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

Tiziana Santini; Julie Martone; Monica Ballarino

doi:10.1007/978-1-0716-0664-3_15

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

Methods Mol Biol. 2021:2157:251-280. doi: 10.1007/978-1-0716-0664-3_15.

Authors

Tiziana Santini¹, Julie Martone², Monica Ballarino³

Affiliations

¹ Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
² Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy.
³ Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy. monica.ballarino@uniroma1.it.

PMID: 32820409
DOI: 10.1007/978-1-0716-0664-3_15

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.

Keywords: Immunofluorescence; In situ hybridization; RNA-FISH; Single-cell detection; lncRNA; ncRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Nucleus / metabolism*
Cytoplasm / metabolism*
Humans
In Situ Hybridization, Fluorescence / methods*
RNA, Long Noncoding / analysis*
RNA, Long Noncoding / metabolism*

Substances

RNA, Long Noncoding