Comparative analysis of the RED1 and RED2 A-to-I RNA editing genes from mammals, pufferfish and zebrafish

Gene

Volumn 250, Issue 1-2, 2000, Pages 41-51

  Slavov, D ^a,b   Clark, M ^b   Gardiner, K ^a  

^a UNIVERSITY OF DENVER   (United States)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Fugu rubripes; Genomic organization; RED1; RED2; RNA editing; Zebrafish

Indexed keywords

ADENOSINE; CELL ENZYME; INOSINE; ISOENZYME; RNA EDITASE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA BASE COMPOSITION; ENZYME ACTIVE SITE; FISH; GENE ISOLATION; GENE STRUCTURE; HUMAN; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN RNA BINDING; RAT; RNA EDITING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; ZEBRA FISH;

ADENOSINE DEAMINASE; AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; DNA; EXONS; FISHES; GENES; HUMANS; INTRONS; MAMMALS; MICE; MOLECULAR SEQUENCE DATA; RNA EDITING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; ZEBRAFISH;

DANIO RERIO; MAMMALIA; TAKIFUGU; TAKIFUGU RUBRIPES; TETRAODONTIDAE;

EID: 0034732896     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(00)00174-8     Document Type: Article

References (29)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
2. Bass B.L. RNA editing and hypermutation by adenosine deamination. Trends Biochem Sci. 22:1997;157-162.
3. Bernardi G. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29:1995;445-476.
4. Burns C.M., Chu H., Rueter S.M., Hutchinson L.K., Canton H., Sanders-Bush E., Emeson R.B. Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature. 387:1997;303-308.
5. Claverie J.-M. Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet. 6:1997;1735-1744.
6. Elgar G., Rattray F., Greystrong J., Brenner S. Genomic structure and nucleotide sequence of the p55 gene of the puffer fish, Fugu rubripes. Genomics. 27:1995;442-446.
7. Elgar G., Sandford R., Aparicio S., Macrae A., Venkatesh B., Brenner S. Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes). Trends Genet. 12:1996;145-150.
8. Feinberg A.P., Vogelstein B. Addendum to a technique for radiolabeling DNA to high specific activity. Anal. Biochem. 137:1989;266-267.
9. Harris N.L. Genotator: a workbench for sequence annotation. Genome Res. 7:1997;754-761.
10. Kim U., Wang Y., Sanford T., Zeng Y., Nishikura K. Molecular cloning of a cDNA for double stranded RNA adenosine deaminase. Proc. Natl. Acad. Sci. USA. 91:1994;11457-11461.
11. Lehrach H., Drmanac R., Hoheisel J., Larin Z., Lennon G., Monaco A.P., Nizetic V., Zehtner G., Poustka A. Hybridization fingerprinting in genome mapping and sequencing. Davies K.E., Tilghman S.M. Genome Analysis 1: Genetic and Physical Mapping. 1990;Cold Spring Harbor Laboratory Press, Boca Raton, FL.
12. Lomeli H., Mosbacher J., Melcher V., Hoger V., Geiger J.R.P., Kuner T., Monyer H., Higuchi M., Bach A., Seeburg P.H. Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science. 266:1994;1709-1713.
13. Maas S., Melcher T., Seeburg P.H. Curr. Opin. Cell Biol. 9:1997;343-349.
14. Melcher T., Mass S., Herb A., Sprengel R., Seeburg P.H., Higuchi M. A mammalian RNA editing enzyme. Nature. 379:1996;460-464.
15. Melcher T., Maas S., Herb A., Sprengel R., Higuchi M., Seeburg P.H. RED2, a brain-specific member of the RNA-specific adenosine deaminase family. J. Biol. Chem. 271:1996;31795-31798.
16. Paschen W., Djuricic B. Regional differences in the extent of RNA editing of the glutamate receptor subunits GluR2 and GluR6 in rat brain. J. Neurosci. Meth. 56:1995;21-29.
17. Paschen W., Schmitt J., Gissel C., Dux E. Developmental changes of RNA editing of glutamate receptor subunits GluR5 and GluR6: in vivo versus in vitro. Dev. Brain Res. 98:1997;271-280.
18. Paul M.S., Bass B.L. Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J. 17:1998;1120-1127.
19. Philibert R., Hawkins G., Damschroder-Williams G., Stubblefield B., Martin B., Ginna E. Direct sequencing of trinucleotide repeats from cosmid genomic DNA template. Anal. Biochem. 225:1995;372-374.
20. Sambrook J., Fritsch E.F., Maniatis E. Molecular Cloning: A Laboratory Manual. second ed. 1989;Cold Spring Harbor Press, Cold Spring Harbor, NY.
21. Seeburg P.H. The role of RNA editing in controlling glutamate receptor channel properties. J. Neurochem. 66:1996;1-6.
22. Slavov D., Crnogorac-Jurcević T., Clark M., Gardiner K. Comparative analysis of the DRADA A-to-I RNA editing gene from mammals pufferfish and zebrafish. Gene. 250:2000;53-60.
23. Slavov D., Hattori M., Sakaki Y., Rosenthal A., Shimizu N., Minoshima S., Kudoh J., Yaspo M.L., Ramser J., Reinhardt R., Reimer C., Clancy K., Rynditch A., Gardiner K. Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21. Gene. 247:2000;215-232.
24. Smith H.C., Gott J.M., Hanson M.R. A guide to RNA editing. RNA. 3:1997;1105-1123.
25. Tassone F., Villard L., Clancy K., Gardiner K. Structures, sequence characteristics, and synteny relationships of the transcription factor E4TF1, the splicing factor U2AF35 and the cystathionine beta synthetase genes from Fugu rubripes. Gene. 326:1999;211-223.
26. Tatusova T., Madden T. BLAST 2 sequences - a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174:1999;247-250.
27. Villard L., Tassone F., Haymowicz M., Welborn R., Gardiner K. Map location, genomic organization and expression patterns of the human RED1 RNA editase. Somat. Cell Mol. Genet. 23:1997;135-145.
28. Wang Y., Zeng Y., Murray J.M., Nishikura K. Genomic organization and chromosomal location of the human dsRNA adenosine deaminase gene: The enzyme for glutamate-activated ion channel RNA editing. J. Mol. Biol. 254:1995;184-195.
29. Zoubak S., Clay O., Bernardi G. The gene distribution of the human genome. Gene. 174:1996;95-102.