Scaffold-associated regions in the human type I interferon gene cluster on the short arm of chromosome 9

Genomics

Volumn 47, Issue 2, 1998, Pages 217-229

  Strissel, Pamela L ^a   Dann, Hadas Arad ^a   Pomykala, Helen M ^a   Diaz, Manuel O ^a   Rowley, Janet D ^a   Olopade, Olufunmilayo I ^a  

^a University of Chicago   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTERFERON;

ARTICLE; CHROMOSOME 9; GENE DELETION; GENE MAPPING; GENE STRUCTURE; GLIOMA CELL; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

EID: 0032518532     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1997.5103     Document Type: Article

References (49)

1. Amati B., Gasser S. Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell. 54:1988;967-978.
2. Anand R., Boehm C., Kazazian H., Vanin E. Molecular characterization of a thalassemia resulting from a 1.4 kilobase deletion. Blood. 72:1988;636-641.
3. Blasquez V., Sperry A., Cockerill P., Garrard W. Protein:DNA interactions at chromosomal loop attachment sites. Gene Regul. II. 31:1989;503-509.
4. Bode J., Maass K. Chromatin domain surrounding the humanInterferon-B. Biochemistry. 27:1988;4706-4711.
5. Broeker, P. L. 1993, University of Chicago, IL.
6. Brotherton T., Zenk D., Kahanic S., Reneker J. Avian nuclear matrix proteins bind very tightly to cellular DNA of the B-globin gene enhancer in a tissue-specific fashion. Biochemistry. 30:1991;5845-5850.
7. 16. Science. 265:1994;415-417.
8. Chen S., Chen Z., Grausz D., Hillion J., d'Auriol L., Flandrin G., Larsen C., Berger R. Molecular cloning of a 5′ segment of the genomic ph1 gene defines a new breakpoint cluster region (bcr2) in Philadelphia-positive acute leukemias. Leukemia. 2:1988;634-641.
9. Cockerill P., Garrard W. 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.
10. Cockerill P., Yuen M., Garrard T. The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J. Biol. Chem. 262:1987;5394-5397.
11. de Lange T. Human telomeres are attached to the nuclear matrix. EMBO J. 2:1992;717-724.
12. Diaz M., Ziemin S., Le Beau M., Pitha P., Smith S., Chilcote R., Rowley J. D. Homozygous deletion of the alpha and beta-1 interferon genes in human leukemia and derived cell lines. Proc. Natl. Acad. Sci. USA. 85:1988;5259-5263.
13. Diaz M. O., Ziemin S., Le Beau M. M., Pitha P., Smith S. D., Chilchote R. R., Rowley J. D. Homozygous deletion of theaB1. Proc. Natl. Acad. Sci. USA. 85:1988;5259-5263.
14. Diaz M. O., Pomykala H., Bohlander S., Maltepe E., Malik K., Brownstein B., Olopade O. I. Structure of the human type-I interferon gene cluster determined from a YAC clone contig. Genomics. 22:1994;540-552.
15. Diaz M. O., Rubin C. M., Hardin A., Ziemin S., Larson R. A., LeBeau M. M., Rowley J. D. Deletions ofIFN. N. Engl. J. Med. 322:1990;77-82.
16. Dijkwel P., Hamlin J. Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells. Mol. Cell Biol. 12:1988;5398-5409.
17. Gasser S., Laemmli U. K. Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes ofD. melanogaster. Cell. 46:1986a;521-530.
18. Gasser S., Laemmli U. K. The organization of chromatin loops: Characterization of a scaffold attachment site. EMBO J. 5:1986b;511-517.
19. Gasser S., Amati B., Cardenas M., Hoffmann J. Studies on scaffold attachment sites and their relation to genome function. Int. Rev. Cytol. 119:1989;57-96.
20. Hall G., Allen G., Loer D., Thompson W., Spiker S. Nuclear scaffolds and scaffold-attachment regions in higher plants. Proc. Natl. Acad. Sci. USA. 88:1991;9320-9324.
21. Hanson R., Ley T. A-T rich scaffold attachment regions flank the hematopoietic serine protease genes clustered on chromosome 14q11.2. Blood. 79:1992;610-618.
22. Henco K., Brosius A., Fujisawa A., Fujisawa J., Haynes R., Hochstadt J., Kovacic T., Pasek M., Schambock A., Schmid J., Todokoro K., Walchli M., Nagata S., Weissmann C. Structural relationship of human interferon alpha genes and pseudogenes. J. Mol. Biol. 185:1985;227-260.
23. James D., Ju H., Carlbom E., Nordenskjold M., Cavenee W., Collin P. S. Chromosome 9 deletion mapping reveals interferon alpha and interferon beta-1 gene deletions in human glial tumors. Cancer Res. 51:1991;1684-1688.
24. Jankelevich S., Kolman J., Bodnar J., Miller G. A nuclear matrix attachment region organizes the Epstein-Barr viral plasmid in Raji cells into a single DNA domain. EMBO J. l:1992;1165-1176.
25. Jarmin A., Higgs D. Nuclear scaffold attachment sites in the human globin gene complexes. EMBO J. 7:1988;3337-3344.
