Long-range chromatin reorganization of the human serpin gene cluster at 14q32.1 Accompanies gene activation and extinction in microcell hybrids

Genomics

Volumn 56, Issue 1, 1999, Pages 22-30

  Rollini, Pierre ^a   Fournier, R E K ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA 1 ANTITRYPSIN; DEOXYRIBONUCLEASE I; RNA; SERINE PROTEINASE INHIBITOR; TRANSCORTIN;

ALLELE; ANIMAL CELL; ARTICLE; CHROMATIN; CHROMATIN STRUCTURE; CHROMOSOME 14Q; GENE; GENE ACTIVATION; GENE CLUSTER; GENE EXPRESSION; HEPATOMA CELL; HUMAN; HUMAN CELL; HYBRID CELL; LIVER; MOUSE; NONHUMAN; PRIORITY JOURNAL; RAT;

EID: 0033557482     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1998.5680     Document Type: Article

References (72)

1. Bao J., Reed-Fourquet L., Sifers R. N., Kidd V. J., Woo S. L. C. Molecular structure and sequence homology of a gene related to α-1 antitrypsin in the human genome. Genomics. 2:1988;165-173.
2. Blau J., Xiao H., McCracken S., O'Hare P., Greenblatt J., Bentley D. Three functional classes of transcriptional activation domains. Mol. Cell. Biol. 16:1996;2044-2055.
3. Boyes J., Felsenfeld G. Tissue-specific factors additively increase the probability of the all-or-none formation of a hypersensitive site. EMBO J. 15:1996;2496-2507.
4. Boyes J., Omichinski J., Clark S., Pikaart M., Felsenfeld G. Perturbation of nucleosome structure by the erythroid transcription factor GATA-1. J. Mol. Biol. 279:1998;529-544.
5. Bulla G. A., DeSimone V., Cortese R., Fournier R. E. K. Extinction of α1-antitrypsin gene expression in somatic cell hybrids: Evidence for multiple controls. Genes Dev. 6:1992;316-327.
6. Bulla G. A., Fournier R. E. K. Direct selection of hepatoma cell variants deficient in α1-antitrypsin gene expression. Somat. Cell. Mol. Genet. 18:1992;361-370.
7. Bulla G. A., Fournier R. E. K. Genetic analysis of a transcriptional activation pathway by using hepatoma cell variants. Mol. Cell. Biol. 14:1994;7086-7094.
8. Byth B. C., Billingsley G. D., Cox D. W. Physical and genetic mapping of the serpin gene cluster at 14q32.1: Allelic association and a unique haplotype associated with α-1 antitrypsin deficiency. Am. J. Hum. Genet. 55:1994;126-133.
9. Chi T., Lieberman P., Ellwood K., Carey M. A general mechanism for transcriptional synergy by eukaryotic activators. Nature. 377:1995;254-257.
10. Cockerill P. N., Garrard W. T. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell. 44:1986;273-282.
11. Costa R. H., Grayson D. R., Darnell J. E. Jr. Multiple hepatocyte-enriched nuclear factors function in the regulation of transthyretin and α1-antitrypsin. Mol. Cell. Biol. 9:1989;1415-1425.
12. Courtois G., Morgan J. G., Campbell L. A., Fourel G., Crabtree G. R. Interaction of a liver-specific nuclear factor with the fibrinogen and α1-antitrypsin promoters. Science. 238:1987;688-692.
13. Danielson P. E., Forss-Petter S., Brow M. A., Calavetta L., Douglass J., Milner R. J., Sutcliffe J. G. P1B15: A cDNA clone of the rat mRNA encoding cyclophilin. DNA. 7:1988;261-267.
14. De Simone V., Ciliberto G., Hardon E., Paonessa G., Palla F., Lundberg L., Cortese R. Cistrans. EMBO J. 6:1987;2759-2766.
15. Dhar V., Skoultchi A. I., Schildkraut C. L. Activation and repression of a β-globin gene in cell hybrids is accompanied by a shift in its temporal replication. Mol. Cell. Biol. 9:1989;3524-3532.
16. Dieken E. S., Epner E. M., Fiering S., Fournier R. E. K., Groudine M. Efficient modification of human chromosomal alleles using recombination-proficient chicken/human microcell hybrids. Nat. Genet. 12:1996;174-182.
17. Dieken E. S., Fournier R. E. K. Homologous modification of human chromosomal genes in chicken B-cell × human microcell hybrids. Methods Companion Methods Enzymol. 9:1996;56-63.
18. Dillon N., Grosveld F. Chromatin domains as potential units of eucaryotic gene function. Curr. Opin. Genet. Dev. 4:1994;260-264.
19. Eissenberg J. C., Elgin S. C. R. Boundary functions in the control of gene expression. Trends Genet. 7:1991;335-340.
20. Elgin S. C. R. The formation and function of DNase I hypersensitive sites in the process of gene activation. J. Biol. Chem. 263:1988;19259-19262.
21. Elgin S. C. R. Heterochromatin and gene regulation inDrosophila. Curr. Opin. Genet. Dev. 6:1996;193-202.
22. Fedor M. J. Chromatin structure and gene expression. Curr. Opin. Cell Biol. 4:1992;436-443.
