A distant cis acting intronic element induces site-selective RNA editing

Nucleic Acids Research

Volumn 40, Issue 19, 2012, Pages 9876-9886

  Daniel, Chammiran ^a   Veno, Morten T ^b   Ekdahl, Ylva ^a   Kjems, Jørgen ^b   Öhman, Marie ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID A RECEPTOR ALPHA3; ADENOSINE; CIS ACTING ELEMENT; INOSINE; METHIONINE; TRANSCRIPTOME;

ADULT; ANIMAL TISSUE; ARTICLE; EXON; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN TISSUE; INTRON; INVERTED REPEAT; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA EDITING; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; SWINE;

ANIMALS; BRAIN; HEK293 CELLS; HELA CELLS; HUMANS; INTRONS; MICE; NUCLEIC ACID CONFORMATION; RATS; RECEPTORS, GABA-A; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA EDITING; RNA SPLICING; SWINE;

MAMMALIA;

EID: 84868106296     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks691     Document Type: Article

References (39)

1. Bass, B.L., Nishikura, K., Keller, W., Seeburg, P.H., Emeson, R.B., O'Connell, M.A., Samuel, C.E. and Herbert, A. (1997) A standardized nomenclature for adenosine deaminases that act on RNA. RNA, 3, 947-949. (Pubitemid 127641487)
2. Jepson, J.E. and Reenan, R.A. (2008) RNA editing in regulating gene expression in the brain. Biochim. Biophys. Acta, 1779, 459-470.
3. Polson, A.G. and Bass, B.L. (1994) Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J., 13, 5701-5711. (Pubitemid 24363038)
4. Källman, A.M., Sahlin, M. and Öhman, M. (2003) ADAR2 AI editing: site selectivity and editing efficiency are separate events. Nucleic Acids Res., 31, 4874-4881. (Pubitemid 37441852)
5. 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. (Pubitemid 30318464)
6. Wahlstedt, H. and Öhman, M. (2011) Site-selective versus promiscuous A-to-I editing. Wiley Interdiscip Rev RNA, 2, 761-771.
7. 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.
8. 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. (Pubitemid 40012220)
9. 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. (Pubitemid 39014477)
10. Lev-Maor, G., Sorek, R., Levanon, E.Y., Paz, N., Eisenberg, E. and Ast, G. (2007) RNA-editing-mediated exon evolution. Genome Biol., 8, R29.
11. Carmi, S., Borukhov, I. and Levanon, E.Y. (2011) Identification of widespread ultra-edited human RNAs. PLoS Genet., 7, e1002317.
12. Dawson, T.R., Sansam, C.L. and Emeson, R.B. (2004) Structure and sequence determinants required for the RNA editing of ADAR2 substrates. J. Biol. Chem., 279, 4941-4951. (Pubitemid 38199090)
13. Stephens, O.M., Haudenschild, B.L. and Beal, P.A. (2004) The binding selectivity of ADAR2's dsRBMs contributes to RNA-editing selectivity. Chem. Biol., 11, 1239-1250. (Pubitemid 39282799)
14. Stefl, R., Oberstrass, F.C., Hood, J.L., Jourdan, M., Zimmermann, M., Skrisovska, L., Maris, C., Peng, L., Hofr, C., Emeson, R.B. et al. (2010) The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove. Cell, 143, 225-237.
15. Bhalla, T., Rosenthal, J.J., Holmgren, M. and Reenan, R. (2004) Control of human potassium channel inactivation by editing of a small mRNA hairpin. Nat. Struct. Mol. Biol., 11, 950-956. (Pubitemid 39315298)
16. Brusa, R., Zimmermann, F., Koh, D.S., Feldmeyer, D., Gass, P., Seeburg, P.H. and Sprengel, R. (1995) Early-onset epilepsy and postnatal lethality associated with an editing-deficient GluR-B allele in mice. Science, 270, 1677-1680. (Pubitemid 26002446)
17. 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. (Pubitemid 27220768)
