Table 1 Overview of m1A detection methods
From: Research progress of N1-methyladenosine RNA modification in cancer
Detection method | Feature | Advantage | Drawback | Function | Article source |
|---|---|---|---|---|---|
2D-TLC | differential retention values(Rf values) | ease and cheap | hydrolysis and 32P labeling steps may have bias | – | [17] |
HPLC | differential retention, enzymatic RNA digestion | faster no radiolabeling | loss of sequence information | analysis of modifications with high abundance | |
LC-MS | HPLC, mass Spectrometry | high accuracy and sensitivity | loss of sequence information | detect and quantify the m1A level in mRNA | |
Primer-extension | block base pairing compared cDNA bands | Precise modification position | RNA targets of high abundance and existing sequence knowledge | validate the new detection technique | [17] |
ARM-Seq | ALKB treatment | sensitive and accuracy | – | Assay escape modification, Analysis of RNA modification and processing sequences | [20] |
m1A-ID-seq | RNA Immu-opreipitaion with ALKB assisted | no cross-reactivity | m1A was difficult to obtain, rely on specific m1A antibody | the first trans-criptomewide characterization of m1A | [21] |
MeRIP-seq-or-m1A-seq | Dimroth rearrangement, immune-oprecipitation | low mutation rate, lower mismatch rate | rely on specific m1A antibody | – | [22] |
m1A-MAP-seq | Immun-oprecipitation, AlkB treatment, TGIRT-mediated RT, ligation-based strand-specific library preparation protocol | Excellent readthrough efficiency and relatively high mutation frequency | TGIRT Under-estimated the m1A level, the sequence context of RNA affect the mutation rate | identify m1A modification at mRNA cap, and GUUCRA tRNA-like sequencemotif | [6] |
m1A-IP-seq | ALKB treatment, immun-oprecipitation, Differential abundance analysis, RT-1306-mediated RT mutation | capture robustly mutation signature, good reproducibility, wide transcriptome coverage, high alignment rate to the genome | data re-producibility worse, false negatives, disable the detection of potential sites at or near the 5′-cap | discovered hundreds of new m1A sites in human mRNA | [6] |
m1A-quant-seq | ALKB treatment spike-in RNA RT1306-mediated RT mutation | Mutation signatures and sensitivity to AlkB treatment are robustly observed | false negatives result, disable the detection of potential sites at or near the 5′-cap | estimate m1A stoichiometries at individual sites in the transcriptome | [6] |
m1A-seq-TGIRT | Immun-oprecipitation, Dimroth rearrangement, TGIRT-mediated RT | identifying individual modified bases, higher misincorporation rates, not require adapter ligation | low truncation rates, low RT activity | redefinition of m1A genome-wide distribution | |
m1A-seq-SS | immunoprecipitation, Dimroth rearrangement, SS-mediated RT | identifying individual modified bases, premature truncations | – | – | [23] |