Table 1 Chemical-assisted sequencing methods for single-base resolution mapping of f5C
From: 5-Formylcytosine is not a prevalent RNA modification in mammalian cells
Method | Chemistry & sensitivity (S) | f5C specificity | target RNA | Number of f5C sites reported | Reference |
|---|---|---|---|---|---|
fCAB RNA-seq | O-ethylhydroxylamine & bisulfite treatment S: low | not tested | mitochondrial-enriched RNA (human) | 1 (f5C34 of mt-tRNAMet) | |
RedBS RNA-seq | Na-borohydride & bisulfite treatment S:low | not tested | mitochondrial-enriched RNA (human) | 1 (f5C34 of mt-tRNAMet) | |
f5C-seq | Pyridine borane (PyBo) S:high | not tested | poly(A)+ RNA (yeast) | 1892 | |
Protonation-dependent sequencing | Cyanoborohydride S: low | ac4C and ca5C cross-reactivity; No cross-reactivity with m5C, hm5C and C | mt-tRNAMet (human) | 1 (f5C34 of mt-tRNAMet) | |
Mal-seq | Malononitrile (Mal) S: low | no cross-reactivity with m5C and hm5C | mt-tRNAMet (human, mouse, yeast, Drosophila, C. elegans) | human, mouse, C. elegans: 1 (f5C34 of mt-tRNAMet), yeast and Drosophila: 0 | |
f5C-seq | 2-picoline borane (PiBo) S: high | not tested | small RNA, poly(A)+ RNA, chromatin-associated RNA (caRNA) of human and mouse cells | human and mouse small RNA: 2 (f5C34 of mt-tRNAMet and f5C/f5Cm34 of ct-tRNALeu); poly(A)+ RNA: >100, caRNA: 3 sites in human and mouse, respectively | |
FIBo-seq | Immunoprecipitation & PyBo S: high | high | rRNA-depleted RNA from mESCs | 1 (f5C34 of mt-tRNAMet) | This study |
