Alon S., Garrett S. C., Levanon E. Y., Olson S., Graveley B. R., Rosenthal J. J. et al. 2015 The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. eLife 4, e05198.

Article  PubMed  PubMed Central  Google Scholar 

Birk M. A., Liscovitch-Brauer N., Dominguez M. J., McNeme S., Yue Y., Hoff J. D. et al. 2023 Temperature-dependent RNA editing in octopus extensively recodes the neural proteome. Cell 186, e2513.

Article  Google Scholar 

Chateigner-Boutin A. L. and Small I. 2011 Organellar RNA editing. Wiley Interdiscip. Rev. RNA 2, 493–506.

Article  PubMed  CAS  Google Scholar 

Chu D. and Wei L. 2019 The chloroplast and mitochondrial C-to-U RNA editing in Arabidopsis thaliana shows signals of adaptation. Plant Direct. 3, e00169.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Dominissini D., Nachtergaele S., Moshitch-Moshkovitz S., Peer E., Kol N., Ben-Haim M. S. et al. 2016 The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441–446.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Duan Y. 2025 Accurate interpretation of inosines in RNAs: recognized as G is more than basepairing with C. Epigenomics 1–6 (in press).

Duan Y., Cai W. and Li H. 2023a Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis. RNA 29, 141–152.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Duan Y., Li H. and Cai W. 2023b Adaptation of A-to-I RNA editing in bacteria, fungi, and animals. Front Microbiol. 14, 1204080.

Article  PubMed  PubMed Central  Google Scholar 

Duan Y., Ma L., Liu J., Liu X., Song F., Tian L. et al. 2024 The first A-to-I RNA editome of hemipteran species Coridius chinensis reveals overrepresented recoding and prevalent intron editing in early-diverging insects. Cell Mol. Life Sci. 81, 136.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Duan Y., Xu Y., Song F., Tian L., Cai W. and Li H. 2023c Differential adaptive RNA editing signals between insects and plants revealed by a new measurement termed haplotype diversity. Biol. Direct. 18, 47.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Eisenberg E. and Levanon E. Y. 2018 A-to-I RNA editing - immune protector and transcriptome diversifier. Nat. Rev. Genet. 19, 473–490.

Article  PubMed  CAS  Google Scholar 

Gao Z., Zha X., Li M., Xia X. and Wang S. 2024 Insights into the m6A demethylases FTO and ALKBH5: structural, biological function, and inhibitor development. Cell Biosci. 14, 108.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ge Z., Quek B. L., Beemon K. L. and Hogg J. R. 2016 Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway. Elife 5, e11155.

Article  PubMed  PubMed Central  Google Scholar 

Graveley B. R., Brooks A. N., Carlson J. W., Duff M. O., Landolin J. M., Yang L. et al. 2011 The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479.

Article  PubMed  CAS  Google Scholar 

Gu X., Zhuang A., Yu J., Yang L., Ge S., Ruan J. et al. 2024 Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1A demethylation of SP100A. Nucleic Acids Res. 52, 2273–2289.

Article  PubMed  CAS  Google Scholar 

He Y. F., Li B. Z., Li Z., Liu P., Wang Y., Tang Q. et al. 2011 Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303–1307.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Higuchi M., Stefan M., Single F. N., Hartner J., Rozov A., Burnashev N. et al. 2000 Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406, 78–81.

Article  PubMed  CAS  Google Scholar 

Jia G., Fu Y., Zhao X., Dai Q., Zheng G., Yang Y. et al. 2011 N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Jonkhout N., Tran J., Smith M. A., Schonrock N., Mattick J. S. and Novoa E. M. 2017 The RNA modification landscape in human disease. RNA 23, 1754–1769.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lerner T., Papavasiliou F. N. and Pecori R. 2018 RNA editors, cofactors, and mRNA targets: an overview of the C-to-U RNA editing machinery and its implication in human disease. Genes (Basel) 10, 10010013.

Article  Google Scholar 

Li C., Xu P., Huang Y., Wang Y., Wu Y., Li H. et al. 2023 RNA methylations in depression, from pathological mechanism to therapeutic potential. Biochem. Pharmacol. 215, 115750.

Article  PubMed  CAS  Google Scholar 

Licht K., Hartl M., Amman F., Anrather D., Janisiw M. P. and Jantsch M. F. 2019 Inosine induces context-dependent recoding and translational stalling. Nucleic Acids Res. 47, 3–14.

Article  PubMed  CAS  Google Scholar 

Liddicoat B. J., Piskol R., Chalk A. M., Ramaswami G., Higuchi M., Hartner J. C. et al. 2015 RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science 349, 1115–1120.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Liu J., Zhao T., Zheng C., Ma L., Song F., Tian L. et al. 2024a An orthology-based methodology as a complementary approach to retrieve evolutionarily conserved A-to-I RNA editing sites. RNA Biol. 21, 29–45.

Article  PubMed  PubMed Central  Google Scholar 

Liu J., Zheng C. and Duan Y. 2024b New comparative genomic evidence supporting the proteomic diversification role of A-to-I RNA editing in insects. Mol. Genet. Genomics 299, 46.

Article  PubMed  CAS  Google Scholar 

Liu W. W., Zheng S. Q., Li T., Fei Y. F., Wang C., Zhang S. et al. 2024c RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct. Target. Ther. 9, 70.

Article  PubMed  PubMed Central  Google Scholar 

Liu Z. and Zhang J. 2018 Most m6A RNA modifications in protein-coding regions are evolutionarily unconserved and likely nonfunctional. Mol. Biol. Evol. 35, 666–675.

Article  PubMed  CAS  Google Scholar 

Ma J., Zhang L., Chen S. and Liu H. 2022 A brief review of RNA modification related database resources. Methods 203, 342–353.

Article  PubMed  CAS  Google Scholar 

Ma L., Zheng C., Liu J., Song F., Tian L., Cai W. et al. 2024 Learning from the codon table: convergent recoding provides novel understanding on the evolution of A-to-I RNA editing. J. Mol. Evol. 92, 488–504.

Article  PubMed  CAS  Google Scholar 

Mauer J. and Jaffrey S. R. 2018 FTO, m6Am, and the hypothesis of reversible epitranscriptomic mRNA modifications. FEBS Lett. 592, 2012–2022.

Article  PubMed  CAS  Google Scholar 

Morita Y., Shibutani T., Nakanishi N., Nishikura K., Iwai S. and Kuraoka I. 2013 Human endonuclease V is a ribonuclease specific for inosine-containing RNA. Nat. Commun. 4, 2273.

Article  PubMed  Google Scholar