Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules
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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 demonstrating 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.
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 demonstrating 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.
참고문헌 (53)
- ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome", Nature, 6, pp.57~74 (2012)
- Djebali, S., "Landscape of transcription in human cells", Nature 489 (2012)
- Dundr, M, "Cold Spring Harb", Perspect. Biol, 2, pp.a000711~ (2010)
- Larson, D. R., "A single molecule view of gene expression", Trends Cell Biol, 19, pp.630~637 (2009)
- Wang, F., "RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues", J. Mol. Diagn, 14, pp.22~29 (2012)
- Levsky, J. M., "Fluorescence in situ hybridization: past, present and future", J. Cell Sci, 116, pp.2833~2838 (2003)
- Tischler, J., "Investigating transcriptional states at single-cell-resolution", Curr. Opin. Biotechnol, 24, pp.69~78 (2012)
- Hanahan, D., "Hallmarks of cancer: the next generation", Cell, 144, pp.646~674 (2011)
- Gall, J. G., "Formation and detection of RNA-DNA hybrid molecules in cytological preparations", Proc. Natl. Acad. Sci. U.S.A, 63, pp.378~383 (1969)
- Kitaoka, M., "Transglutaminase-mediated in situ hybridization (TransISH) system: a new methodology for simplified mRNA detection", Anal. Chem, 17, pp.5885~5891 (2012)
- Qian, X., "Recent developments in signal amplification methods for in situ hybridization", Diagn. Mol. Pathol, 12, pp.1~13 (2003)
- Tautz, D, "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, pp.81~85 (1989)
- Femino, A. M., "Visualization of single RNA transcripts in situ", Science, 280, pp.585~590 (1998)
- Itzkovitz, S., "Validating transcripts with probes and imaging technology", Nat. Methods, 8, pp.S12~S19 (2011)
- Raj, A., "Imaging individual mRNA molecules using multiple singly labeled probes", Nat. Methods, 5, pp.877~879 (2008)
- Raj, A., "Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes", Methods Enzymol, 472, pp.365~386 (2010)
- Shih, J. D., "Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA", Nucleic Acids Res, 39, pp.7740~7749 (2011)
- Tholouli, E., "Imaging of multiple mRNA targets using quantum dot based in situ hybridization and spectral deconvolution in clinical biopsies", Biochem. Biophys. Res. Commun, 348, pp.628~636 (2006)
- Harland, R. M., "In situ hybridization: an improved whole-mount method for Xenopus embryos", Methods Cell Biol, 36, pp.685~695 (1991)
- McNally, J. G., "Three-dimensional imaging by deconvolution microscopy", Methods, 19, pp.373~385 (1999)
- Neve, R. M., "A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes", Cancer Cell, 10, pp.515~527 (2006)
- Chubb, J. R., "Bursts and pulses: insights from single cell studies into transcriptional mechanisms", Curr. Opin. Genet. Dev, 20, pp.478~484 (2010)
- Markaki, Y., "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, pp.412~426 (2012)
- Player, A. N., "Single-copy gene detection using branched DNA (bDNA) in situ hybridization", J. Histochem. Cytochem, 49, pp.603~612 (2001)
- Lunde, B. M., "RNAbinding proteins: modular design for efficient function", Nat. Rev. Mol. Cell Biol, 8, pp.479~490 (2007)
- Speel, E. J., "Improved mRNA in situ hybridization on formaldehyde-fixed and paraffin-embedded tissue using signal amplification with different haptenized tyramides", Histochem. Cell Biol, 110, pp.571~577 (1998)
- Clay, H., "Multiplex fluorescent in situ hybridization in zebrafish embryos using tyramide signal amplification", Zebrafish, 2, pp.105~111 (2005)
- Chen, C. H., "Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization", Anal. Chem, 83, pp.7269~7275 (2011)
- Kawakami, S., "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, pp.15~21 (2010)
- Gao, X., "In vivo molecular and cellular imaging with quantum dots", Curr. Opin. Biotechnol, 16, pp.63~72 (2005)
- Alivisatos, A. P., "Quantum dots as cellular probes", Annu. Rev. Biomed. Eng, 7, pp.55~76 (2005)
- Chan, P., "Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization", Nucleic Acids Res, 33, pp.e161~ (2005)
- Nilsson, M., "Lock and roll: single-molecule genotyping in situ using padlock probes and rolling-circle amplification", Histochem. Cell Biol, 126, pp.159~164 (2006)
- Larsson, C., "In situ detection and genotyping of individual mRNA molecules", Nat. Methods, 7, pp.395~397 (2010)
- Weibrecht, I., "Simultaneous visualization of both signaling cascade activity and end-point gene expression in single cells", PLoS One, 6, pp.e20148~ (2011)
- Lichtman, J. W., "Fluorescence microscopy", Nat. Methods, 2, pp.910~919 (2005)
- Nederlof, P. M., "Multiple fluorescence in situ hybridization", Cytometry, 11, pp.126~131 (1990)
- Jakt, L. M., "A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization", Development, 140, pp.216~225 (2013)
- Speicher, M. R., "Karyotyping human chromosomes by combinatorial multi- fluor FISH", Nat. Genet, 12, pp.368~375 (1996)
- Levsky, J. M., "Single-cell gene expression profiling", Science, 297, pp.836~840 (2002)
- Lubeck, E., "Single-cell systems biology by super-resolution imaging and combinatorial labeling", Nat. Methods, 9, pp.743~748 (2012)
- Wang, D. O., "A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes", RNA, 18, pp.166~175 (2012)
- McKee, A. E., "Systems perspectives on mRNA processing", Cell Res, 17, pp.581~590 (2007)
- Boulon, S., "Intra-nuclear RNA trafficking: insights from live cell imaging", Biochimie, 84, pp.805~813 (2002)
- Politz, J. C., "Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells", Curr. Biol, 9, pp.285~291 (1999)
- Tyagi, S., "Molecular beacons: probes that fluoresce upon hybridization", Nat. Biotechnol, 14, pp.303~308 (1996)
- Bratu, D. P., "Visualizing the distribution and transport of mRNAs in living cells", Proc. Natl. Acad. Sci. U.S.A, 100, pp.13308~13313 (2003)
- Bertrand, E., "Localization of ASH1 mRNA particles in living yeast", Mol. Cell, 2, pp.437~445 (1998)
- Dictenberg, J., "Genetic encoding of fluorescent RNA ensures a bright future for visualizing nucleic acid dynamics", Trends. Biotechnol, 30, pp.621~626 (2012)
- Shaner, N. C., "A guide to choosing fluorescent proteins", Nat. Methods, 2, pp.905~909 (2005)
- Paige, J. S., "RNA mimics of green fluorescent protein", Science, 333, pp.642~646 (2011)
- Paige, J. S., "Fluorescence imaging of cellular metabolites with RNA", Science, 335, pp.1194~
- Rajapakse, I., "On emerging nuclear order", J. Cell Biol, 192, pp.711~721 (2011)