18. Higuchi, M., Single, F.N., Köhler, M., Sommer, B., Sprengel, R. and Seeburg, P.H. (1993) RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell, 75, 1361-1370. (Pubitemid 24021910)
19. 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.
20. Sommer, B., Köhler, M., Sprengel, R. and Seeburg, P.H. (1991) RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell, 67, 11-19. (Pubitemid 121001421)
21. Farrant, M. and Kaila, K. (2007) The cellular, molecular and ionic basis of GABA(A) receptor signalling. Prog. Brain Res., 160, 59-87. (Pubitemid 46702286)
22. Ohlson, J., Pedersen, J.S., Haussler, D. and Öhman, M. (2007) Editing modifies the GABA(A) receptor subunit alpha3. RNA, 13, 698-703. (Pubitemid 46641528)
23. Wahlstedt, H., Daniel, C., Ensterö, M. and Öhman, M. (2009) Large-scale mRNA sequencingdetermines global regulation of RNA editing during brain development. Genome Res., 19, 978-986.
24. Nimmich, M.L., Heidelberg, L.S. and Fisher, J.L. (2009) RNA editing of the GABAA receptor a3 subunit alters the functional properties of recombinant receptors Neurosci. Res., 63, 288-293.
25. Rula, E.Y., Lagrange, A.H., Jacobs, M.M., Hu, N., Macdonald, R.L. and Emeson, R.B. (2008) Developmental modulation of GABA(A) receptor function by RNA editing. J. Neurosci., 28, 6196-6201.
26. Daniel, C., Wahlstedt, H., Ohlson, J., Björk, P. and Öhman, M. (2011) Adenosine-to-inosine RNA editing affects trafficking of the gamma-aminobutyric acid type A (GABA(A)) receptor. J Biol Chem, 286, 2031-2040.
27. Tian, N., Yang, Y., Sachsenmaier, N., Muggenhumer, D., Bi, J., Waldsich, C., Jantsch, M.F. and Jin, Y. (2011) A structural determinant required for RNA editing. Nucleic Acids Res., 39, 5669-5681.
28. Desterro, J.M., Keegan, L.P., Lafarga, M., Berciano, M.T., O'Connell, M. and Carmo-Fonseca, M. (2003) Dynamic association of RNA-editing enzymes with the nucleolus. J. Cell Sci., 116, 1805-1818. (Pubitemid 36582167)
29. Bratt, E. and Öhman, M. (2003) Coordination of editing and splicing of glutamate receptor pre-mRNA. RNA, 9, 309-318. (Pubitemid 36246170)
30. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415. (Pubitemid 37442169)
31. Ding, Y., Chan, C.Y. and Lawrence, C.E. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166. (Pubitemid 41132387)
32. Ding, Y. and Lawrence, C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301. (Pubitemid 38008457)
33. 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. (Pubitemid 30460214)
34. Laurencikiene, J., Källman, A.M., Fong, N., Bentley, D.L. and Öhman, M. (2006) RNA editing and alternative splicing: the importance of co-transcriptional coordination. EMBO Rep., 7, 303-307.
35. Ryman, K., Fong, N., Bratt, E., Bentley, D.L. and Öhman, M. (2007) The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript. RNA, 13, 1071-1078. (Pubitemid 46984897)
36. Patterson, J.B. and Samuel, C.E. (1995) Expression and regulation by interferon of a double-stranded-RNA-specific adenosine deaminase from human cells: evidence for two forms of the deaminase. Mol. Cell Biol., 15, 5376-5388.
37. Amaral, A.J., Ferretti, L., Megens, H.J., Crooijmans, R.P., Nie, H., Ramos-Onsins, S.E., Perez-Enciso, M., Schook, L.B. and Groenen, M.A. (2011) Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One, 6, e14782.
38. Aruscavage, P.J. and Bass, B.L. (2000) A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing. RNA, 6, 257-269. (Pubitemid 30091596)
39. 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. (Pubitemid 34650978)