26. Jenuwein T., Forrester W. C., Fernandez-Herrero, Laible G., Dull M., Grosschedl R. Extension of chromatin accessibility by nuclear matrix attachment regions. Nature. 385:1997;269-272.
27. Kamb A., Gruis N. A., Weaver-Feldhauf J., Liu Q., Harshman K., Tautigian, Stockert E., Day R. S. III, Johnson B. E., Skolnick M. H. A cell cycle regulator potentially involved in genesis of many tumor types. Science. 264:1994;436-439.
28. Laemmli U. K., Kas E., Poljak L., Adachi Y. Scaffold associated regions: cis-acting determinants of chromatin structural loops and functional domains. Curr. Opin. Genet. Dev. 2:1992;275-285.
29. Maher J. F., Nathans D. Multivalent DNA-binding properties of the HMG-I proteins. Proc. Natl. Acad. Sci. USA. 93:1996;6716-6720.
30. Maniatis T., Fritsch E., Sambrook J. Molecular Cloning: A Laboratory Manual. 1982;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
31. Middleton P., Prince R., Williamson I., Taylor P., Reid M., Jackson G., Katz F., Chessells J., Proctor S. Alpha interferon gene deletions in adults, children and infants with acute lymphoblastic leukemia. Leukemia. 5:1991;680-682.
32. Mirkovitch J., Mirault M., Laemmli U. K. Organization of the higher-order chromatin loop: Specific DNA attachment sites on nuclear scaffold. Cell. 39:1984;223-232.
33. Nobori T., Miura K., Wu D. J., Lois A., Takabayashi K., Carson D. Deletions of the cyclin-dependent kinase-4 inhibitor gene in multiple human cancers. Nature. 368:1994;753-7566.
34. INK4. Proc. Natl. Acad. Sci. USA. 91:1994;11045-11049.
35. Olopade O., Bohlander S., Pomykala H., Maltepe E., Van Melle E., LeBeau, Diaz M. Mapping of the shortest region of overlap of deletion of the short arm of chromosome 9 associated with human neoplasia. Genomics. 14:1992a;1-7.
36. Olopade O., Jenkins R., Ransom D., Malik K., Pomykala H., Nobori T., Cowan J., Rowley J., Diaz M. Molecular analysis of deletions of the short arm of chromosome 9 in human gliomas. Cancer Res. 52:1992b;2523-2529.
37. Olopade O. I., Pomykala H. M., Hagos F., Sveen L. W., Espinsoa R., Dreyling M. H., Gursky S., Stadler W. M., Le Beau M. M., Bohlander S. K. Construction of a 2.8 megabase yeast artificial chromosome contig and cloning of a human methylthioadenosine phosphorylase gene from the tumor suppressor region on 9p21. Proc. Natl. Acad. Sci. USA. 92:1995;6489-6493.
38. Pegoraro L., Matera L., Ritz J., Levis A., Palumbo A., Biagini G. Establishment of a Ph1-positive human cell line (BV173). J. Natl. Cancer Inst. 70:1983;447-451.
39. Phi-Van L., Stratling W. The matrix attachment regions of the chicken lysozyme gene co-map with the boundaries of the chromatin domain. EMBO J. 7:1988;655-664.
40. Pomykala H. M., Bohlander S. K., Broeker P. L., Olopade O. I., Diaz M. Breakpoint junctions of chromosome 9p deletions in two human glioma cell lines. Mol. Cell. Biol. 14:1994;7604-7610.
41. Scheuermann R. H., Chen U. A developmental-specific factor binds to suppressor sites flanking the immunoglobulin heavy-chain enhancer. Genes Dev. 3:1989;1255-1266.
42. Sperry A., Blasquez V., Garrard W. Dysfunction of chromosomal loop attachment sites: Illegitimate recombination linked to matrix association regions and topoisomerase II. Proc. Natl. Acad. Sci. USA. 86:1989;5497-5501.
43. Stadler W., Sherman J., Bohlander S., Roulston D., Dreyling M., Rukstalis D., Olopade O. I. Homozygous deletions within chromosomal bands 9p21-22 in bladder cancer. Cancer Res. 54:1994;2060-2063.
44. Strick R., Laemmli U. K. SARs are cis DNA elements of chromosome dynamics: Synthesis of a SAR repressor protein. Cell. 83:1995;1137-1148.
45. Strissel P. L., Espinosa R. III, Rowley J. D., Swift H. Scaffold attachment sites map to centromeric DNA. Chromosoma. 105:1996;122-133.
46. Strissel Broeker P. L., Gill Super H., Thirman M. J., Pomykala H., Yonebayshi Y., Tanabe S., Zeleznik-Le N., Rowley J. D. Distribution of 11q23 breakpoints within theMLL. Blood. 87:1996;1912-1922.
47. Thirman M. J., Gill H. J., Burnett R. C., Mbangkollo D., McCabe N. R., Kobayashi H., Ziemin-Van Der Poel S., Kaneko, Ulk Morgan R., Sandberg A. A., Chaganti R. S. K., Larson R. A., Le Beau M. M., Diaz M. O., Rowley J. D. Rearrangement of theMLL. N. Engl. J. Med. 329:1993;909-914.
48. Ullrich A., Gray A., Goeddel V. V., Dull T. J. Nucleotide sequence of a portion of human chromosome 9 containing a leukocyte interferon gene cluster. J. Mol. Biol. 156:1982;467-486.
49. Vaux. Technical tips. Trends Genet. 8:1992;81.