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

Volumn 226, Issue 2, 1999, Pages 211-223

  Tassone, Flora ^a   Villard, Laurent ^a   Clancy, Kevin ^a   Gardiner, Katheleen ^a  

^a UNIVERSITY OF DENVER   (United States)

Author keywords

Base composition; Gene structure; Pufferfish; Regulation

Indexed keywords

AMYLOID PRECURSOR PROTEIN; CYSTATHIONINE BETA SYNTHASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR E4TF1; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; CHROMOSOME 21Q; COSMID; CPG ISLAND; DNA BASE COMPOSITION; FISH; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; ISOCHORE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SPLICING; SYNTENY;

AMINO ACID SEQUENCE; AMYLOID BETA-PROTEIN PRECURSOR; ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; CPG ISLANDS; CYSTATHIONINE BETA-SYNTHASE; DNA; DNA PRIMERS; EXONS; FISHES; GA-BINDING PROTEIN TRANSCRIPTION FACTOR; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; RIBONUCLEOPROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS;

ANIMALIA; MAMMALIA; TAKIFUGU; TAKIFUGU RUBRIPES; TETRAODONTIDAE;

EID: 0033590615     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(98)00559-9     Document Type: Article

References (48)

1. Altschul S.F., Madden T.L., Schaffer R.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. Aparicio S., Morrison A., Gould A., Gilthorpe J., Chaudhuri C., Rigby P., Krumlauf R., Brenner S. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl. Acad. Sci. USA. 92:1995;1684-1688.
3. Baxendale S., Abdulla S., Elgar G., Buck D., Berks M., Micklem G., Durbin R., Bates G., Brenner S., Beck S., Lehrach H. Comparative sequence analysis of the human and pufferfish Huntington's disease genes. Nature Genet. 10:1995;67-77.
4. Bernardi G. The human genome: organisation and evolutionary history. Annu. Rev. Genet. 29:1995;445-476.
5. Brenner S., Elgar G., Sandford R., Macrae A., Venkatesh B., Aparicio S. Characterization of the pufferfish (Fugu) genome as a compact-model vertebrate genome. Nature. 366:1993;567-571.
6. Chinenov Y., Schmidt T., Yang X.Y., Martin M.E. Identification of redox-sensitive cysteines in GA-binding protein-alpha that regulate DNA binding and heterodimerization. J. Biol. Chem. 273:1998;6203-6209.
7. Chrast R., Chen H., Morris M.A., Antonarakis S.E. Mapping of the human transcription factor GABPA (E4TF1-60) gene to chromosome 21. Genomics. 28:1995;119-122.
8. Coutelle O., Nyakatura G., Taudien S., Elgar G., Brenner S., Platzer M., Drescher B., Jouet M., Kenwrick S., Rosenthal A. The neural cell adhesion molecular L1: genomic organization and differential splicing is conserved between man and the pufferfish Fugu. Gene. 208:1998;7-15.
9. Duret L., Mouchiroud D., Gautier C. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40:1994;308-317.
10. 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.
11. 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.
12. Gardiner K. Clonability and gene distribution on human chromosome 21: reflections of junk DNA content? Gene. 205:1997;39-46.
13. Gardiner K., Horisberger M., Kraus J., Tantravahi U., Korenberg J., Rao V., Reddy S., Patterson D. Analysis of human chromosome 21: correlation of physical and cytogenetic maps; gene and CpG island distributions. EMBO J. 9:1990;25-34.
14. Gardiner K., Aissani B., Bernardi G. A compositional map of human chromosome 21. EMBO J. 9:1990;1853-1858.
15. Goto M., Shimizu T., Sawada J., Sawa C., Watanabe H., Ichikawa H., Ohira M., Handa H. Assignment of the E4TF1-60 gene to human chromosome 21q21.2-q21.3. Gene. 166:1995;337-338.
16. Harris N.L. Genotator: A workbench for sequence annotation. Genome Res. 7:1997;754-761.
17. Hattori M., Tsukahara F., Furuhata Y., Tanahashi H., Hirose M., Saito M., Tsukuni S., Sakaki Y. A novel method for making nested deletions and its application for sequencing of a 300 kb region of human APP locus. Nucleic Acids Res. 25:1997;1802-1808.
18. How G.-F., Venkatesh B., Brenner S. Conserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor. Genome Res. 6:1996;1185-1191.
19. Kamura T., Handa H., Hamasaki N., Kitajima S. Characterization of the human thrombopoietin gene promoter. A possible role of an Ets transcription factor, E4TF1/GABP. J. Biol. Chem. 272:1997;11361-11368.
20. Kery V., Bukovská G., Kraus J.P. Transsulfuration depends on heme in addition to pyridoxal 5′-phosphate. Cystathionine β-synthase is a heme protein. J. Biol. Chem. 269:1994;25283-25288.
21. Koh C.G., Oon S.H., Brenner S. Serine/threonine phosphatases of the pufferfish, Fugu rubripes. Gene. 198:1997;223-228.
22. Koop B.G., Nadeau J.H. Pufferfish and a new paradigm for comparative genome analysis. Proc. Natl. Acad. Sci. USA. 93:1996;1363-1365.
23. Kraus J.P. Biochemistry and molecular genetics of cystathionine beta-synthase deficiency. Eur. J. Pediatr. 157:1998;S50-S53.
