Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Sep 20;11(18):e4154.
doi: 10.21769/BioProtoc.4154.

Quantitative Analysis of RNA Editing at Specific Sites in Plant Mitochondria or Chloroplasts Using DNA Sequencing

Yang Yang  1 , Weixing Shan  1
Affiliations

Quantitative Analysis of RNA Editing at Specific Sites in Plant Mitochondria or Chloroplasts Using DNA Sequencing

Yang Yang et al. Bio Protoc. .

Abstract

Cytidine-to-uridine (C-to-U) RNA editing is one of the most important post-transcriptional RNA processing in plant mitochondria and chloroplasts. Several techniques have been developed to detect the RNA editing efficiency in plant mitochondria and chloroplasts, such as poisoned primer extension (PPE) assays, high-resolution melting (HRM) analysis, and DNA sequencing. Here, we describe a method for the quantitative detection of RNA editing at specific sites by sequencing cDNA from plant leaves to further evaluate the effect of different treatments or plant mutants on the C to U RNA editing in mitochondria and chloroplasts.

Keywords: C to U RNA editing; Chloroplasts; DNA sequencing; Editing extent; Mitochondria.

PubMed Disclaimer

Conflict of interest statement

Competing interestsThe authors declare no conflict of interests.

Figures

Figure 1.
Figure 1.. Workflow of the RNA editing analysis of specific sites in mitochondria and chloroplasts
Figure 2.
Figure 2.. Analysis of RNA editing extent by Bioedit.
The blue arrows mark the targeted nucleotide peaks, and the black hollow boxes mark the reads of the peak heights.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Barkan A. and Small I.(2014). Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol 65: 415-442. - PubMed
    1. Bentolila S., Heller W. P., Sun T., Babina A. M., Friso G., van Wijk K. J. and Hanson M. R.(2012). RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proc Natl Acad Sci U S A 109(22): E1453-1461. - PMC - PubMed
    1. Brehme N., Bayer-Csaszar E., Glass F. and Takenaka M.(2015). The DYW Subgroup PPR Protein MEF35 Targets RNA Editing Sites in the Mitochondrial rpl16, nad4 and cob mRNAs in Arabidopsis thaliana . PLoS One 10(10): e0140680. - PMC - PubMed
    1. Chateigner-Boutin A. L. and Small I.(2007). A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res 35(17): e114. - PMC - PubMed
    1. Dahan J. and Mireau H.(2013). The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes. RNA Biol 10(9): 1469-1476. - PMC - PubMed

LinkOut - more resources