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Visualization of Nuclear and Cytoplasmic Long Noncoding RNAs at Single-Cell Level by RNA-FISH

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Book cover Capturing Chromosome Conformation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2157))

Abstract

The RNA fluorescence in situ hybridization (RNA-FISH) methodology offers an attractive strategy to deepen our knowledge on the long noncoding RNA biology. In this chapter, we provide a comprehensive overview of the current RNA-FISH protocols available for imaging nuclear and cytoplasmic lncRNAs within cells or tissues. We describe a multicolor approach optimized for the simultaneous visualization of these transcripts with their specific molecular interactors, such as proteins or DNA sequences. Common challenges faced by this methodology such as cell-type specific permeabilization, target accessibility, image acquisition, and post-acquisition analyses are also discussed.

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Acknowledgments

This work was partially supported by grants from Sapienza University (prot. RM11715C7C8176C1 and RM11916B7A39DCE5) and FFABR 2017 to M.B. Panel a of Fig. 4 was reprinted from Cell, 2011, 147(2), Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I., “A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA”, Pages 358-69, Copyright (2011), with permission from Elsevier. License number: 4398770836312. The authors declare no competing financial interests.

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Authors and Affiliations

  1. Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy

    Tiziana Santini

  2. Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy

    Julie Martone & Monica Ballarino

Authors
  1. Tiziana Santini
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  2. Julie Martone
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  3. Monica Ballarino
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Corresponding author

Correspondence to Monica Ballarino .

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Editors and Affiliations

  1. Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy

    Beatrice Bodega

  2. Istituto Nazionale di Genetica Molecolare, Milan, Italy

    Chiara Lanzuolo

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Santini, T., Martone, J., Ballarino, M. (2021). Visualization of Nuclear and Cytoplasmic Long Noncoding RNAs at Single-Cell Level by RNA-FISH. In: Bodega, B., Lanzuolo, C. (eds) Capturing Chromosome Conformation. Methods in Molecular Biology, vol 2157. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0664-3_15

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  • DOI: https://doi.org/10.1007/978-1-0716-0664-3_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0663-6

  • Online ISBN: 978-1-0716-0664-3

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