A database of experimental results on globin gene expression

Genomics

Volumn 53, Issue 3, 1998, Pages 325-337

  Riemer, Cathy ^b   ElSherbini, Ahmed ^a   Stojanovic, Nikola ^b   Schwartz, Scott ^b   Kwitkin, Paul B ^b   Miller, Webb ^b   Hardison, Ross ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b The Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DATA BASE; DNA SEQUENCE; GENE EXPRESSION; GENE MUTATION; GENE STRUCTURE; GLOBIN GENE; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EUKARYOTA; MAMMALIA; PROKARYOTA;

EID: 0032213674     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1998.5524     Document Type: Article

References (36)

1. Arnold K., Gosling J. The Java Programming Language. 1996;Addison-Wesley, Reading, MA.
2. Benson D. A., Boguski M. S., Lipman D. J., Ostell J., Ouellette B. F. F. GenBank. Nucleic Acids Res. 26:1998;1-7.
3. Berners-Lee T., Cailliau R., Groff J., Pollerman B. World-Wide Web: The information universe. Electr. Networking. 2:1992;52-58.
4. Caterina J. J., Ciavatta D. J., Donze D., Behringer R. R., Townes T. M. Multiple elements in human β-globin locus control region 5′ HS2 are involved in enhancer activity and position-independent transgene expression. Nucleic Acids Res. 22:1994;1006-1011.
5. Chamberlin D. D., Astrahan M. M., Eswaran K. P., Griffiths P. P., Lorie R. A., Mehl J. W., Reisner P., Wade B. W. SEQUEL 2: A unified approach to data definition, manipulation, and control. IBM J. Res. Dev. 20:1976;560-575.
6. Chao K.-M., Hardison R., Miller W. Recent developments in linear-space alignment methods: A survey. J. Comput. Biol. 1:1994;271-291.
7. Chui D. H. K., Hardison R., Riemer C., Miller W., Carver M. F. H., Molchanova T. P., Efremov G. D., Huisman T. H. J. An electronic database of human hemoglobin variants on the World Wide Web. Blood. 91:1998;2643-2644.
8. Codd E. F. A relational model for large shared data banks. Comm. ACM. 13:1970;377-387.
9. Collis P., Antoniou M., Grosveld F. Definition of the minimal requirements within the human β-globin gene and the dominant control region for high level expression. EMBO J. 9:1990;233-240.
10. Crossley M., Orkin S. Regulation of the β-globin locus. Curr. Opin. Genet. Dev. 3:1993;232-237.
11. Elmasri R., Navathe S. Fundamentals of Database Systems. 1989;Benjamin/Cummings, Redwood City, CA.
12. Elnitski L., Miller W., Hardison R. Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the β-globin locus control region: Role of basic helix-loop-helix proteins. J. Biol. Chem. 272:1997;369-378.
13. Fasman K., Letovsky S., Cottingham R., Kingsbury D. The GDB human genome database anno 1997. Nucleic Acids Res. 25:1997;72-80.
14. Forrester W. C., Novak U., Gelinas R., Groudine M. Molecular analysis of the human β-globin locus activation region. Proc. Natl. Acad. Sci. USA. 86:1989;5439-5443.
15. Grosveld F., Antoniou M., Berry M., de Boer E., Dillon N., Ellis J., Fraser P., Hanscombe O., Hurst J., Imam A., Lindenbaum M., Philipsen S., Pruzina S., Strouboulis J., Raguz-Bolognesi S., Talbot D. The regulation of human globin gene switching. Philos. Trans. R. Soc. London B Biol. Sci. 339:1993;183-191.
16. Gumucio D. L., Heilstedt-Williamson H., Gray T. A., Tarle S. A., Shelton D. A., Tagle D., Slightom J., Goodman M., Collins F. S. Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human γ and ε globin genes. Mol. Cell. Biol. 12:1992;4919-4929.
17. Gumucio D. L., Shelton D. A., Bailey W. J., Slightom J. L., Goodman M. Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the ε-globin gene. Proc. Natl. Acad. Sci. USA. 90:1993;6018-6022.
18. Hardison R., Chao K.-M., Schwartz S., Stojanovic N., Ganetsky M., Miller W. Globin gene server: A prototype e-mail database server featuring extensive multiple alignments and data compilation. Genomics. 21:1994;344-353.