24. Lalioti M.D., Gos A., Green M.R., Rossier C., Morris M.A., Antonarakis S.E. The gene for human U2 snRNP auxiliary factor small 35-kDa subunit (U2AF1) maps to the progressive myoclonus epilepsy (EPM1) critical region on chromosome 21q22.3. Genomics. 33:1996;298-300.
25. Maheshwar M.M., Sandford R., Nellist M., Cheadle J.P., Sgotto B., Vaudin M., Sampson J.R. Comparative analysis and genomic structure of the tuberous sclerosis 2 (TSC2) gene in human and pufferfish. Hum. Mol. Gen. 5:1996;131-137.
26. Mason P.J., Stevens D.J., Luzzatto L., Brenner S., Aparicio S. Genomic structure and sequence of the Fugu rubripes glucose-6-phosphate dehydrogenase gene (G6PD). Genomics. 26:1995;587-591.
27. Mudd, S.H., Levy, H.L., Skovby, F., 1995. Disorders of transsulfuration. In: Scriver, C.R., Beaudet, A.L., Sly, W.S., Valle, D. (Eds.), The Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill, New York, pp. 1279-1327.
28. Munke M., Kraus J.P., Ohura T., Francke U. The gene for cystathionine beta-synthase (CBS) maps to the subtelomeric region on human chromosome 21q and to proximal mouse chromosome 17. Am. J. Hum. Genet. 42:1988;550-559.
29. Philibert R., Hawkins G., Wamschroder-Williams P., Stubblefield B., Martin B., Genna E. Direct sequencing of trinucleotide repeats from cosmid genomic DNA template. Analyt. Biochem. 225:1995;372-374.
30. 2 leukocyte integrin) transcription. J. Biol. Chem. 270:1995;23627-23633.
31. Sambrook, J., Fritsch, E.F., Maniatis, E., 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Press, Boca Raton, FL.
32. Sathasivam K., Baxendale S., Mangiarini L., Bertaux F., Hetherington C., Kanazawa I., Lehrach H., Bates G.P. Aberrant processing of the Fugu HD (FrHD) mRNA in mouse cells and in transgenic mice. Hum. Mol. Gen. 12:1997;2141-2149.
33. Savoysky E., Mizuno T., Sowa Y., Watanabe H., Sawada J.-i., Nomura H., Ohsugi Y., Handa H., Sakai T. The retinoblastoma binding factor 1 (RBF-1) site in RB gene promoter binds preferentially E4TF1, a member of the Ets transcription factors family. Oncogene. 9:1994;1839-1846.
34. Sawada J.-i., Goto M., Sawa C., Watanabe H., Handa H. Transcriptional activation through the tetrameric complex formation of E4TF1 subunits. EMBO J. 13:1994;1396-1402.
35. Schuler G.D., Boguski M.S., Stewart E.A., Stein L.D., Gyapay G., Rice K.et al. A gene map of the human genome. Science. 274:1996;547-562.
36. Swaroop M., Bradley K., Ohura T., Tahara T., Roper M.D., Rosenberg L.E., Kraus J.P. Rat cystathionine β-synthase. Gene organization and alternative splicing. J. Biol. Chem. 267:1992;11455-11461.
37. Tanzi R.E., Gusella J.R., Watkins P.C., Bruns G.A.P., St. George-Hyslop P., Van Keuren M.L., Patterson D., Pagan S., Kurnit D.M., Neve R.L. Amyloid β protein gene: cDNA, mRNA distribution, and genetic linkage near the Alzheimer locus. Science. 235:1987;880-884.
38. Tronchere H., Wang J., Fu X.D. A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA. Nature. 388:1997;397-400.
39. Trower M.K., Orton S.M., Purvis I.J., Sanseau P., Riley J., Christodoulou C., Burt D., See C.G., Elgar G., Sherrington R., Rogaev E.I., St. George-Hyslop P., Brenner S., Dykes C.W. Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease (AD3 locus). Proc. Natl. Acad. Sci. USA. 93:1996;1366-1369.
40. Venkatesh B., Brenner S. Genomic structure and sequence of the pufferfish (Fugu rubripes) growth hormone-encoding gene: a comparative analysis of teleost growth hormone genes. Gene. 187:1997;211-215.
41. Venkatesh B., Si-Hoe S.L., Murphy D., Brenner S. Transgenic rats reveal functional conservation of regulatory controls between the Fugu isotocin and rat oxytocin genes. Proc. Natl. Acad. Sci. USA. 94:1997;12462-12466.
42. Villard L., Tassone F., Crnogorac-Jurcevic T., Clancy K., Gardiner K. Analysis of pufferfish homologues of the AT-rich human APP gene. Gene. 210:1998;17-24.
43. Virbasius J.V., Virbasius C.A., Scarpulla R.C. Identity of GABP with NRF-2, a multisubunit activator of cytochrome oxidase expression, reveals a cellular role for an ETS domain activator of viral promoters. Genes Dev. 7:1993;380-392.
44. Watanabe H., Sawada J.-I., Yano K.-I., Yamaguchi K., Goto M., Handa H. cDNA cloning of transcription factor E4TF1 subunits with Ets and Notch motifs. Mol. Cell. Biol. 13:1993;1385-1391.
45. 1 and its linkage to DOC-2 in pufferfish Fugu rubripes. Gene. 200:1997;203-211.
46. Zhang M., Zamore P.D., Carmo-Fonseca M., Lamond A.I., Green M.R. Cloning and intracellular localization of the U2 small nuclear ribonucleoprotein auxiliary factor small subunit. Proc. Natl. Acad. Sci. USA. 89:1992;8769-8773.
47. Zoubak S., Clay O., Bernardi G. The gene distribution of the human genome. Gene. 174:1996;95-102.
48. Zuo P., Maniatis T. The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes Dev. 10:1996;1356-1368.