Electronic access to sequence alignments, experimental results, and human mutations as an aid to studying globin gene regulation

Genomics

Volumn 47, Issue 3, 1998, Pages 429-437

  Hardison, Ross ^a   Riemer, Cathy ^b   Chui, David H K ^c   Huisman, Titus H J ^d   Miller, Webb ^b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b Pennsylvania State University   (United States)

^c MCMASTER UNIVERSITY   (Canada)

^d MEDICAL COLLEGE OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GLOBIN;

ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; DNA SEQUENCE; GENE MUTATION; GENOTYPE; HEMOGLOBINOPATHY; HUMAN; HUMAN CELL; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EID: 0032005167     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1997.5147     Document Type: Article

References (49)

1. Burset M. R., Guigó R. Evaluation of gene structure prediction programs. Genomics. 34:1996;353-367.
2. 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.
3. Chao K.-M., Hardison R., Miller W. Recent developments in linear-space alignment methods: A survey. J. Comput. Biol. 1:1994;271-291.
4. 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. 1998.
5. Collins F. S., Weissman S. M. The molecular genetics of human hemoglobin. Prog. Nucleic Acids Res. Mol. Biol. 31:1984;315-462.
6. Cooper D. N., Krawczak M. Human Gene Mutation. 1993;BIOS Sci. Oxford.
7. Cotton R. G. H., Scriver C. R., McKusick V. A. Locus-specific mutation databases: A resource. Genome Dig. January:1996;6.
8. 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.
9. Fasman K., Letovsky S., Cottingham R., Kingsbury D. The GDB human genome database anno 1997. Nucleic Acids Research. 25:1997;72-80.
10. Feng D.-F., Doolittle R. F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25:1987;351-360.
11. Flint J., Thomas K., Micklem G., Raynham H., Clark K., Doggett N. A., King A., Higgs D. R. The relationship between chromosome structure and function at a human telomeric region. Nature Genet. 15:1997;252-257.
12. Grosveld F., van Assendelft G. B., Greaves D., Kollias G. Position-independent, high-level expression of the human β-globin gene in transgenic mice. Cell. 51:1987;975-985.
13. Gumucio D., Shelton D., Zhu W., Millinoff D., Gray T., Bock J., Slightom J., Goodman M. Evolutionary strategies for the elucidation ofcistrans. Mol. Phylogenet. Evol. 5:1996;18-32.
14. 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.
15. 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.
16. Hardison R. Hemoglobins from bacteria to man: Evolution of different patterns of gene expression. J. Exp. Biol. 1998.
17. 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.
18. Hardison R., Elnitski L., Goldstrohm A., ElSherbini A., Riemer C., Schwartz S., Stojanovic N., Miller W. Globin Gene Server: An aid to studying the regulation of mammalian globin genes. Molecular Biology of Hemoglobin Switching. 1995;Intercept, Andover. p. 405-426.
19. Hardison R., Oeltjen J., Miller W. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7:1997a;959-966.
20. 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. 205:1997b;73-94.
21. Hardison R., Xu J., Jackson J., Mansberger J., Selifonova O., Grotch B., Biesecker J., Petrykowska H., Miller W. Comparative analysis of the locus control region of the rabbit β-like globin gene cluster: HS3 increases transient expression of an embryonic ε-globin gene. Nucleic Acids Res. 21:1993;1265-1272.
22. Hug B. A., Moon A. M., Ley T. J. Structure and function of the murine β-globin locus control region 5′ HS-3. Nucleic Acids Res. 21:1992;5771-5778.
23. Huisman T. H. J., Carver M. F. H., Baysal E. A Syllabus of Thalassemia Mutations (1997). 1997;The Sickle Cell Anemia Foundation, Augusta.
24. Huisman T. H. J., Carver M. F. H., Efremov G. D. A Syllabus of Human Hemoglobin Variants (1996). 1996;The Sickle Cell Anemia Foundation, Augusta.
