Processes 2018, 6,42
18. Paz, N. Altered adenosine-to-inosine RNA editing in human cancer. Genome Res. 2007, 17, 1586–1595.
[CrossRef][PubMed]
19. Blow, M.J.; Grocock, R.J.; van Dongen, S.; Enright, A.J.; Dicks, E.; Futreal, P.A.; Stratton, M.R. RNA editing of
human microRNAs. Genome Biol. 2006, 7, R27. [CrossRef][PubMed]
20. Kim, V.N. MicroRNA biogenesis: Coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 2005, 6, 376–385.
[CrossRef][PubMed]
21. Zamore, P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002, 297, 2056–2060.
22. He, L.; Hannon, G.J. MicroRNAs: Small RNAs with a big role in gene regulation. Nat. Rev. Genet. 2004, 5,
522–531. [CrossRef][PubMed]
23. Maegdefessel, L. The emerging role of microRNAs in cardiovascular disease. J. Intern. Med. 2014, 276,
633–644. [CrossRef][PubMed]
24. Sun, E.; Shi, Y. MicroRNAs: Small molecules with big roles in neurodevelopment and diseases. Exp. Neurol.
2014, 268, 46–53. [CrossRef][PubMed]
25. Jansson, M.D.; Lund, A.H. MicroRNA and cancer. Mol. Oncol. 2012, 6, 590–610. [CrossRef][PubMed]
26. Ota, H. ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene
silencing. Cell 2013, 153, 575–589. [CrossRef][PubMed]
27. Yang, W. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases.
Nat. Struct. Mol. Biol. 2006, 13, 13–21. [CrossRef][PubMed]
28. Kawahara, Y.; Zinshteyn, B.; Chendrimada, T.P.; Shiekhattar, R.; Nishikura, K. RNA editing of the
microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep. 2007, 8, 763–769.
[CrossRef][PubMed]
29. Kawahara, Y.; Zinshteyn, B.; Sethupathy, P.; Iizasa, H.; Hatzigeorgiou, A.G.; Nishikura, K. Redirection
of silencing targets by adenosine-to-inosine editing of miRNAs. Science 2007, 315, 1137–1140. [CrossRef]
[PubMed]
30. Nakano, M.; Fukami, T.; Gotoh, S.; Takamiya, M.; Aoki, Y.; Nakajima, M. RNA Editing Modulates Human
Hepatic Aryl Hydrocarbon Receptor Expression by Creating MicroRNA Recognition Sequence. J. Biol. Chem.
2016, 291, 894–903. [CrossRef][PubMed]
31. Zhang, L.; Yang, C.S.; Varelas, X.; Monti, S. Altered RNA editing in 3 ′ UTR perturbs microRNA-mediated
regulation of oncogenes and tumor-suppressors. Sci. Rep. 2016, 6, 23226. [CrossRef][PubMed]
32. Soundararajan, R.; Stearns, T.M.; Griswold, A.L.; Mehta, A.; Czachor, A.; Fukumoto, J.; Kolliputi, N.
Detection of canonical A-to-G editing events at 3 ′ UTRs and microRNA target sites in human lungs using
next-generation sequencing. Oncotarget 2015, 6, 35726–35736. [CrossRef][PubMed]
33. Nakano, M.; Fukami, T.; Gotoh, S.; Nakajima, M. A-to-I RNA Editing Up-regulates Human Dihydrofolate
Reductase in Breast Cancer. J. Biol. Chem. 2017, 292, 4873–4884. [CrossRef][PubMed]
34. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data.
Bioinformatics 2014, 30, 2114–2120. [CrossRef][PubMed]
35. Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S.L. TopHat2: Accurate alignment
of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14, R36.
[CrossRef][PubMed]
36. Li, H. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25, 2078–2079. [CrossRef]
[PubMed]
37. Levanon, E.Y. Systematic identification of abundant A-to-I editing sites in the human transcriptome.
Nat. Biotechnol. 2004, 22, 1001–1005. [CrossRef][PubMed]
38. Kozomara, A.; Griffiths-Jones, S. miRBase: Annotating high confidence microRNAs using deep sequencing
data. Nucleic Acids Res. 2014, 42, D68–D73. [CrossRef][PubMed]
39. Camacho, C.; Coulouris, G.; Avagyan, V.; Ma, N.; Papadopoulos, J.; Bealer, K.; Madden, T.L. BLAST+:
Architecture and applications. BMC Bioinform. 2009, 10, 421. [CrossRef][PubMed]
40. Thompson, J.D.; Gibson, T.J.; Higgins, D.G. Multiple Sequence Alignment Using ClustalW and ClustalX.
Curr. Protocals Bioinform. 2002.[ CrossRef][PubMed]
41. Borchert, G.M. Adenosine deamination in human transcripts generates novel microRNA binding sites.
Hum. Mol. Genet. 2009, 18, 4801–4807. [CrossRef][PubMed]
42. Rosenthal, J.J.; Seeburg, P.H. A-to-I RNA editing: Effects on proteins key to neural excitability. Neuron 2012,
74, 432–439. [CrossRef][PubMed]
