Abstract
Post-transcriptional modifications are essential mechanisms for mRNA biogenesis and function in eukaryotic cells. Beyond well-characterized events such as splicing, capping, and polyadenylation, there are several others, as RNA editing mechanisms and regulation of transcription mediated by miRNAs that are taking increasing attention in the last years. RNA editing through A-to-I deamination increases transcriptomic complexity, generating different proteins with amino acid substitution from the same transcript. On the other hand, miRNAs can regulate gene expression modulating target mRNA decay and translation. Interestingly, recent studies highlight the possibility that miRNAs might undergo editing themselves. This mainly translates in the degradation or uncorrected maturation of miRNAs but also in the recognition of different targets. The presence of edited and unedited forms of the same miRNA may have important biological implications in both health and disease. Here we review ongoing investigations on miRNA RNA editing with the aim to shed light on the growing importance of this mechanism in adding complexity to post-transcriptional regulation of gene expression.
Similar content being viewed by others
References
Bentley DL (2014) Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15(3):163–175. https://doi.org/10.1038/nrg3662
Orlandi C, Barbon A, Barlati S (2012) Activity regulation of adenosine deaminases acting on RNA (ADARs). Mol Neurobiol 45(1):61–75. https://doi.org/10.1007/s12035-011-8220-2
Bass BL, Weintraub H (1988) An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell 55(6):1089–1098
Athanasiadis A, Rich A, Maas S (2004) Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol 2(12):e391. https://doi.org/10.1371/journal.pbio.0020391
Daniel C, Lagergren J, Ohman M (2015) RNA editing of non-coding RNA and its role in gene regulation. Biochimie 117:22–27. https://doi.org/10.1016/j.biochi.2015.05.020
Wagner RW, Smith JE, Cooperman BS, Nishikura K (1989) A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Natl Acad Sci U S A 86(8):2647–2651
Bass BL, Nishikura K, Keller W, Seeburg PH, Emeson RB, O'Connell MA, Samuel CE, Herbert A (1997) A standardized nomenclature for adenosine deaminases that act on RNA. RNA 3(9):947–949
Bass BL (2002) RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem 71:817–846. https://doi.org/10.1146/annurev.biochem.71.110601.135501
Kim U, Wang Y, Sanford T, Zeng Y, Nishikura K (1994) Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing. Proc Natl Acad Sci U S A 91(24):11457–11461
Melcher T, Maas S, Herb A, Sprengel R, Seeburg PH, Higuchi M (1996) A mammalian RNA editing enzyme. Nature 379(6564):460–464. https://doi.org/10.1038/379460a0
Chen CX, Cho DS, Wang Q, Lai F, Carter KC, Nishikura K (2000) A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains. RNA 6(5):755–767
Herbert A, Alfken J, Kim YG, Mian IS, Nishikura K, Rich A (1997) A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc Natl Acad Sci U S A 94(16):8421–8426
George CX, Samuel CE (1999) Human RNA-specific adenosine deaminase ADAR1 transcripts possess alternative exon 1 structures that initiate from different promoters, one constitutively active and the other interferon inducible. Proc Natl Acad Sci U S A 96(8):4621–4626
Sansam CL, Wells KS, Emeson RB (2003) Modulation of RNA editing by functional nucleolar sequestration of ADAR2. Proc Natl Acad Sci U S A 100(24):14018–14023. https://doi.org/10.1073/pnas.2336131100
Cho DS, Yang W, Lee JT, Shiekhattar R, Murray JM, Nishikura K (2003) Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA. J Biol Chem 278(19):17093–17102. https://doi.org/10.1074/jbc.M213127200
Valente L, Nishikura K (2007) RNA binding-independent dimerization of adenosine deaminases acting on RNA and dominant negative effects of nonfunctional subunits on dimer functions. J Biol Chem 282(22):16054–16061. https://doi.org/10.1074/jbc.M611392200