23. Felsenfeld G. Chromatin as an essential part of the transcriptional mechanism. Nature. 355:1992;219-224.
24. Forrester W. C., Thompson C., Elder J. T., Groudine M. A developmentally stable chromatin structure in the human β-globin gene cluster. Proc. Natl. Acad. Sci. USA. 83:1986;1359-1363.
25. Forrester W. C., Takegawa S., Papayannopoulou T., Stamatoyannopoulos G., Groudine M. Evidence for a locus activation region: The formation of developmentally stable hypersensitive sites in globin-expressing hybrids. Nucleic Acids Res. 15:1987;10159-10177.
26. Forrester W. C., Epner E., Driscoll M. C., Enver T., Brice M., Papayannopoulou T., Groudine M. A deletion of the human β-globin locus activation region causes a major alteration in chromatin structure and replication across the entire β-globin locus. Genes Dev. 4:1990;1637-1649.
27. Frain M., Swart G., Monaci P., Nicosia A., Stämpfli S., Frank R., Cortese R. The liver-specific transcription factor LF-B1 contains a highly diverged homeobox DNA binding domain. Cell. 59:1989;145-157.
28. Gourdeau H., Fournier R. E. K. Genetic analysis of mammalian cell differentiation. Annu. Rev. Cell Biol. 6:1990;69-94.
29. Gross D. S., Garrard W. T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57:1988;159-197.
30. Grosveld F., van Assendelft G. B., Greaves D. R., Kollias G. Position-independent, high-level expression of the human β-globin gene in transgenic mice. Cell. 51:1987;975-985.
31. Hafeez W., Ciliberto G., Perlmutter D. H. Constitutive and modulated expression of the human α-1 antitrypsin gene. J. Clin. Invest. 89:1992;1214-1222.
32. Hammond G. L., Smith C. L., Goping I. S., Underhill D. A., Harley M. J., Reventos J., Musto N. A., Gunsalus G. L., Bardin C. W. Primary structure of human corticosteroid binding globulin, deduced from hepatic and pulmonary cDNAs, exhibits homology with serine protease inhibitors. Proc. Natl. Acad. Sci. USA. 84:1987;5153-5157.
33. Hanna-Rose W., Hansen U. Active repression mechanisms of eukaryotic transcription repressors. Trends Genet. 12:1996;229-234.
34. Hill C. S., Treisman R. Transcriptional regulation by extracellular signals: Mechanisms and specificity. Cell. 80:1995;199-211.
35. Hofker M. H., Nelen M., Klasen E. C., Nukiwa T., Curiel D., Crystal R. G., Frants R. R. Cloning and characterization of an α-1 antitrypsin like gene 12 kb downstream of the genuine α-1 antitrypsin gene. Biochem. Biophys. Res. Commun. 155:1988;634-642.
36. Hohn P. A., Popescu N. C., Hanson R. D., Salvesen G., Ley T. J. Genomic organization and chromosomal localization of the human cathepsin G gene. J. Biol. Chem. 264:1989;13412-13419.
37. Ip Y. T., Fournier R. E. K., Chalkley R. Extinction of phosphoenolpyruvate carboxykinase gene expression is associated with loss of a specific chromatin-binding protein from a far upstream domain. Mol. Cell. Biol. 10:1990;3782-3787.
38. Johnson P. F., McKnight S. L. Eukaryotic transcriptional regulatory proteins. Annu. Rev. Biochem. 58:1989;799-839.
39. Kelsey G. D., Povey S., Bygrave A. E., Lovell-Badge R. H. Species- and tissue-specific expression of human α-1 antitrypsin in transgenic mice. Genes Dev. 1:1987;161-171.
40. Kelsey G. D., Parkar M., Povey S. The human alpha-1-antitrypsin-related sequence: Isolation and investigation of its expression. Ann. Hum. Genet. 52:1988;151-160.
41. Kioussis D., Festenstein R. Locus control regions: Overcoming heterochromatin-induced gene inactivation in mammals. Curr. Opin. Genet. Dev. 7:1997;614-619.
42. Laemmli U. K., Kas E., Poljak L., Adachi Y. Scaffold-associated regions:cis. Curr. Opin. Genet. Dev. 2:1992;275-285.
43. Li Y., Shen R.-F., Tsai S. Y., Woo S. L. C. Multiple hepatictransin vitro. Mol. Cell Biol. 8:1988;4362-4369.
44. Lin Y. S., Carey M., Ptashne M., Green M. R. How different eukaryotic transcriptional activators can cooperate promiscuously. Nature. 345:1990;359-361.
45. Lugo T. G., Handelin B., Killary A. M., Housman D. E., Fournier R. E. K. Isolation of microcell hybrid clones containing retroviral vector insertions into specific human chromosomes. Mol. Cell. Biol. 7:1987;2814-2820.
46. Maniatis T., Goodbourn S., Fischer J. A. Regulation of inducible and tissue-specific gene expression. Science. 236:1987;1237-1245.
