701
Views
0
CrossRef citations to date
0
Altmetric
Commentary

Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts

, , , , & ORCID Icon
Article: 2304503 | Received 20 Oct 2023, Accepted 08 Jan 2024, Published online: 29 Jan 2024

References

  • Zhang P, Zhu Y, Guo Q, et al. On the origin and evolution of RNA editing in metazoans. Cell Rep. 2023;42(2):112112. doi: 10.1016/j.celrep.2023.112112
  • Eisenberg E, Levanon EY. A-to-I RNA editing — immune protector and transcriptome diversifier. Nat Rev Genet. 2018;19(8):473–14. doi: 10.1038/s41576-018-0006-1
  • Alon S, Garrett SC, Levanon EY, et al. The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. Elife. 2015;4:4. doi: 10.7554/eLife.05198
  • Gommans WM, Mullen SP, Maas S. RNA editing: a driving force for adaptive evolution? BioEssays. 2009;31(10):1137–1145. doi: 10.1002/bies.200900045
  • Yablonovitch AL, Deng P, Jacobson D, et al. The evolution and adaptation of A-to-I RNA editing. PloS Genet. 2017;13(11):e1007064. doi: 10.1371/journal.pgen.1007064
  • Duan Y, Xu Y, Song F, et al. Differential adaptive RNA editing signals between insects and plants revealed by a new measurement termed haplotype diversity. Biol Direct. 2023;18(1):47. doi: 10.1186/s13062-023-00404-7
  • Liscovitch-Brauer N, Alon S, Porath HT, et al. Trade-off between transcriptome plasticity and genome evolution in cephalopods. Cell. 2017;169(2):191–202 e111. doi: 10.1016/j.cell.2017.03.025
  • Duan Y, Li H, Cai W. Adaptation of A-to-I RNA editing in bacteria, fungi, and animals. Front Microbiol. 2023;14:1204080. doi: 10.3389/fmicb.2023.1204080
  • Zhan D, Zheng C, Cai W, et al. The many roles of A-to-I RNA editing in animals: functional or adaptive? Front Biosci (Landmark Ed). 2023;28(10):256. doi: 10.31083/j.fbl2810256
  • Edera AA, Gandini CL, Sanchez-Puerta MV. Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria. Plant Mol Biol. 2018;97(3):215–231. doi: 10.1007/s11103-018-0734-9
  • Duan Y, Cai W, Li H. Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis. RNA. 2023;29(2):141–152. doi: 10.1261/rna.079450.122
  • Bian Z, Ni Y, Xu JR, et al. A-to-I mRNA editing in fungi: occurrence, function, and evolution. Cell Mol Life Sci. 2019;76(2):329–340. doi: 10.1007/s00018-018-2936-3
  • Liu H, Wang Q, He Y, et al. Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes. Genome Res. 2016;26(4):499–509. doi: 10.1101/gr.199877.115
  • Liu H, Li Y, Chen D, et al. A-to-I RNA editing is developmentally regulated and generally adaptive for sexual reproduction in Neurospora crassa. Proc Natl Acad Sci USA. 2017;114(37):E7756–E7765. doi: 10.1073/pnas.1702591114
  • Jiang D, Zhang J. The preponderance of nonsynonymous A-to-I RNA editing in coleoids is nonadaptive. Nat Commun. 2019;10(1):5411. doi: 10.1038/s41467-019-13275-2
  • Xin K, Zhang Y, Fan L, et al. Liu H: experimental evidence for the functional importance and adaptive advantage of A-to-I RNA editing in fungi. Proc Natl Acad Sci USA. 2023;120(12):e2219029120. doi: 10.1073/pnas.2219029120
  • Duan Y, Ma L, Song F, et al. Autorecoding A-to-I RNA editing sites in the adar gene underwent compensatory gains and losses in major insect clades. RNA. 2023;29(10):1509–1519. doi: 10.1261/rna.079682.123
  • Ma L, Zheng C, Xu S, et al. A full repertoire of hemiptera genomes reveals a multi-step evolutionary trajectory of auto-RNA editing site in insect adar gene. RNA Biol. 2023;20(1):703–714. doi: 10.1080/15476286.2023.2254985
  • Popitsch N, Huber CD, Buchumenski I, et al. A-to-I RNA editing uncovers hidden signals of adaptive genome evolution in animals. Genome Biol Evol. 2020;12(4):345–357. doi: 10.1093/gbe/evaa046
  • Palladino MJ, Keegan LP, O’Connell MA, et al. dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing. RNA. 2000;6(7):1004–1018. doi: 10.1017/S1355838200000248
  • Savva YA, Jepson JE, Sahin A, et al. Auto-regulatory RNA editing fine-tunes mRNA re-coding and complex behaviour in Drosophila. Nat Commun. 2012;3(1):790. doi: 10.1038/ncomms1789
  • Zhang R, Deng P, Jacobson D, et al. Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing. PloS Genet. 2017;13(2):e1006563. doi: 10.1371/journal.pgen.1006563
  • Zhang Y, Duan Y. Genome-wide analysis on driver and passenger RNA editing sites suggests an underestimation of adaptive signals in insects. Genes (Basel). 2023;14(10):1951. doi: 10.3390/genes14101951
  • Picardi E, D’Erchia AM, Lo Giudice C, et al. Rediportal: a comprehensive database of A-to-I RNA editing events in humans. Nucleic Acids Res. 2017;45(D1):D750–D757. doi: 10.1093/nar/gkw767
  • Ramaswami G, Li JB. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 2014;42(Database issue):D109–113. doi: 10.1093/nar/gkt996
  • An NA, Ding W, Yang XZ, et al. Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates. Genome Biol. 2019;20(1):24. doi: 10.1186/s13059-019-1638-y
  • Licht K, Kapoor U, Amman F, et al. A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing. Genome Res. 2019;29(9):1453–1463. doi: 10.1101/gr.242636.118
  • Adetula AA, Fan X, Zhang Y, et al. Landscape of tissue-specific RNA editome provides insight into co-regulated and altered gene expression in pigs (sus-scrofa). RNA Biol. 2021;18(sup1):439–450. doi: 10.1080/15476286.2021.1954380
  • Porath HT, Schaffer AA, Kaniewska P, et al. A-to-I RNA editing in the earliest-diverging eumetazoan phyla. Mol Biol Evol. 2017;34(8):1890–1901. doi: 10.1093/molbev/msx125
  • Keegan LP, McGurk L, Palavicini JP, et al. O’Connell MA: functional conservation in human and Drosophila of metazoan ADAR2 involved in RNA editing: loss of ADAR1 in insects. Nucleic Acids Res. 2011;39(16):7249–7262. doi: 10.1093/nar/gkr423
  • Grenier JK, Arguello JR, Moreira MC, et al. Global diversity lines - a five-continent reference panel of sequenced drosophila melanogaster strains. G3 (Bethesda). 2015;5(4):593–603. doi: 10.1534/g3.114.015883
  • Kuehn BM. 1000 genomes project promises closer look at variation in human genome. JAMA. 2008;300(23):2715. doi: 10.1001/jama.2008.823
  • Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780. doi: 10.1093/molbev/mst010
  • Abascal F, Zardoya R, Telford MJ. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 2010;38: W7–W13. doi: 10.1093/nar/gkq291