Higuchi M, Single FN, Kohler M, Sommer B, Sprengel R, Seeburg PH (1993) RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell 75(7):1361–1370
Burns CM, Chu H, Rueter SM, Hutchinson LK, Canton H, Sanders-Bush E, Emeson RB (1997) Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature 387(6630):303–308. https://doi.org/10.1038/387303a0
Bhalla T, Rosenthal JJ, Holmgren M, Reenan R (2004) Control of human potassium channel inactivation by editing of a small mRNA hairpin. Nat Struct Mol Biol 11(10):950–956. https://doi.org/10.1038/nsmb825
Daniel C, Wahlstedt H, Ohlson J, Bjork P, Ohman M (2011) Adenosine-to-inosine RNA editing affects trafficking of the gamma-aminobutyric acid type A (GABA(A)) receptor. J Biol Chem 286(3):2031–2040. https://doi.org/10.1074/jbc.M110.130096
Behm M, Ohman M (2016) RNA editing: a contributor to neuronal dynamics in the mammalian brain. Trends Genet 32(3):165–175. https://doi.org/10.1016/j.tig.2015.12.005
Kawahara Y, Grimberg A, Teegarden S, Mombereau C, Liu S, Bale TL, Blendy JA, Nishikura K (2008) Dysregulated editing of serotonin 2C receptor mRNAs results in energy dissipation and loss of fat mass. J Neurosci 28(48):12834–12844. https://doi.org/10.1523/JNEUROSCI.3896-08.2008
Hood JL, Emeson RB (2012) Editing of neurotransmitter receptor and ion channel RNAs in the nervous system. Curr Top Microbiol Immunol 353:61–90. https://doi.org/10.1007/82_2011_157
Nishikura K (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321–349. https://doi.org/10.1146/annurev-biochem-060208-105251
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853–858. https://doi.org/10.1126/science.1064921
Guo D, Barry L, Lin SS, Huang V, Li LC (2014) RNAa in action: from the exception to the norm. RNA Biol 11(10):1221–1225. https://doi.org/10.4161/15476286.2014.972853
Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294(5543):858–862. https://doi.org/10.1126/science.1065062
Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294(5543):862–864. https://doi.org/10.1126/science.1065329
Tomaselli S, Bonamassa B, Alisi A, Nobili V, Locatelli F, Gallo A (2013) ADAR enzyme and miRNA story: a nucleotide that can make the difference. Int J Mol Sci 14(11):22796–22816. https://doi.org/10.3390/ijms141122796
Li Z, Rana TM (2014) Therapeutic targeting of microRNAs: current status and future challenges. Nat Rev Drug Discov 13(8):622–638. https://doi.org/10.1038/nrd4359
Yi R, Qin Y, Macara IG, Cullen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17(24):3011–3016. https://doi.org/10.1101/gad.1158803
Hock J, Meister G (2008) The Argonaute protein family. Genome Biol 9(2):210. https://doi.org/10.1186/gb-2008-9-2-210
Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20(5):515–524. https://doi.org/10.1101/gad.1399806
Bhat SS, Jarmolowski A, Szweykowska-Kulinska Z (2016) MicroRNA biogenesis: epigenetic modifications as another layer of complexity in the microRNA expression regulation. Acta Biochim Pol 63(4):717–723. https://doi.org/10.18388/abp.2016_1370
Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304(5670):594–596. https://doi.org/10.1126/science.1097434
Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122(4):553–563. https://doi.org/10.1016/j.cell.2005.07.031
Chen PY, Meister G (2005) microRNA-guided posttranscriptional gene regulation. Biol Chem 386(12):1205–1218. https://doi.org/10.1515/BC.2005.139
Meister G (2007) miRNAs get an early start on translational silencing. Cell 131(1):25–28. https://doi.org/10.1016/j.cell.2007.09.021
Hutvagner G, Simard MJ (2008) Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9(1):22–32. https://doi.org/10.1038/nrm2321
