's guide to deconvolution in light microscopy. Biotechniques 31(1076-8):1080, 1082 passim
27. Levsky JM, Braut SA, Singer RH (2003) Single cell gene expression pro filing: multiplexed expression fluorescence in situ hybridization (FISH) application to the analysis of cultured cells. http://www.singerlab.org/ protocols
28. Tam R, Shopland LS, Johnson CV, McNeil JA, Lawrence JB (2002) Applications of RNA FISH for visualizing gene expression and nuclear architecture. In: Beatty B, Mai S, Squire J (eds) FISH: a practical approach. Oxford University Press, New York, p 93
29. Brown JM, Buckle VJ (2010) Detection of nascent RNA transcripts by fluorescence in situ hybridization. Methods Mol Biol 659:33-50
30. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Meth 5:877-879
31. Carlton PM, Boulanger J, Kervrann C et al (2010) Fast live simultaneous multiwavelength four-dimensional optical microscopy. Proc Natl Acad Sci USA 107:16016-16022
32. Dobbie IM, King E, Parton RM, Carlton PM, Sedat JW, Swedlow JR, Davis I (2011) OMX: a new platform for multimodal, multichannel wide-field imaging. Cold Spring Harb Protoc 2011:899-909
33. Salic A, Mitchison TJ (2008) A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc Natl Acad Sci USA 105:2415-2420
34. Cordes T, Maiser A, Steinhauer C, Schermelleh L, Tinnefeld P (2011) Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy. Phys Chem Chem Phys 13:6699-6709