47. Mirkovitch J., Mirault M. E., Laemmli U. K. Organization of the higher-order chromatin loop: Specific DNA attachment site on nuclear scaffold. Cell. 39:1984;223-232.
48. Mirkovitch J., Darnell J. E. Jr. Rapid in vivo footprinting technique identifies proteins bound to the TTR gene in the mouse liver. Genes Dev. 5:1991;83-93.
49. Mitchell P. J., Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 245:1989;371-378.
50. Monaci P., Nicosia A., Cortese R. Two different liver-specific factors stimulate in vitro transcription from the human α1-antitrypsin promoter. EMBO J. 7:1988;2075-2087.
51. Morgan K., Scobie G., Kalsheker N. A. Point mutation in a 3′ flanking sequence of the alpha-1-antitrypsin gene associated with chronic respiratory disease occurs in a regulatory sequence. Hum. Mol. Genet. 2:1993;253-257.
52. Namciu S. J., Blochlinger K. B., Fournier R. E. K. Human matrix attachment regions insulate transgene expression from chromosomal position effects inDrosophila melanogaster. Mol. Cell. Biol. 18:1998;2382-2391.
53. Opdecamp K., Szpirer C., Szpirer J. Major chromatin changes accompany extinction of α-fetoprotein gene in hepatoma × fibroblast hybrids. Somat. Cell. Mol. Genet. 17:1991;49-55.
54. Perlino E., Cortese R., Ciliberto G. The human α-1 antitrypsin gene is transcribed from two different promoters in macrophages and hepatocytes. EMBO J. 6:1987;2767-2771.
55. Perlmutter D. H., Sessions Cole F., Kilbridge P., Rossing T. H., Colten H. R. Expression of the α-1 proteinase inhibitor gene in human monocytes and macrophages. Proc. Natl. Acad. Sci. USA. 82:1985;795-799.
56. Perlmutter D. H., Daniels J. D., Auerbach H. S., De Schryver-Kecskemeti K., Winter H. S., Alpers D. H. The α-1 antitrypsin gene is expressed in a human intestinal epithelial cell line. J. Biol. Chem. 264:1989;9485-9490.
57. Porter M. B., Fournier R. E. K. Isolation and characterization of human hepatoma cells with targeted insertions of agpt. Somat. Cell Mol. Genet. 22:1996;311-327.
58. Potempa J., Korzus E., Travis J. The serpin superfamily of proteinase inhibitors: Structure, function, and regulation. J. Biol. Chem. 269:1994;15957-15960.
59. Rollini P., Fournier R. E. K. Molecular linkage of the human α-1 antitrypsin and corticosteroid-binding globulin genes on chromosome 14q32.1. Mamm. Genome. 8:1997a;913-916.
60. Rollini P., Fournier R. E. K. A 370-kb cosmid contig of the serpin gene cluster on human chromosome 14q32.1: Molecular linkage of the genes encoding α-1 antichymotrypsin, protein C inhibitor, kallistatin, α-1 antitrypsin and corticosteroid-binding globulin. Genomics. 46:1997b;409-415.
61. Rüther U., Tripodi M., Cortese R., Wagner E. F. The human alpha-1-antitrypsin gene is efficiently expressed from two tissue-specific promoters in transgenic mice. Nucleic Acids Res. 15:1987;7519-7529.
62. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
63. Sefton L., Kelsey G., Kearney P., Povey S., Wolfe J. A physical map of the human PI and AACT genes. Genomics. 7:1990;382-388.
64. Shapero M. H., Langston A. A., Fournier R. E. K. Tissue-specific extinguisher loci in the human genome: A screening study based on random marking and transfer of human chromosomes. Somat. Cell Mol. Genet. 20:1994;215-231.
65. Sifers R. N., Carlson J. A., Clift S. M., DeMayo F. J., Bullock D. W., Woo S. L. C. Tissue specific expression of the human alpha-1-antitrypsin gene in transgenic mice. Nucleic Acids Res. 15:1987;1459-1475.
66. Sladek F. M., Zhong W., Lai E., Darnell J. E. Jr. Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily. Genes Dev. 4:1990;2353-2365.
67. Svaren J., Horz W. Regulation of gene expression by nucleosomes. Curr. Opin. Genet. Dev. 6:1996;164-170.
68. Tjian R., Maniatis T. Transcriptional activation: A complex puzzle with few easy pieces. Cell. 77:1994;5-8.
69. Tso J. Y., Sun X.-H., Kao T., Reece K. S., Wu R. Isolation and characterization of rat and human glyceraldehyde-3-phosphate dehydrogenase cDNAs: Genomic complexity and molecular evolution of the gene. Nucleic Acids Res. 13:1985;2485-2502.
70. 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.
71. Underhill D. A., Hammond G. L. Organization of the human corticosteroid binding globulin gene and analysis of its 5′-flanking region. Mol. Endocrinol. 3:1989;1448-1454.
72. Weintraub H., Groudine M. Chromosomal subunits in active genes have an altered conformation. Science. 193:1976;848-856.