Zealy RW, Wrenn SP, Davila S, Min KW, Yoon JH (2017) microRNA-binding proteins: specificity and function. Wiley interdisciplinary reviews RNA. https://doi.org/10.1002/wrna.1414
Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115(2):199–208
Vitsios DM, Davis MP, van Dongen S, Enright AJ (2017) Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis. Nucleic Acids Res 45(3):1079–1090. https://doi.org/10.1093/nar/gkw1031
Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T et al (2010) miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res 38(Database issue):D137–D141. https://doi.org/10.1093/nar/gkp888
Sim SE, Lim CS, Kim JI, Seo D, Chun H, Yu NK, Lee J, Kang SJ et al (2016) The brain-enriched microRNA miR-9-3p regulates synaptic plasticity and memory. J Neurosci 36(33):8641–8652. https://doi.org/10.1523/JNEUROSCI.0630-16.2016
Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR (2006) RNA editing of human microRNAs. Genome Biol 7(4):R27. https://doi.org/10.1186/gb-2006-7-4-r27
Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K (2007) Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315(5815):1137–1140. https://doi.org/10.1126/science.1138050
Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K (2008) Frequency and fate of microRNA editing in human brain. Nucleic Acids Res 36(16):5270–5280. https://doi.org/10.1093/nar/gkn479
Garcia-Lopez J, Hourcade Jde D, Del Mazo J (2013) Reprogramming of microRNAs by adenosine-to-inosine editing and the selective elimination of edited microRNA precursors in mouse oocytes and preimplantation embryos. Nucleic Acids Res 41(10):5483–5493. https://doi.org/10.1093/nar/gkt247
Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R, Nishikura K (2006) Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 13(1):13–21. https://doi.org/10.1038/nsmb1041
Weissbach R, Scadden AD (2012) Tudor-SN and ADAR1 are components of cytoplasmic stress granules. RNA 18(3):462–471. https://doi.org/10.1261/rna.027656.111
Scadden AD (2005) The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nat Struct Mol Biol 12(6):489–496. https://doi.org/10.1038/nsmb936
Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R, Nishikura K (2007) RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep 8(8):763–769. https://doi.org/10.1038/sj.embor.7401011
Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A, Jantsch MF (2014) ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res 42(19):12155–12168. https://doi.org/10.1093/nar/gku844
Ota H, Sakurai M, Gupta R, Valente L, Wulff BE, Ariyoshi K, Iizasa H, Davuluri RV et al (2013) ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing. Cell 153(3):575–589. https://doi.org/10.1016/j.cell.2013.03.024
Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS et al (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433(7027):769–773. https://doi.org/10.1038/nature03315
Zhang B, Wang Q, Pan X (2007) MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210(2):279–289. https://doi.org/10.1002/jcp.20869
Mendell JT (2005) MicroRNAs: critical regulators of development, cellular physiology and malignancy. Cell Cycle 4(9):1179–1184. https://doi.org/10.4161/cc.4.9.2032
Chen CZ, Li L, Lodish HF, Bartel DP (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303(5654):83–86. https://doi.org/10.1126/science.1091903
Wienholds E, Plasterk RH (2005) MicroRNA function in animal development. FEBS Lett 579(26):5911–5922. https://doi.org/10.1016/j.febslet.2005.07.070
Wang Y, Xu X, Yu S, Jeong KJ, Zhou Z, Han L, Tsang YH, Li J et al (2017) Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers. Genome Res 27:1112–1125. https://doi.org/10.1101/gr.219741.116
Nemlich Y, Greenberg E, Ortenberg R, Besser MJ, Barshack I, Jacob-Hirsch J, Jacoby E, Eyal E et al (2013) MicroRNA-mediated loss of ADAR1 in metastatic melanoma promotes tumor growth. J Clin Invest 123(6):2703–2718. https://doi.org/10.1172/JCI62980
