A Nonsequencing Approach for the Rapid Detection of RNA Editing

Summary

Rapid detection and reliable quantification of RNA editing events at a genomic scale remain challenging and currently rely on direct RNA sequencing methods. The protocol described here uses microtemperature gradient gel electrophoresis (µTGGE) as a simple, quick, and portable method of detecting RNA editing.

Abstract

RNA editing is a process that leads to posttranscriptional sequence alterations in RNAs. Detection and quantification of RNA editing rely mainly on Sanger sequencing and RNA sequencing techniques. However, these methods can be costly and time-consuming. In this protocol, a portable microtemperature gradient gel electrophoresis (µTGGE) system is used as a nonsequencing approach for the rapid detection of RNA editing. The process is based on the principle of electrophoresis, which uses high temperatures to denature nucleic acid samples as they move across a polyacrylamide gel. Across a range of temperatures, a DNA fragment forms a gradient of fully double-stranded DNA to partially separated strands and then to entirely separated single-stranded DNA. RNA-edited sites with distinct nucleotide bases produce different melting profiles in µTGGE analyses. We used the µTGGE-based approach to characterize the differences between the melting profiles of four edited RNA fragments and their corresponding nonedited (wild-type) fragments. Pattern Similarity Scores (PaSSs) were calculated by comparing the band patterns produced by the edited and nonedited RNAs and were used to assess the reproducibility of the method. Overall, the platform described here enables the detection of even single base mutations in RNAs in a straightforward, simple, and cost-effective manner. It is anticipated that this analysis tool will aid new molecular biology findings.

Introduction

Single nucleotide variants (SNVs) in genomic RNA, including A-to-I, C-to-U, and U-to-C variants, can indicate RNA editing events. However, the detection of SNVs in RNA remains a technically challenging task. Conventionally, the ratio of edited to nonedited RNA is determined by direct sequencing, allele-specific real-time polymerase chain reaction (PCR), or denaturing high-performance liquid chromatography (HPLC) approaches^1,2,3,4,5,6. However, these approaches are not part....

Protocol

1. Optimization of the target fragment

NOTE: Four edited genes were used in the development of this protocol, including two nuclear genes (AT2G16586 and AT5G02670) from A. thaliana, and the genes encoding blue fluorescent protein (BFP) and enhanced green fluorescent protein (EGFP) expressed in HEK293 cells.

1. To identify gene fragments with different melting profiles, representing edited versus nonedited regions, generate predicted melting curves using the uMelt HETS web-based tool, an extension of the original uMelt software¹³.
   NOTE: This tool predicts the shapes of melting....

Results

Use of µTGGE to identify single nucleotide base changes in RNA editing events
Four edited genes were used for this protocol (Table 1), including the BFP gene produced in HEK293 cells (with C-to-U RNA editing by the deaminase enzymes of apolipoprotein B mRNA editing enzyme complex; APOBEC1¹⁵), the EGFP gene containing the ochre stop codon (TAA) produced in HEK293 cells (with A-to-I RNA editing by adenosine deaminase acting on RNA 1; ADAR1¹⁶

Discussion

RNA editing plays an important role in biology; however, current methods of detecting RNA editing, such as chromatography and sequencing, present several challenges due to their high cost, excessive time requirements, and complexity. The protocol described here is a simple, rapid, and cost-effective method of detecting RNA editing that uses a portable, microsized, TGGE-based system. This system can be used to differentiate between edited and nonedited genes prior to Sanger sequencing. Specifically, edited and nonedited g.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
2U ExoI	Takara	2650A	Exonuclease I
40(w/v)%-acrylamide/bis (19:1)	Thermo fisher	AM9022
Ammonium persulfate (APS)	Thermo Fisher	17874
Centrifuge Mini spin	eppendorf	5452000034
Digital dry bath/ block heater	Thermo fisher	NA
Gold Taq Polymerase Master mixture	Promega	M7122
LATaq DNA polymerase	TAKARA	RR002A	Taq Polymerase
micro-TGGE  cassette holder	BioSeeds Corp.	BS-GE-CH
micro-TGGE apparatus	Lifetech Corp.	TG
micro-TGGE gel cassette	BioSeeds Corp.	BS-TGGE-C
NanoDrop 1000	Thermo fisher	ND-1000	Spectrophotometer
Plant Rneasy Mini kit	Qiagen	74904
ReverTra Ace Master Mix	TOYOBO	TRT101	M-MLV (Moloney Murine Leukemia Virus) reverse transcriptase
Rneasy Mini kit	Qiagen	74104
Shrimp Alkaline Phosphatase	Takara	2660B
SYBR Gold nucleic acid gel stain	Thermo fisher	S11494
TBE buffer	Thermo fisher	B52
Tetramethylethylenediamine (TEMED)	Nacalai tesque	33401-72
Urea, Nuclease and protease tested	Nacalai tesque	35940-65