Matrix attachment regions and transcription units in a polygenic mammalian locus overlapping two isochores

Journal of Cellular Biochemistry

Volumn 67, Issue 4, 1997, Pages 541-551

  Fernandez, Maria Aparecida ^a,b   Baron, Bruno ^a   Prigent, Magali ^a   Toledo, Franck ^a   Buttin, Gérard ^a   Debatisse, Michelle ^a  

^a INSTITUT PASTEUR   (France)

^b STATE UNIVERSITY OF MARINGÁ   (Brazil)

Author keywords

Chromatin loops; Chromosome organization; Compositional mapping; Gene cluster

Indexed keywords

COMPLEMENTARY DNA; CYTOSINE; GUANINE;

ANIMAL CELL; ARTICLE; CELL NUCLEUS MATRIX; CHINESE HAMSTER; CONTROLLED STUDY; CPG ISLAND; DNA SEQUENCE; GENE LOCUS; GENETIC TRANSCRIPTION; HUMAN; ISOCHORE; LUNG FIBROBLAST; NONHUMAN; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; ANIMALS; BASE COMPOSITION; CELL LINE; CHROMOSOME MAPPING; CLONING, MOLECULAR; CONSENSUS SEQUENCE; CRICETINAE; CRICETULUS; DINUCLEOSIDE PHOSPHATES; DNA TOPOISOMERASES, TYPE II; DROSOPHILA; LUNG; MOLECULAR SEQUENCE DATA; NUCLEAR MATRIX; RECOMBINATION, GENETIC; RESTRICTION MAPPING; TRANSCRIPTION, GENETIC;

ANIMALIA; CRICETINAE; CRICETULUS GRISEUS; EUKARYOTA; MAMMALIA;

EID: 0030682467     PISSN: 07302312     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-4644(19971215)67:4<541::AID-JCB11>3.0.CO;2-C     Document Type: Article

References (48)