19. Hardison R., Slightom J. L., Gumucio D. L., Goodman M., Stojanovic N., Miller W. Locus control regions of mammalian β-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights. Gene. 205:1997;73-94.
20. Hardison R., Riemer C., Chui D. H. K., Huisman T. H. J., Miller W. Electronic access to sequence alignments, experimental results and human mutations as an aid to studying globin gene regulation. Genomics. 47:1998a;429-437.
21. Hardison R. C., Chui D. H. K., Riemer C., Miller W., Carver M. F. H., Molchanova T. P., Efremov G. D., Huisman T. H. J. Access to "A Syllabus of Human Hemoglobin Variants (1996)" via the World Wide Web. Hemoglobin. 22:1998b;113-127.
22. Jackson J. D., Petrykowska H., Philipsen S., Miller W., Hardison R. Role of DNA sequences outside the cores of DNase hypersensitive sites (HSs) in functions of the β-globin locus control region: Domain opening and synergism between HS2 and HS3. J. Biol. Chem. 271:1996;11871-11878.
23. Lam L. T., Bresnick E. H. A novel DNA-binding protein, HS2NF5, interacts with a functionally important sequence of the human β-globin locus control region. J. Biol. Chem. 271:1996;32421-32429.
24. Miller J. L., Walsh C. E., Ney P. A., Samulski R. J., Nienhuis A. W. Single-copy transduction and expression of human γ-globin in K562 erythroleukemia cells using recombinant adeno-associated virus vectors: the effects of mutations in NF-E2 and GATA1 binding motifs within the hypersensitive site 2 enhancer. Blood. 82:1993;1900-1906.
25. Moi P., Kan Y. W. Synergistic enhancement of globin gene expression by activator protein-1-like proteins. Proc. Natl. Acad. Sci. USA. 87:1990;9000-9004.
26. Motohashi H., Shavit J. A., Igarashi K., Yamamoto M., Engel J. D. The world according to Maf. Nucleic Acids Res. 25:1997;2953-2959.
27. Ousterhout J. K. Tcl and the Tk Toolkit. 1994.
28. Pistor P., Traunmueller R. A database language for sets, lists and tables. Inform. Systems. 11:1986;323-336.
29. Roth M. A., Korth H. F., Batory D. S. SQL/NF: A query language for ¬1NF relational databases. Inform. Systems. 12:1987;99-114.
30. Salas F., Haas J., Stoeckert C. J. Jr., Overton G. C. Bioinformatics: German Conference on Bioinformatics, GCB '96. 1997;Springer Verlag, Berlin. p. 52-61.
31. Schuler G., Epstein J., Ohkawa H., Kans J. Entrez: Molecular biology database and retrieval system. Methods Enzymol. 266:1996;141-162.
32. Slightom J., Bock J., Tagle D., Gumucio D., Goodman M., Stojanovic N., Jackson J., Miller W., Hardison R. The complete sequences of the galago and rabbit β-globin locus control regions: Extended sequence and functional conservation outside the cores of DNase hypersensitive sites. Genomics. 39:1997;90-94.
33. Sorrentino B., Ney P., Bodine D., Nienhuis A. W. A 46 base pair enhancer sequence within the locus activating region is required for induced expression of the γ-globin gene during erythroid differentiation. Nucleic Acids Res. 18:1990;2721-2731.
34. Stamatoyannopoulos, G. Nienhuis, A. W. 1994, The Molecular Basis of Blood Diseases, G. StamatoyannopoulosA. W. NienhuisP. W. MajerusH. Varmus, 107, 155, Saunders, Philadelphia.
35. Tuan D., Abeliovich A., Lee-Oldham M., Lee D. Identification of regulatory elements of human β-like globin genes. Stamatoyannopoulos G., Nienhuis A. W. Progress in Clinical Biological Research, Developmental Control of Globin Gene Expression. 1987;211-220 A. R. Liss, New York.
36. vanAssendelft G. B., Hanscombe O., Grosveld F., Greaves D. The β-globin dominant control region activates homologous and heterologous promoters in a tissue-specific manner. Cell. 56:1989;969-977.