Table 3.

Experimental method of A>I(G) RNA-edited sites.

“De Novo” A>I(G)-RNA-Edited Sites
Method	Observations	Ref.
Sanger sequencing	Accurate, but very tedious to compare DNA and RNA.	[89]
Comparative genomics	-	[91]
Biochemical method (Inosine)	-	[92]
Inosine Chemical Erasing (ICE) sequencing	Many false positives.	[93,94]
eEndoV and hEndoV	To isolate and enrich edited transcripts in RNA before sequencing, optimizing the coverage of editing sites with low expression levels.	[95,96]
Slic-seq	RNase T1 + hEndoV + EndoVIPER-seq.	[97]
NGS and RNA-seq	Identification with high throughput. Requires meticulous methods to separate authentic from false results.	[98,99,100]
mmPCR-seq	Measures RNA-editing levels in samples with low expression levels. Complements RNA-seq.	[101]
Third-generation sequencing (L-GIREMI, PacBio, and ONT)	Identifies RNA-editing sites in long-read RNA-seq data.	[105,107]
Specific A>I(G)-RNA-edited sites
Method	Observations	Ref.
RESSq-PCR	Rapid and cost-effective method and compatible with qRT-PCR SYBR. Requires highly sensitive primer design strategies.	[102]
Padlock Probe + RCA	PCR and in situ hybridization. Requires the design of a panel of barcoded padlock probes to examine specifics editing RNA sites changes. Allows spatiotemporal resolution on cells or tissues.	[103,104]