25. Jackson J. D., Miller W., Hardison R. C. Sequences within and flanking hypersensitive sites 3 and 2 of the β-globin locus control region required for synergistic versus additive interaction with the ε-globin gene promoter. Nucleic Acids Res. 24:1996a;4327-4335.
26. 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. 271:1996b;11871-11878.
27. Jimenez G., Gale K. B., Enver T. The mouse β-globin locus control region: Hypersensitive sites 3 and 4. Nucleic Acids Res. 20:1992;5797-5803.
28. Koop B. F. Human and rodent sequence comparisons: A mosaic model of genomic evolution. Trends Genet. 11:1995;367-371.
29. Lam L., 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.
30. Lander E. S. The new genomics: Global views of biology. Science. 274:1996;536-539.
31. Li Q., Powers P. A., Smithies O. Nucleotide sequence of 16-kilobase pairs of DNA 5′ to the human ε-globin gene. J. Biol. Chem. 260:1985;14901-14910.
32. Li Q., Zhou B., Powers P., Enver T., Stamatoyannopoulos G. β-Globin locus activation regions: Conservation of organization, structure and function. Proc. Natl. Acad. Sci. USA. 87:1990;8207-8211.
33. Liu D., Chang J. C., Moi P., Jiu W., Kan Y. W., Curtin P. T. Dissection of the enhancer activity of β-globin 5′ DNase I-hypersensitive site 2 in transgenic mice. Proc. Natl. Acad. Sci. USA. 89:1992;3899-3903.
34. Margot J., Hardison R. DNase I and nuclease S1 sensitivity of the rabbit β1 globin gene in nuclei and in supercoiled plasmids. J. Mol. Biol. 184:1985;195-210.
35. McKusick V. A. Genomics: Structural and functional studies of genomes. Genomics. 45:1997;244-249.
36. Miller, W. ElSherbini, A. Peck, J. Riemer, C. Schwartz, S. Stojanovic, N. Hardison, R. 1995, A database for globin gene expression data, In, Proceedings of the 28th Hawaii Conference on System Sciences, V, Biotechnology Computing, L. HunterB. Shriver, 62, 71, IEEE Comput. Soc. Los Alamitos, CA.
37. Moon A. M., Ley T. J. Conservation of the primary structure, organization, and function of the human and mouse β-globin locus-activating regions. Proc. Natl. Acad. Sci. USA. 87:1990;7693-7697.
38. Myers E., Selznick S., Zhang Z., Miller W. Progressive multiple alignment with constraints. J. Comput. Biol. 3:1996;563-572.
39. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:1970;443-453.
40. Riemer, C. ElSherbini, A. Stojanovic, N. Schwartz, S. Kwitkin, P. B. Peck, J. Gudjonsson, G. Miller, W. Hardison, R. 1997, A database of experimental results on gene expression on the Globin Gene Server.
41. Shehee R., Loeb D. D., Adey N. B., Burton F. H., Casavant N. C., Cole P., Davies C. J., McGraw R. A., Schichman S. A., Severynse D. M., Voliva C. F., Weyter F. W., Wisely G. B., Edgell M. H., Hutchison C. A. Nucleotide sequence of the BALB/c mouse β-globin complex. J. Mol. Biol. 205:1989;41-62.
42. 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.
43. Stojanovic, N. Berman, P. Gumucio, D. L. Hardison, R. C. Miller, W. 1997, A linear-time algorithm for the 1-mismatch problem, In, Algorithms and Data Structures, F. DehneA. Rau-ChaplinJ.-R. SackR. Tamassia, 126, 135, Springer, New York.
44. Stormo G. Consensus patterns in DNA. Methods Enzymol. 183:1990;211-221.
45. Tagle D., Stanhope M. J., Siemieniak D. R., Benson P., Goodman M., Slightom J. L. The β-globin gene cluster of the prosimian primateGalago crassicaudatus: Genomics. 13:1992;741-760.
46. Tagle D. A., Koop B. F., Goodman M., Slightom J., Hess D. L., Jones R. T. Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus. J. Mol. Biol. 203:1988;7469-7480.
47. Townes T. M., Fitzgerald M. C., Lingrel J. B. Triplication of a four-gene set during evolution of the goat β-globin locus produced three genes now expressed differentially during development. Proc. Natl. Acad. Sci. USA. 81:1984;6589-6593.
48. Tuan D., Solomon W., Li Q., London I. M. The β-like globin gene domain in human erythroid cells. Proc. Natl. Acad. Sci. USA. 82:1985;6384-6388.
49. Uberbacher E. C., Mural R. J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA. 88:1991;11261-11265.