Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA-FISH

Kun Huang; Blake C Meyers; Jeffrey L Caplan

doi:10.1007/978-1-0716-3766-1_7

Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA-FISH

Methods Mol Biol. 2024:2784:101-111. doi: 10.1007/978-1-0716-3766-1_7.

Authors

Kun Huang^{1

2

3}, Blake C Meyers^{4

5

6}, Jeffrey L Caplan^{7

8}

Affiliations

¹ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
² Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
³ Molecular Imaging Core, Dana-Farber Cancer Institute, Boston, USA.
⁴ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA. bmeyers@danforthcenter.org.
⁵ Donald Danforth Plant Science Center, St. Louis, MO, USA. bmeyers@danforthcenter.org.
⁶ Division of Plant Science and Technology, University of Missouri - Columbia, Columbia, MO, USA. bmeyers@danforthcenter.org.
⁷ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA. jcaplan@udel.edu.
⁸ Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA. jcaplan@udel.edu.

PMID: 38502481
DOI: 10.1007/978-1-0716-3766-1_7

Abstract

Plant small RNAs are 21-24 nucleotide, noncoding RNAs that function as regulators in plant growth and development. Colorimetric detection of plant small RNAs was made possible with the introduction of locked nucleic acid probes. However, fluorescent detection of plant small RNAs has been challenging due to the high autofluorescence from plant tissue. Here we report a fluorescent in situ detection method for plant small RNAs. This method can be applied to most plant samples and tissue types and also can be adapted for single-molecule detection of small RNAs with super-resolution microscopy.

Keywords: Autofluorescence; Confocal; FISH; In situ hybridization; Linear spectral unmixing; Plant; Quantification; RNAs; SIM; STORM; Small RNAs; Spectra.

MeSH terms

Coloring Agents
In Situ Hybridization, Fluorescence / methods
Nucleic Acid Probes*
Plants / genetics
RNA, Plant / genetics
RNA, Untranslated*

Substances

RNA, Untranslated
Nucleic Acid Probes
RNA, Plant
Coloring Agents