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Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers

Yang, Weibing and Schuster, Christoph and Prunet, Nathanaël and Dong, Qingkun and Landrein, Benoit and Wightman, Raymond and Meyerowitz, Elliot M. (2020) Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers. Plant Physiology, 182 (1). pp. 147-158. ISSN 0032-0889. PMCID PMC6945838. doi:10.1104/pp.19.00980. https://resolver.caltech.edu/CaltechAUTHORS:20191118-081715086

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Abstract

In addition to transcriptional regulation, gene expression is further modulated through mRNA spatiotemporal distribution, by RNA movement between cells, and by RNA localization within cells. Here, we have adapted RNA fluorescence in situ hybridization (FISH) to explore RNA localization in Arabidopsis (Arabidopsis thaliana). We show that RNA FISH on sectioned material can be applied to investigate the tissue and subcellular localization of meristem and flower development genes, cell cycle transcripts, and plant long noncoding RNAs. We also developed double RNA FISH to dissect the coexpression of different mRNAs at the shoot apex and nuclear-cytoplasmic separation of cell cycle gene transcripts in dividing cells. By coupling RNA FISH with fluorescence immunocytochemistry, we further demonstrate that a gene’s mRNA and protein may be simultaneously detected, for example revealing uniform distribution of PIN-FORMED1 (PIN1) mRNA and polar localization of PIN1 protein in the same cells. Therefore, our method enables the visualization of gene expression at both transcriptional and translational levels with subcellular spatial resolution, opening up the possibility of systematically tracking the dynamics of RNA molecules and their cognate proteins in plant cells.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1104/pp.19.00980DOIArticle
http://www.plantphysiol.org/content/182/1/147/tab-figures-dataPublisherSupplemental Data
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945838PubMed CentralArticle
ORCID:
AuthorORCID
Yang, Weibing0000-0002-2379-5729
Schuster, Christoph0000-0002-1948-2367
Prunet, Nathanaël0000-0002-8939-5920
Landrein, Benoit0000-0002-2371-9996
Wightman, Raymond0000-0003-1295-4875
Meyerowitz, Elliot M.0000-0003-4798-5153
Alternate Title:Visualization of RNA Localization by FISH, Visualization of Protein Coding, Long Non-coding and Nuclear RNAs by FISH in Sections of Shoot Apical Meristems and Developing Flowers
Additional Information:© 2020 American Society of Plant Biologists. Received August 8, 2019; Accepted November 5, 2019; Published November 13, 2019. We thank Jim Murray for sharing the H4::DB-VENUS seeds. We also thank Detlef Weigel for providing the Non-Radioactive in Situ Hybridisation with Arabidopsis Floral Tissue protocol. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Elliot M. Meyerowitz (meyerow@caltech.edu). W.Y. and E.M.M. designed the research; W.Y. performed most of the experiments; C.S. helped to generate some of the probes; N.P., Q.D., and B.L. carried out fluorescent reporter analysis; W.Y. and E.M.M. analyzed the data and wrote the article with contributions from R.W. and C.S. This work was funded by the Gatsby Charitable Foundation (through fellowship GAT3395/DAA). E.M.M. is supported by the Howard Hughes Medical Institute. The Microscopy and Histology Facilities at the Sainsbury Laboratory are supported by The Gatsby Charitable Foundation. Q.D. is supported by the Graduate Student Oversea Study Program South China Agricultural University (2018LHPY011).
Funders:
Funding AgencyGrant Number
Gatsby Charitable FoundationGAT3395/DAA
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
South China Agricultural University2018LHPY011
Issue or Number:1
PubMed Central ID:PMC6945838
DOI:10.1104/pp.19.00980
Record Number:CaltechAUTHORS:20191118-081715086
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191118-081715086
Official Citation:Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers. Weibing Yang, Christoph Schuster, Nathanaël Prunet, Qingkun Dong, Benoit Landrein, Raymond Wightman, Elliot M. Meyerowitz. Plant Physiology Jan 2020, 182 (1) 147-158; DOI: 10.1104/pp.19.00980
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:99888
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:18 Nov 2019 18:35
Last Modified:16 Nov 2021 17:50

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