A method to find tissue-specific novel sites of selective adenosine deamination

Nucleic Acids Research

Volumn 33, Issue 19, 2005, Pages 1-7

  Ohlson, Johan ^a   Ensterö, Mats ^a   Sjöberg, Britt Marie ^a   Öhman, Marie ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; ADENOSINE DEAMINASE; ADENOSINE DEAMINASE 2; DOUBLE STRANDED RNA; INOSINE; UNCLASSIFIED DRUG; DSRNA ADENOSINE DEAMINASE;

ANIMAL TISSUE; ARTICLE; BINDING SITE; CONTROLLED STUDY; DEAMINATION; ENZYME BINDING; IMMUNOPRECIPITATION; IN VIVO STUDY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEIN RNA BINDING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBONUCLEASE PROTECTION ASSAY; RNA EDITING; RNA SEQUENCE; ANIMAL; BRAIN; DNA MICROARRAY; EVALUATION; IMMUNOLOGY; ISOLATION AND PURIFICATION; METABOLISM; NUCLEASE PROTECTION ASSAY;

ANIMALIA; METAZOA;

ADENOSINE; ADENOSINE DEAMINASE; ANIMALS; BRAIN; DEAMINATION; IMMUNOPRECIPITATION; INOSINE; MICE; NUCLEASE PROTECTION ASSAYS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA EDITING;

EID: 28544447032     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni169     Document Type: Article

References (29)

1. Bass,B.L. (2002) RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem., 71, 817-846.
2. Morse,D.P. and Bass,B.L. (1999) Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA. Proc. Natl Acad. Sci. USA, 96, 6048-6053.
3. Morse,D.P., Aruscavage,P.J. and Bass,B.L. (2002) RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc. Natl Acad. Sci. USA, 99, 7906-7911.
4. Levanon,E.Y., Eisenberg,E., Yelin,R., Nemzer,S., Hallegger,M., Shemesh,R., Fligelman,Z.Y., Shoshan,A., Pollock,S.R., Sztybel,D. et al. (2004) Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol., 22, 1001-1005.
5. Blow,M., Futreal,P.A., Wooster,R. and Stratton,M.R. (2004) A survey of RNA editing in human brain. Genome Res., 14, 2379-2387.
6. Athanasiadis,A., Rich,A. and Maas,S. (2004) Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol., 2, e391.
7. Hume,R.I., Dingledine,R. and Heinemann,S.F. (1991) Identification of a site in glutamate receptor subunits that controls calcium permeability. Science, 253, 1028-1031.
8. Burnashev,N., Monyer,H., Seeburg,P.H. and Sakmann,B. (1992) Divalent ion permeability of AMPA receptor channels is dominated by the edited form of a single subunit. Neuron, 8, 189-198.
9. Lomeli,H., Mosbacher,J., Melcher,T., Hoger,T., Geiger,J.R., Kuner,T., Monyer,H., Higuchi,M., Bach,A. and Seeburg,P.H. (1994) Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science, 266, 1709-1713.
10. Seeburg,P.H., Higuchi,M. and Sprengel,R. (1998) RNA editing of brain glutamate receptor channels: Mechanism and physiology. Brain Res. Brain. Res. Rev., 26, 217-229.
11. Burns,C.M., Chu,H., Rueter,S.M., Hutchinson,L.K., Canton,H., Sanders-Bush,E. and Emeson,R.B. (1997) Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature, 387, 303-308.
12. Paul,M.S. and Bass,B.L. (1998) Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J., 17, 1120-1127.
13. Ule,J., Jensen,K.B., Ruggiu,M., Mele,A., Ule,A. and Darnell,R.B. (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science, 302, 1212-1215.
14. Tenenbaum,S.A., Lager,P.J., Carson,C.C. and Keene,J.D. (2002) Ribonomics: Identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods, 26, 191-198.
15. Klaue,Y., Källman,A.M., Bonin,M., Nellen,W. and Öhman,M. (2003) Biochemical analysis and scanning force microscopy reveal productive and non-productive ADAR2 binding to RNA substrates. RNA, 9, 839-846.
16. Öhman,M., Källman,A.M. and Bass,B.L. (2000) In vitro analysis of the binding of ADAR2 to the pre-mRNA encoding the GluR-B R/G site. RNA, 6, 687-697.
17. Lai,F., Drakas,R. and Nishikura,K. (1995) Mutagenic analysis of double-stranded RNA adenosine deaminase, a candidate enzyme for RNA editing of glutamate-gated ion channel transcripts. J. Biol. Chem., 270, 17098-17105.
18. Stephens,O.M., Yi-Brunozzi,H.Y. and Beal,PA. (2000) Analysis of the RNA-editing reaction of ADAR2 with structural and fluorescent analogues of the GluR-B R/G editing site. Biochemistry, 39, 12243-12251.
19. Fierro-Monti,I. and Mathews,M.B. (2000) Proteins binding to duplexed RNA: One motif, multiple functions. Trends Biochem. Sci., 25, 241-246.
20. Nanduri,S., Carpick,B.W., Yang,Y., Williams,B.R. and Qin,J. (1998) Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation. EMBO J., 17, 5458-5465.
21. Ryter,J.M. and Schultz,S.C. (1998) Molecular basis of double-stranded RNA-protein interactions: Structure of a dsRNA-binding domain complexed with dsRNA. EMBO J., 17, 7505-7513.
22. Källman,A.M., Sahlin,M. and Öhman,M. (2003) ADAR2 A→I editing: site selectivity and editing efficiency are separate events. Nucleic Acids Res., 31, 4874-4881.
23. Chanfreau,G., Buckle,M. and Jacquier,A. (2000) Recognition of a conserved class of RNA tetraloops by Saccharomyces cerevisiae RNase III. Proc. Natl Acad. Sci. USA, 97, 3142-3147.
24. Ramos,A., Grunert,S., Adams,J., Micklem,D.R., Proctor,M.R., Freund,S., Bycroft,M., St Johnston,D. and Varani,G. (2000) RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J., 19, 997-1009.
25. Nagel,R. and Ares,M.,Jr (2000) Substrate recognition by a eukaryotic RNase III: The double-stranded RNA-binding domain of Rnt1p selectively binds RNA containing a 5′-AGNN-3′ tetraloop. RNA, 6, 1142-1156.
26. Leulliot,N., Quevillon-Cheruel,S., Graille,M., Van Tilbeurgh,H., Leeper,T.C., Godin,K.S., Edwards,T.E., Sigurdsson,S.T., Rozenkrants,N., Nagel,R.J. et al. (2004) A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III. EMBO J., 23, 2468-2477.
27. Higuchi,M., Maas,S., Single,F.N., Hartner,J., Rozov,A., Burnashev,N., Feldmeyer,D., Sprengel,R. and Seeburg,P.H. (2000) Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature, 406, 78-81.
28. Akbarian,S., Smith,M.A. and Jones,E.G. (1995) Editing for an AMPA receptor subunit RNA in prefrontal cortex and striatum in Alzheimer's disease, Huntington's disease and schizophrenia. Brain Res., 699, 297-304.
29. Sodhi,M.S., Burnet,P.W., Makoff,A.J., Kerwin,R.W. and Harrison,P.J. (2001) RNA editing of the 5-HT(2C) receptor is reduced in schizophrenia. Mol. Psychiatry, 6, 373-379.