Genome-wide evaluation and discovery of vertebrate A-to-I RNA editing sites

Biochemical and Biophysical Research Communications

Volumn 412, Issue 3, 2011, Pages 407-412

  Maas, S ^a,c   Godfried Sie, C P ^a   Stoev, I ^b   Dupuis, D E ^a   Latona, J ^a   Porman, A M ^a   Evans, B ^a   Rekawek, P ^a   Kluempers, V ^a   Mutter, M ^a   Gommans, W M ^a   Lopresti, D ^b  

^a LEHIGH UNIVERSITY   (United States)

^b Lehigh University   (United States)

^c InteRNA Technologies BV   (Netherlands)

Author keywords

ADAR; Adenosine deamination; Inosine; RNA editing

Indexed keywords

ADENOSINE; COATOMER PROTEIN; COATOMER PROTEIN COMPLEX SUBUNIT ALPHA; COMPLEMENTARY DNA; CYCLIN DEPENDENT KINASE; CYCLIN DEPENDENT KINASE 13; GUANOSINE; INOSINE; RNA; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CODON; GENETIC ANALYSIS; GENETIC CODE; GENETIC DATABASE; HUMAN; MOLECULAR CLONING; MOUSE; NONHUMAN; PRIORITY JOURNAL; RNA EDITING; SCORING SYSTEM;

ADENINE; ANIMALS; BASE SEQUENCE; GENOME, HUMAN; GENOMICS; HUMANS; INOSINE; MICE; RNA EDITING; TRANSCRIPTOME;

MAMMALIA; VERTEBRATA;

EID: 80052273429     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2011.07.075     Document Type: Article

References (18)

1. Bass B.L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 2002, 71:817-846.
2. Farajollahi S., Maas S. Molecular diversity through RNA editing: a balancing act. Trends Genet. 2010, 26:221-230.
3. Athanasiadis A., Rich A., Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2004, 2:e391.
4. Levanon E.Y., Eisenberg E., Yelin R., Nemzer S., Hallegger M., Shemesh R., Fligelman Z.Y., Shoshan A., Pollock S.R., Sztybel D., Olshansky M., Rechavi G., Jantsch M.F. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 2004, 22:1001-1005.
5. Hoopengardner B., Bhalla T., Staber C., Reenan R. Nervous system targets of RNA editing identified by comparative genomics. Science 2003, 301:832-836.
6. Clutterbuck D.R., Leroy A., O'Connell A.M., Semple C.A. A bioinformatic screen for novel A-I RNA editing sites reveals re-coding editing in BC10. Bioinformatics 2005.
7. Gommans W.M., Tatalias N.E., Sie C.P., Dupuis D., Vendetti N., Smith L., Kaushal R., Maas S. Screening of human SNP database identifies recoding sites of A-to-I RNA editing. RNA 2008, 14:2074-2085.
8. Levanon E.Y., Hallegger M., Kinar Y., Shemesh R., Djinovic-Carugo K., Rechavi G., Jantsch M.F., Eisenberg E. Evolutionarily conserved human targets of adenosine to inosine RNA editing. Nucleic Acids Res. 2005, 33:1162-1168.
9. Wahlstedt H., Daniel C., Enstero M., Ohman M. Large-scale mRNA sequencing determines global regulation of RNA editing during brain development. Genome Res. 2009.
10. Li J.B., Levanon E.Y., Yoon J.K., Aach J., Xie B., Leproust E., Zhang K., Gao Y., Church G.M. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 2009, 324:1210-1213.
11. Kuhn R.M., Karolchik D., Zweig A.S., Trumbower H., Thomas D.J., Thakkapallayil A., Sugnet C.W., Stanke M., Smith K.E., Siepel A., Rosenbloom K.R., Rhead B., Raney B.J., Pohl A., Pedersen J.S., Hsu F., Hinrichs A.S., Harte R.A., Diekhans M., Clawson H., Bejerano G., Barber G.P., Baertsch R., Haussler D., Kent W.J. The UCSC genome browser database: update 2007. Nucleic Acids Res. 2007, 35:D668-D673.
12. M. Enstero, O. Akerborg, D. Lundin, B. Wang, T.S. Furey, M. Ohman, and J. Lagergren, A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. BMC Bioinformatics 11 (2010) 6.
13. Gommans W.M., Mullen S.P., Maas S. RNA editing: a driving force for adaptive evolution?. BioEssays 2009, 31:1137-1145.
14. Shah S.P., Morin R.D., Khattra J., Prentice L., Pugh T., Burleigh A., Delaney A., Gelmon K., Guliany R., Senz J., Steidl C., Holt R.A., Jones S., Sun M., Leung G., Moore R., Severson T., Taylor G.A., Teschendorff A.E., Tse K., Turashvili G., Varhol R., Warren R.L., Watson P., Zhao Y., Caldas C., Huntsman D., Hirst M., Marra M.A., Aparicio S. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2009, 461:809-813.
15. Nickel W., Brugger B., Wieland F.T. Vesicular transport: the core machinery of COPI recruitment and budding. J. Cell Sci. 2002, 115:3235-3240.
16. Beck R., Ravet M., Wieland F.T., Cassel D. The COPI system: molecular mechanisms and function. FEBS Lett. 2009, 583:2701-2709.
17. Even Y., Durieux S., Escande M.L., Lozano J.C., Peaucellier G., Weil D., Geneviere A.M. CDC2L5, a Cdk-like kinase with RS domain, interacts with the ASF/SF2-associated protein p32 and affects splicing in vivo. J. Cell. Biochem. 2006, 99:890-904.
18. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., Sirotkin K. DbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29:308-311.