Browse > Article
http://dx.doi.org/10.5483/BMBRep.2013.46.2.016

Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules  

Kwon, Sunjong (Department of Biomedical Engineering, Oregon Health & Science University)
Publication Information
BMB Reports / v.46, no.2, 2013 , pp. 65-72 More about this Journal
Abstract
In situ detection of RNAs is becoming increasingly important for analysis of gene expression within and between intact cells in tissues. International genomics efforts are now cataloging patterns of RNA transcription that play roles in cell function, differentiation, and disease formation, and they are demon-strating the importance of coding and noncoding RNA transcripts in these processes. However, these techniques typically provide ensemble averages of transcription across many cells. In situ hybridization-based analysis methods complement these studies by providing information about how expression levels change between cells within normal and diseased tissues, and they provide information about the localization of transcripts within cells, which is important in understanding mechanisms of gene regulation. Multi-color, single-molecule fluorescence in situ hybridization (smFISH) is particularly useful since it enables analysis of several different transcripts simultaneously. Combining smFISH with immunofluorescent protein detection provides additional information about the association between transcription level, cellular localization, and protein expression in individual cells.
Keywords
Breast cancer; ERBB2; FISH; Ribonucleoprotein (RNP); RNA; Single-molecule imaging;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Tautz, D. and Pfeifle, C. (1989) A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback. Chromosoma 98, 81-85.   DOI   ScienceOn
2 Femino, A. M., Fay, F. S., Fogarty, K. and Singer, R. H. (1998) Visualization of single RNA transcripts in situ. Science 280, 585-590.   DOI   ScienceOn
3 Itzkovitz, S. and van Oudenaarden, A. (2011) Validating transcripts with probes and imaging technology. Nat. Methods 8, S12-S19.   DOI   ScienceOn
4 Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. and Tyagi, S. (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877-879.   DOI   ScienceOn
5 Raj, A. and Tyagi, S. (2010) Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes. Methods Enzymol. 472, 365-386.   DOI   ScienceOn
6 Shih, J. D., Waks, Z., Kedersha, N. and Silver, P. A. (2011) Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA. Nucleic Acids Res. 39, 7740-7749.   DOI   ScienceOn
7 Tholouli, E., Hoyland, J. A., Di Vizio, D., O'Connell, F., Macdermott, S. A., Twomey, D., Levenson, R., Yin, J. A., Golub, T. R., Loda, M. and Byers, R. (2006) Imaging of multiple mRNA targets using quantum dot based in situ hybridization and spectral deconvolution in clinical biopsies. Biochem. Biophys. Res. Commun. 348, 628-636.   DOI   ScienceOn
8 Harland, R. M. (1991) In situ hybridization: an improved whole-mount method for Xenopus embryos. Methods Cell Biol. 36, 685-695.   DOI
9 McNally, J. G., Karpova, T., Cooper, J. and Conchello, J. A. (1999) Three-dimensional imaging by deconvolution microscopy. Methods 19, 373-385.   DOI   ScienceOn
10 Neve, R. M., Chin, K., Fridlyand, J., Yeh, J., Baehner, F. L., Fevr, T., Clark, L., Bayani, N., Coppe, J. P., Tong, F., Speed, T., Spellman, P. T., DeVries, S., Lapuk, A., Wang, N. J., Kuo, W. L., Stilwell, J. L., Pinkel, D., Albertson, D. G., Waldman, F. M., McCormick, F., Dickson, R. B., Johnson, M. D., Lippman, M., Ethier, S., Gazdar, A. and Gray, J. W. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10, 515-527.   DOI   ScienceOn
