Nakae A, Tanaka T, Miyake K, Hase M, Mashimo T. Comparing methods of detection and quantitation of RNA editing of rat glycine receptor alpha3.
Int J Biol Sci 2008;
4:397-405. [PMID:
18974845 PMCID:
PMC2575349 DOI:
10.7150/ijbs.4.397]
[Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 10/20/2008] [Indexed: 11/13/2022] Open
Abstract
Background: Recently, it has become evident that RNA editing-related
changes are important in the modulation of neuronal information processing.
Alternatively edited transcripts, when meagerly present, are hard to detect.
Significant functional consequences may result, however, from small differences
in editing efficiency. Moreover, it is difficult to evaluate the ratio of edited
transcripts. The glycine receptor alpha3 subunit (GlyR alpha3) is expressed in
the spinal cord, and transcripts of GlyR alpha3 are susceptible to RNA editing.
The physiological role of this editing is still unclear. To analyze changes in
RNA editing in various animal models, we need reliable and practical ways to
detect and quantitate GlyR alpha3 RNA editing.
Results: We identified and assessed different ways of detecting
edited RNA transcripts, including direct sequencing, denaturing high performance
chromatography (DHPLC), allele-specific real-time PCR with TaqMan probes, and
PCR with allele-specific primers. Using PCR with allele-specific primers on
standard PCR products for edited and nonedited GlyR alpha3, we were able to
detect as little as a 0.5% incidence of edited transcripts. We were able to
detect a 5% incidence of RNA editing using direct sequencing and 2% using DHPLC.
We could accurately determine the ratio of edited to non-edited RNA using DHPLC,
direct sequencing, and allele-specific real-time PCR with TaqMan probes.
Conclusion: We demonstrated exact and sensitive methods of detecting
RNA editing. In prepared samples, we showed means of quantitating the incidence
of editing of a particular site. The demonstrated methodologies should be very
useful when extended to the evaluation of other types of RNA editing and single
base mutations.
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