142
18. Paz, N. Altered adenosine-to-inosine RNA editing in human cancer. Genome Res. 2007, 17, 1586–1595.
[CrossRef][PubMed]
19. Blow, M.J.; Grocock, R.J.; van Dongen, S.; Enright, A.J.; Dicks, E.; Futreal, P.A.; Stratton, M.R. RNA editing of
human microRNAs. Genome Biol. 2006, 7, R27. [CrossRef][PubMed]
20. Kim, V.N. MicroRNA biogenesis: Coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 2005, 6, 376–385.
[CrossRef][PubMed]
21. Zamore, P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002, 297, 2056–2060.
22. He, L.; Hannon, G.J. MicroRNAs: Small RNAs with a big role in gene regulation. Nat. Rev. Genet. 2004, 5,
522–531. [CrossRef][PubMed]
23. Maegdefessel, L. The emerging role of microRNAs in cardiovascular disease. J. Intern. Med. 2014, 276,
633–644. [CrossRef][PubMed]
24. Sun, E.; Shi, Y. MicroRNAs: Small molecules with big roles in neurodevelopment and diseases. Exp. Neurol.
2014, 268, 46–53. [CrossRef][PubMed]
25. Jansson, M.D.; Lund, A.H. MicroRNA and cancer. Mol. Oncol. 2012, 6, 590–610. [CrossRef][PubMed]
26. Ota, H. ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene
silencing. Cell 2013, 153, 575–589. [CrossRef][PubMed]
27. Yang, W. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases.
Nat. Struct. Mol. Biol. 2006, 13, 13–21. [CrossRef][PubMed]
28. Kawahara, Y.; Zinshteyn, B.; Chendrimada, T.P.; Shiekhattar, R.; Nishikura, K. RNA editing of the
microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep. 2007, 8, 763–769.
[CrossRef][PubMed]
29. Kawahara, Y.; Zinshteyn, B.; Sethupathy, P.; Iizasa, H.; Hatzigeorgiou, A.G.; Nishikura, K. Redirection
of silencing targets by adenosine-to-inosine editing of miRNAs. Science 2007, 315, 1137–1140. [CrossRef]
[PubMed]
30. Nakano, M.; Fukami, T.; Gotoh, S.; Takamiya, M.; Aoki, Y.; Nakajima, M. RNA Editing Modulates Human
Hepatic Aryl Hydrocarbon Receptor Expression by Creating MicroRNA Recognition Sequence. J. Biol. Chem.
2016, 291, 894–903. [CrossRef][PubMed]
31. Zhang, L.; Yang, C.S.; Varelas, X.; Monti, S. Altered RNA editing in 3 ′ UTR perturbs microRNA-mediated
regulation of oncogenes and tumor-suppressors. Sci. Rep. 2016, 6, 23226. [CrossRef][PubMed]
32. Soundararajan, R.; Stearns, T.M.; Griswold, A.L.; Mehta, A.; Czachor, A.; Fukumoto, J.; Kolliputi, N.
Detection of canonical A-to-G editing events at 3 ′ UTRs and microRNA target sites in human lungs using
next-generation sequencing. Oncotarget 2015, 6, 35726–35736. [CrossRef][PubMed]
33. Nakano, M.; Fukami, T.; Gotoh, S.; Nakajima, M. A-to-I RNA Editing Up-regulates Human Dihydrofolate
Reductase in Breast Cancer. J. Biol. Chem. 2017, 292, 4873–4884. [CrossRef][PubMed]
34. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data.
Bioinformatics 2014, 30, 2114–2120. [CrossRef][PubMed]
35. Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S.L. TopHat2: Accurate alignment
of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14, R36.
[CrossRef][PubMed]
36. Li, H. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25, 2078–2079. [CrossRef]
[PubMed]
37. Levanon, E.Y. Systematic identification of abundant A-to-I editing sites in the human transcriptome.
Nat. Biotechnol. 2004, 22, 1001–1005. [CrossRef][PubMed]
38. Kozomara, A.; Griffiths-Jones, S. miRBase: Annotating high confidence microRNAs using deep sequencing
data. Nucleic Acids Res. 2014, 42, D68–D73. [CrossRef][PubMed]
39. Camacho, C.; Coulouris, G.; Avagyan, V.; Ma, N.; Papadopoulos, J.; Bealer, K.; Madden, T.L. BLAST+:
Architecture and applications. BMC Bioinform. 2009, 10, 421. [CrossRef][PubMed]
40. Thompson, J.D.; Gibson, T.J.; Higgins, D.G. Multiple Sequence Alignment Using ClustalW and ClustalX.
Curr. Protocals Bioinform. 2002.[ CrossRef][PubMed]
41. Borchert, G.M. Adenosine deamination in human transcripts generates novel microRNA binding sites.
Hum. Mol. Genet. 2009, 18, 4801–4807. [CrossRef][PubMed]
42. Rosenthal, J.J.; Seeburg, P.H. A-to-I RNA editing: Effects on proteins key to neural excitability. Neuron 2012,
74, 432–439. [CrossRef][PubMed]
142