11 Chubb, J. R. and Liverpool, T. B. (2010) Bursts and pulses: insights from single cell studies into transcriptional mechanisms. Curr. Opin. Genet. Dev. 20, 478-484   DOI   ScienceOn
12 Markaki, Y., Smeets, D., Fiedler, S., Schmid, V. J., Schermelleh, L., Cremer, T. and Cremer, M. (2012) The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture. Bioessays 34, 412-426.   DOI   ScienceOn
13 Player, A. N., Shen, L. P., Kenny, D., Antao, V. P. and Kolberg, J. A. (2001) Single-copy gene detection using branched DNA (bDNA) in situ hybridization. J. Histochem. Cytochem. 49, 603-612.   DOI   ScienceOn
14 Lunde, B. M., Moore, C. and Varani, G. (2007) RNAbinding proteins: modular design for efficient function. Nat. Rev. Mol. Cell Biol. 8, 479-490.   DOI   ScienceOn
15 Speel, E. J., Saremaslani, P., Roth, J., Hopman, A. H. and Komminoth, P. (1998) Improved mRNA in situ hybridization on formaldehyde-fixed and paraffin-embedded tissue using signal amplification with different haptenized tyramides. Histochem. Cell Biol. 110, 571-577.   DOI
16 Clay, H. and Ramakrishnan, L. (2005) Multiplex fluorescent in situ hybridization in zebrafish embryos using tyramide signal amplification. Zebrafish 2, 105-111.   DOI   ScienceOn
17 Alivisatos, A. P., Gu, W. and Larabell, C. (2005) Quantum dots as cellular probes. Annu. Rev. Biomed. Eng. 7, 55-76.   DOI   ScienceOn
18 Chen, C. H., Cho, S. H., Chiang, H. I., Tsai, F., Zhang, K. and Lo, Y. H. (2011) Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization. Anal. Chem. 83, 7269-7275.   DOI   ScienceOn
19 Kawakami, S., Kubota, K., Imachi, H., Yamaguchi, T., Harada, H. and Ohashi, A. (2010) Detection of single copy genes by two-pass tyramide signal amplification fluorescence in situ hybridization (Two-Pass TSA-FISH) with single oligonucleotide probes. Microbes Environ. 25, 15-21.   DOI   ScienceOn
20 Gao, X., Yang, L., Petros, J. A., Marshall, F. F., Simons, J. W. and Nie, S. (2005) In vivo molecular and cellular imaging with quantum dots. Curr. Opin. Biotechnol. 16, 63-72.   DOI   ScienceOn
21 Chan, P., Yuen, T., Ruf, F., Gonzalez-Maeso, J. and Sealfon, S. C. (2005) Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization. Nucleic Acids Res. 33, e161.   DOI   ScienceOn
22 Nilsson, M. (2006) Lock and roll: single-molecule genotyping in situ using padlock probes and rolling-circle amplification. Histochem. Cell Biol. 126, 159-164.   DOI
23 Larsson, C., Grundberg, I., Soderberg, O. and Nilsson, M. (2010) In situ detection and genotyping of individual mRNA molecules. Nat. Methods 7, 395-397.   DOI   ScienceOn
24 Weibrecht, I., Grundberg, I., Nilsson, M. and Söderberg, O. (2011) Simultaneous visualization of both signaling cascade activity and end-point gene expression in single cells. PLoS One 6, e20148.   DOI
25 Lichtman, J. W. and Conchello, J. A. (2005) Fluorescence microscopy. Nat. Methods 2, 910-919.   DOI   ScienceOn
26 Levsky, J. M., Shenoy, S. M., Pezo, R. C. and Singer, R. H. (2002) Single-cell gene expression profiling. Science 297, 836-840.   DOI   ScienceOn
27 Nederlof, P. M., van der Flier, S., Wiegant, J., Raap, A. K., Tanke, H. J., Ploem, J. S. and van der Ploeg, M. (1990) Multiple fluorescence in situ hybridization. Cytometry 11, 126-131.   DOI   ScienceOn
28 Jakt, L. M., Moriwaki, S. and Nishikawa, S. (2013) A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization. Development 140, 216-225.   DOI   ScienceOn
29 Speicher, M. R., Gwyn Ballard, S. and Ward, D. C. (1996) Karyotyping human chromosomes by combinatorial multi- fluor FISH. Nat. Genet. 12, 368-375.   DOI   ScienceOn
30 Lubeck, E. and Cai, L. (2012) Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat. Methods 9, 743-748.   DOI   ScienceOn
