Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by preventing the translation of specific messenger RNAs. Adenosine deaminases acting on RNAs (ADARs) catalyze adenosine-to-inosine (A-to-I) RNA editing, the conversion of adenosines into inosines, in double-stranded RNAs. Because inosine preferentially base pairs with cytidine, this conversion is equivalent to an adenosine to guanosine change. Over the past seven years, an increasing number of edited adenosines have been identified in miRNAs. Editing of miRNAs affects their biogenesis, causes their degradation or alters the set of messenger RNAs that they regulate. Recently, ADARs have been shown to also affect the miRNA phenomenon by sequestering miRNAs or by editing the messenger RNAs they regulate. This article reviews the recent attempts to identify miRNA editing sites and elucidate the effects of ADARs on miRNA expression and function.
Keywords
- Mature miRNAs
- Editing Site
- Seed Sequence
- Guide Strand
- Dicer Cleavage
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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- A:
-
Adenosine
- I:
-
Inosine
- G:
-
Guanosine
- U:
-
Uridine
- C:
-
Cytidine
- UTR:
-
Untranslated region
- dsRNA:
-
Double-stranded RNA
- ADAR:
-
Adenosine deaminase acting on RNA
- miRNA:
-
MicroRNA
- pri-miRNA:
-
Primary miRNA
- pre-miRNA:
-
Precursor miRNA
- mRNA:
-
Messenger RNA
- pre-mRNA:
-
Precursor messenger RNA
- siRNA:
-
Small interfering RNA
- cDNA:
-
Complementary DNA
- Tudor-SN:
-
Tudor staphylococcal nuclease
- EBV:
-
Epstein-Barr virus
- DFFA:
-
DNA fragmentation factor alpha
- PRPS1:
-
Phosphoribosyl pyrophosphate synthetase 1
References
Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R (2008) Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 22:2773–2785
Bass BL (2002) RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem 71:817–846
Bass BL, Weintraub H (1988) An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell 55:1089–1098
Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res 21:203–215
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:R27
Borchert GM, Gilmore BL, Spengler RM, Xing Y, Lanier W, Bhattacharya D, Davidson BL (2009) Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum Mol Genet 18:4801–4807
Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP (2010) Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24:992–1009
de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J, Suzuki H, Hayashizaki Y (2010) Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 20:257–264
Gottwein E, Cai X, Cullen BR (2006) A novel assay for viral microRNA function identifies a single nucleotide polymorphism that affects Drosha processing. J Virol 80:5321–5326
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27:91–105
Heale BS, Keegan LP, McGurk L, Michlewski G, Brindle J, Stanton CM, Caceres JF, O’Connell MA (2009) Editing independent effects of ADARs on the miRNA/siRNA pathways. EMBO J 28:3145–3156
Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K (2010) Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency. J Biol Chem 285:33358–33370
Jin Y, Zhang W, Li Q (2009) Origins and evolution of ADAR-mediated RNA editing. IUBMB Life 61:572–578
Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R, Nishikura K (2007a) RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep 8:763–769
Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K (2007b) Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315:1137–1140
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 36:5270–5280
Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126–139
Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11:597–610
Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, Humphries RK (2008) In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 18:1787–1797
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401–1414
Liang H, Landweber LF (2007) Hypothesis: RNA editing of microRNA target sites in humans? RNA 13:463–467
Linsen SE, de Wit E, de Bruijn E, Cuppen E (2010) Small RNA expression and strain specificity in the rat. BMC Genomics 11:249
Luciano DJ, Mirsky H, Vendetti NJ, Maas S (2004) RNA editing of a miRNA precursor. RNA 10:1174–1177
Morin RD, O’Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18:610–621
Nishikura K (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321–349
Okada C, Yamashita E, Lee SJ, Shibata S, Katahira J, Nakagawa A, Yoneda Y, Tsukihara T (2009) A high-resolution structure of the pre-microRNA nuclear export machinery. Science 326:1275–1279
Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207
Ryan BM, Robles AI, Harris CC (2010) Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer 10:389–402
Scadden AD (2005) The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nat Struct Mol Biol 12:489–496
Scadden AD, Smith CW (2001) Specific cleavage of hyper-edited dsRNAs. EMBO J 20:4243–4252
Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, Thor T, Vandesompele J, Eggert A, Schreiber S, Rahmann S, Schramm A (2010) Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Res 38:5919–5928
Siomi H, Siomi MC (2010) Posttranscriptional regulation of microRNA biogenesis in animals. Mol Cell 38:323–332
Sun G, Yan J, Noltner K, Feng J, Li H, Sarkis DA, Sommer SS, Rossi JJ (2009) SNPs in human miRNA genes affect biogenesis and function. RNA 15:1640–1651
Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hornquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N et al (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41:553–562
Wulff BE, Sakurai M, Nishikura K (2011) Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing. Nat Rev Genet 12:81–85
Yang W, Wang Q, Howell KL, Lee JT, Cho DS, Murray JM, Nishikura K (2005) ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells. J Biol Chem 280:3946–3953
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 13:13–21
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Wulff, BE., Nishikura, K. (2011). Modulation of MicroRNA Expression and Function by ADARs. In: Samuel, C. (eds) Adenosine Deaminases Acting on RNA (ADARs) and A-to-I Editing. Current Topics in Microbiology and Immunology, vol 353. Springer, Berlin, Heidelberg. https://doi.org/10.1007/82_2011_151
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DOI: https://doi.org/10.1007/82_2011_151
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