Abstract
It is now clear that long noncoding RNAs (lncRNAs) regulate a number of aspects of nuclear organization and gene expression. An important tool for the study of the distribution and function of lncRNAs is RNA fluorescence in situ hybridization (RNA-FISH). The protocols presented in this chapter describe this method in detail and also mention a number of critical points that must be considered when performing this technique.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Femino AM et al (1998) Visualization of single RNA transcripts in situ. Science 280:585–590
Narimatsu R, Patterson BK (2005) High-throughput cervical cancer screening using intracellular human papillomavirus E6 and E7 mRNA quantification by flow cytometry. Am J Clin Pathol 123:716–723
Popescu NC et al (1993) A Burkitt lymphoma cell line with integrated Epstein-Barr virus at a stable chromosome modification site. Virology 195:248–251
Fan Y et al (2001) Determination of transgenic loci by expression FISH. Genomics 71:66–69
Bridger JM et al (2005) Nuclear RNAs confined to a reticular compartment between chromosome territories. Exp Cell Res 302:180–193
Clemson CM et al (1996) XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 132:259–275
Dirks RW, Raap AK (1995) Cell-cycle-dependent gene expression studied by two-colour fluorescent detection of a mRNA and histone mRNA. Histochem Cell Biol 104:391–395
Gribnau J et al (2000) Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol Cell 5:377–386
Hutchinson JN et al (2007) A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8:39
Lampel S et al (1997) Nuclear RNA accumulations contain released transcripts and exhibit specific distributions with respect to Sm antigen foci. DNA Cell Biol 16:1133–1142
Lawrence JB, Singer RH, Marselle LM (1989) Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization. Cell 57:493–502
Miles J et al (2007) Intergenic transcription, cell-cycle and the developmentally regulated epigenetic profile of the human beta-globin locus. PLoS One 2:e630
van de Corput MP, Grosveld FG (2001) Fluorescence in situ hybridization analysis of transcript dynamics in cells. Methods 25:111–118
Zirbel RM et al (1993) Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res 1:93–106
Braidotti G (2001) RNA-FISH to analyze allele-specific expression. Methods Mol Biol 181:169–180
Herzing LB, Cook EH Jr, Ledbetter DH (2002) Allele-specific expression analysis by RNA-FISH demonstrates preferential maternal expression of UBE3A and imprint maintenance within 15q11–q13 duplications. Hum Mol Genet 11:1707–1718
Levsky JM et al (2002) Single-cell gene expression profiling. Science 297:836–840
Dirks RW, Daniel KC, Raap AK (1995) RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization. J Cell Sci 108:2565–2572
Huang S, Spector DL (1996) Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J Cell Biol 133:719–732
Xing Y et al (1993) Higher level organization of individual gene transcription and RNA splicing. Science 259:1326–1330
Raj A, Tyagi S (2010) Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes. Methods Enzymol 472:365–386
Raj A et al (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5:877–879
Raj A et al (2010) Variability in gene expression underlies incomplete penetrance. Nature 463:913–918
So LH et al (2011) General properties of transcriptional time series in Escherichia coli. Nat Genet 43:554–560
Trcek T et al (2011) Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell 147:1484–1497
Vargas DY et al (2011) Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147:1054–1065
Zenklusen D, Larson DR, Singer RH (2008) Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol 15:1263–1271
Tripathi V et al (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925–938
Acknowledgments
Research in the KVP lab is supported by grants from NIH/NIGMS (GM088252) and American Cancer Society (RSG-11-174-01-RMC). TH is an HHMI investigator.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Tripathi, V., Fei, J., Ha, T., Prasanth, K.V. (2015). RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells. In: Carmichael, G. (eds) Regulatory Non-Coding RNAs. Methods in Molecular Biology, vol 1206. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1369-5_11
Download citation
DOI: https://doi.org/10.1007/978-1-4939-1369-5_11
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1368-8
Online ISBN: 978-1-4939-1369-5
eBook Packages: Springer Protocols