31 Wang, D. O., Matsuno, H., Ikeda, S., Nakamura, A., Yanagisawa, H., Hayashi, Y. and Okamoto, A. (2012) A quick and simple FISH protocol with hybridization- sensitive fluorescent linear oligodeoxynucleotide probes. RNA 18, 166-175.   DOI
32 McKee, A. E. and Silver, P. A. (2007) Systems perspectives on mRNA processing. Cell Res. 17, 581-590.   DOI   ScienceOn
33 Boulon, S., Basyuk, E., Blanchard, J. M., Bertrand, E. and Verheggen, C. (2002) Intra-nuclear RNA trafficking: insights from live cell imaging. Biochimie. 84, 805-813.   DOI   ScienceOn
34 Politz, J. C., Tuft, R. A., Pederson, T. and Singer, R. H. (1999) Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr. Biol. 9, 285-291.   DOI   ScienceOn
35 Tyagi, S. and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303-308.   DOI   ScienceOn
36 Shaner, N. C., Steinbach, P. A. and Tsien, R. Y. (2005) A guide to choosing fluorescent proteins. Nat. Methods 2, 905-909.   DOI   ScienceOn
37 Bratu, D. P., Cha, B. J., Mhlanga, M. M., Kramer, F. R. and Tyagi, S. (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc. Natl. Acad. Sci. U.S.A. 100, 13308-13313.   DOI   ScienceOn
38 Bertrand, E., Chartrand, P., Schaefer, M., Shenoy, S. M., Singer, R. H. and Long, R. M. (1998) Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2, 437-445.   DOI   ScienceOn
39 Dictenberg, J. (2012) Genetic encoding of fluorescent RNA ensures a bright future for visualizing nucleic acid dynamics. Trends. Biotechnol. 30, 621-626.   DOI   ScienceOn
40 Paige, J. S., Wu, K. Y. and Jaffrey, S. R. (2011) RNA mimics of green fluorescent protein. Science 333, 642-646.   DOI
41 Paige, J. S., Nguyen-Duc, T., Song, W. and Jaffrey, S. R. (2012) Fluorescence imaging of cellular metabolites with RNA. Science 335, 1194.   DOI
42 Rajapakse, I. and Groudine M. (2011) On emerging nuclear order. J. Cell Biol. 192, 711-721.   DOI   ScienceOn
43 Levsky, J. M. and Singer, R. H. (2003) Fluorescence in situ hybridization: past, present and future. J. Cell Sci. 116, 2833-2838.   DOI   ScienceOn
44 ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 6, 57-74.
45 Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Roder, M., Kokocinski, F., Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L. H., Shahab, A., Skancke, J., Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guigo, R., and Gingeras, T. R. (2012) Landscape of transcription in human cells. Nature 489, 101-108.   DOI   ScienceOn
46 Dundr, M. and Misteli, T. (2010) Biogenesis of nuclear bodies. Cold Spring Harb. Perspect. Biol. 2, a000711.   DOI   ScienceOn
47 Larson, D. R., Singer, R. H. and Zenklusen, D. (2009) A single molecule view of gene expression. Trends Cell Biol. 19, 630-637.   DOI   ScienceOn
48 Wang, F., Flanagan, J., Su, N., Wang, L. C., Bui, S., Nielson, A., Wu, X., Vo, H. T., Ma, X. J. and Luo, Y. (2012) RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 14, 22-29.   DOI   ScienceOn
49 Tischler, J. and Surani, M. A. (2012) Investigating transcriptional states at single-cell-resolution. Curr. Opin. Biotechnol. 24, 69-78.
50 Hanahan, D. and Weinberg, R. A. (2011) Hallmarks of cancer: the next generation. Cell 144, 646-674.   DOI   ScienceOn
51 Gall, J. G. and Pardue, M. L. (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc. Natl. Acad. Sci. U.S.A. 63, 378-383.   DOI   ScienceOn
52 Kitaoka, M., Mitsumori, M., Hayashi, K., Hiraishi, Y., Yoshinaga, H., Nakano, K., Miyawaki, K., Noji, S., Goto, M. and Kamiya, N. (2012) Transglutaminase-mediated in situ hybridization (TransISH) system: a new methodology for simplified mRNA detection. Anal. Chem. 17, 5885-5891.
53 Qian, X. and Lloyd, R. V. (2003) Recent developments in signal amplification methods for in situ hybridization. Diagn. Mol. Pathol. 12, 1-13.   DOI   ScienceOn