Shoshan E, Mobley AK, Braeuer RR, Kamiya T, Huang L, Vasquez ME, Salameh A, Lee HJ et al (2015) Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis. Nat Cell Biol 17(3):311–321. https://doi.org/10.1038/ncb3110
Tomaselli S, Galeano F, Alon S, Raho S, Galardi S, Polito VA, Presutti C, Vincenti S et al (2015) Modulation of microRNA editing, expression and processing by ADAR2 deaminase in glioblastoma. Genome Biol 16:5. https://doi.org/10.1186/s13059-014-0575-z
Paul D, Sinha AN, Ray A, Lal M, Nayak S, Sharma A, Mehani B, Mukherjee D et al (2017) A-to-I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme. Sci Rep 7(1):2466. https://doi.org/10.1038/s41598-017-02397-6
Salvi A, Abeni E, Portolani N, Barlati S, De Petro G (2013) Human hepatocellular carcinoma cell-specific miRNAs reveal the differential expression of miR-24 and miR-27a in cirrhotic/non-cirrhotic HCC. Int J Oncol 42(2):391–402. https://doi.org/10.3892/ijo.2012.1716
Zhang L, Yao J, Li W, Zhang C (2017) Micro-RNA-21 regulates cancer-associated fibroblast-mediated frug resistance in pancreatic cancer. Oncol Res. https://doi.org/10.3727/096504017X14934840662335
Ekdahl Y, Farahani HS, Behm M, Lagergren J, Ohman M (2012) A-to-I editing of microRNAs in the mammalian brain increases during development. Genome Res 22(8):1477–1487. https://doi.org/10.1101/gr.131912.111
Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C et al (2010) Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24(10):992–1009. https://doi.org/10.1101/gad.1884710
Schratt G (2009) microRNAs at the synapse. Nat Rev Neurosci 10(12):842–849. https://doi.org/10.1038/nrn2763
Vessey JP, Vaccani A, Xie Y, Dahm R, Karra D, Kiebler MA, Macchi P (2006) Dendritic localization of the translational repressor Pumilio 2 and its contribution to dendritic stress granules. J Neurosci 26(24):6496–6508. https://doi.org/10.1523/JNEUROSCI.0649-06.2006
Vessey JP, Schoderboeck L, Gingl E, Luzi E, Riefler J, Di Leva F, Karra D, Thomas S et al (2010) Mammalian Pumilio 2 regulates dendrite morphogenesis and synaptic function. Proc Natl Acad Sci U S A 107(7):3222–3227. https://doi.org/10.1073/pnas.0907128107
Christensen M, Schratt GM (2009) microRNA involvement in developmental and functional aspects of the nervous system and in neurological diseases. Neurosci Lett 466(2):55–62. https://doi.org/10.1016/j.neulet.2009.04.043
McNeill E, Van Vactor D (2012) MicroRNAs shape the neuronal landscape. Neuron 75(3):363–379. https://doi.org/10.1016/j.neuron.2012.07.005
Issler O, Chen A (2015) Determining the role of microRNAs in psychiatric disorders. Nat Rev Neurosci 16(4):201–212. https://doi.org/10.1038/nrn3879
Alon S, Mor E, Vigneault F, Church GM, Locatelli F, Galeano F, Gallo A, Shomron N et al (2012) Systematic identification of edited microRNAs in the human brain. Genome Res 22(8):1533–1540. https://doi.org/10.1101/gr.131573.111
Warnefors M, Liechti A, Halbert J, Valloton D, Kaessmann H (2014) Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol 15(6):R83. https://doi.org/10.1186/gb-2014-15-6-r83
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115(7):787–798
Funding
This work was supported by 2014 CARIPLO Foundation Biomedical Research conducted by Young Researchers 2014-1133 to LM. We thank Dr. Stefano Saloriani for the help in depicting Fig. 1.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of Interest
The authors declare that they have no conflict of interest.
Rights and permissions
About this article
Cite this article
Mingardi, J., Musazzi, L., De Petro, G. et al. miRNA Editing: New Insights into the Fast Control of Gene Expression in Health and Disease. Mol Neurobiol 55, 7717–7727 (2018). https://doi.org/10.1007/s12035-018-0951-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12035-018-0951-x