1. Adachi Y, Käs E, Laemmli UK (1989): Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J 8:3997-4006.
2. Ardeshir F, Giulotto E, Zieg J, Brison O, Liao WSL, Stark G (1983): Structure of amplified DNA in different Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate. Mol Cell Biol 3:2076-2088.
3. Baron B, Fernandez MA, Carignon S, Toledo F, Buttin G, Debatisse M (1996): GNAI3, GNAT2, AMPD2, GSTM are clustered in 120 kb of Chinese hamster chromosome 1q. Mammalian Genome 7:429-432.
4. Baron B, Fernandez MA, Toledo F, Le Roscouët D, Mayau V, Martin N, Buttin G, Debatisse M (1994): The highly conserved Chinese hamster GNAiS gene maps less than 60 kb from the AMPD2 gene and lacks the intronic U6 snRNA present in its human counterpart. Genomics 24: 288-294.
5. Bereznev R, Coffey D (1974): Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410-1419.
6. Bernardi G (1995): The human genome: Organization and evolutionary history. Annu Rev Genetics 29:445-476.
7. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J (1985): The mosaic genome of warm-blooded vertebrates. Science 228:953-958.
8. Blasquez VC, Xu M, Moses SC, Garrard WT (1989): Immunoglobulin kappa gene expression after stable integration. I. Role of the intronic MAR and enhancer in plasmacytoma cells. J Biol Chem 264:21183-21189.
9. Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, Kohwi-Shigematsu T (1992): Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255:195-197.
10. Bonifer C, Vidal M, Grosveld F, Sippel AE (1990): Tissue specific and position independent expression of the complete gene domain for chicken lysozyme in transgenic mice. EMBO J 9:2843-2848.
11. Brun C, Dang Q, Miassod R (1990): Studies of a 800 kilo-base DNA stretch of the Drosophila X chromosome: Comapping of a subclass of scaffold-attached regions with sequences able to replicate autonomously in Saccharomyces Cerevisiae. Mol Cell Biol 10:5455-5463.
12. Cockerill PN (1990): Nuclear matrix attachment occurs in several regions of the IgH locus. Nucl Acids Res 18:2643-2648.
13. Cockerill PN, Garrard WT (1986): Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44:273-282.
14. Debatisse M, Hyrien O, Petit-Koskas E, Robert de Saint Vincent B, Buttin G (1986): Segregation and rearrangement of coamplified genes in different lineages of mutant cells that overproduce adenylate deaminase. Mol Cell Biol 6:1776-1781.
15. Debatisse M, Toledo F, Robert De Saint Vincent B, Buttin G (1992): Amplification of the adenylate deaminase 2 and linked genes in Chinese hamster lung fibroblasts. In Kellems RE (ed): "Gene Amplification in Mammalian Cells - A Comprehensive Guide." New York: Marcel Dekker Inc., pp 173-183.
16. Dijkwell PA, Hamlin JL (1988): 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 8:5398-5409.
17. Farache G, Razin SV, Rzeszowska-Wolny J, Moreau J, Recillas Targa F, Scherrer K (1990): Mapping of structural and transcription-related matrix attachment sites in the alpha-globin gene domain of avian erythroblasts and erythrocytes. Mol Cell Biol 10:5349-5358.
18. Gardiner K (1996): Base composition and gene distribution: Critical patterns in mammalian genome organization. TIG 12:519-524.
19. Garrard W (1991): Histone H1 and the conformation of transcriptionally active chromatin. BioEssays 13:87-88.
20. Gasser SM, Laemmli UK (1987): A glimpse at chromosomal order. TIG 3:16-22.
21. Hanson RD, Ley TJ (1992): A-T-rich scaffold attachment regions flank the hematopoietic serine protease genes clustered on chromosome 14q11.2. Blood 79:610-618.
22. Hyrien O, Debatisse M, Buttin G, Robert De Saint Vincent B (1986): A hotspot for novel amplification joints in a mosaic of Alu-like repeats and palindromic A + T-rich DNA. EMBO J 6:2401-2408.
23. Iarovaia O, Hancock R, Lagarkova M, Miassod R, Razin SV (1996): Mapping of genomic DNA loop organization in a 500-Kilobase region of the Drosophila X chromosome by the topoisomerase II-mediated DNA loop excision protocol. Mol Cell Biol 16:302-308.
24. Jarman AP, Higgs DR (1988): Nuclear scaffold attachment sites in the human globin gene complexes. EMBO J 7:3337-3344.
25. Kalos M, Fournier RE (1995): Position-independent transgene expression mediated by boundary elements from the apolipoprotein B chromatin domain. Mol Cell Biol 15:198-207.
26. Käs E, Izaurralde E, Laemmli UK (1989): Specific inhibition of DNA binding to nuclear scaffolds and histone H1 by distamycin: The role of oligo(dA)-oligo(dT) tracts. J Mol Biol 210:587-599.
27. Käs E, Poljak L, Adachi Y, Laemmli UK (1993): A model for chromatin opening: Stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin. EMBO J 12:115-126.
28. Kay V, Bode J (1994): Binding specificity of a nuclear scaffold: Supercoiled, single-stranded, and scaffold-attached-region DNA. Biochemistry 33:367-374.
29. Klehr D, Maass K, Bode J (1991): Scaffold-attached regions from three human interferon b domains can be used to enhance the stable expression of genes under the control of various promoters. Biochemistry 30:1264-1270.
30. Laemmli UK, Käs E, Poljak L, Adachi Y (1992): Scaffod-associated regions: cis-acting determinants of chromatin structural loops and functional domains. Curr Opin Cell Biol 2:275-285.
31. Levy-Wilson B, Fortier C (1989): The limits of the DNase I-sensitive domain of the human apolipoprotein gene coincide with the locations of chromosomal anchorage loops and define the 5′ and the 3′ boundaries of the gene. J Biol Chem 264:21196-21204.
32. Luderus MEE, Den Blaauwen JL, De Smit OJB, Compton DA Van Driel R (1994): Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove. Mol Cell Biol 14:6297-6305.
33. Macaya G, Thiery J, Bernardi G (1976): An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108:237-254.
34. McKnight RA, Shamay A, Sankaran L, Wall RJ, Hennighausen L (1992): Matrix-attachment regions can impart position-independent regulation of a tissue-specific gene in transgenic mice. Proc Natl Acad Sci USA 89:6943-6947.
35. Mirkovitch J, Mirault ME, Laemmli UK (1984): Organization of the higher-order chromatin loop: Specific DNA attachment sites on nuclear scaffold. Cell 39:223-232.
36. Mirkovitch J, Spierer P, Laemmli UK (1986): Genes and loops in 320,000 base pairs of the Drosophila melanogaster chromosome. J Mol Biol 190:255-258.
37. Nelson HCM, Finch JT, Luisi BF, Klug A (1987): The structure of an Oligo(dA)-Oligo(dT) tract and its biological implications. Nature 330:221-226.
38. Phi-Van L, Stratling WH (1988): The matrix attachment regions of the chicken lysozyme gene co-map with the boundaries of the chromatin domain. EMBO J 7:655-664.
39. Phi-Van L, Stratling WH (1996): Dissection of the ability of the chicken lysozyme gene 5′ matrix attachment region to stimulate transgene expression and to dampen position effects. Biochemistry 35:10735-10742.
40. Phi-Van L, Von Kries JP, Ostertag W, Stratling WH (1990): The chicken lysozyme 5′ matrix attachment region increases transcription from a heterologous promoter in heterologous cells and dampens position effects on the expression of transfected genes. Mol Cell Biol 10:2302-2307.
41. Probst H, Herzog R (1985): DNA regions associated with the nuclear matrix of Ehrlich ascites cells expose single-stranded sites after deproteinization. Eur J Biochem 146:167-171.
42. Razin SV, Petrov P, Hancock R (1991): Precise location of the alpha-globin gene cluster within one of the 20 ts 300-kilobase DNA fragments released by cleavage of the chicken chromosomal DNA at topoisomerase II sites in vivo: Evidence that the fragments are DNA loops or domains. Proc Natl Acad Sci USA 88:8515-8519.
43. Sambrook J, Fritsch EF, Maniatis T (1989): New York:
44. Sperry AO, Blasquez VC, Garrard WT (1989): Dysfunction of chromosomal loop attachment sites: Illegitimate recombination linked to matrix association regions and topoisomerase II. Proc Natl Acad Sci USA 86:5497-5501.
45. Stief A, Winter AM, Stratling WH, Sippel AE (1989): A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature 341:343-345.
46. Surdej P, Got C, Rosset R, Miassod R (1990): Supragenic loop organization: Mapping in Drosophila embryos of scaffold-associated regions on a 800 kilobase DNA continuum cloned from the 14B-15B first chromosome region. Nucl Acids Res 18:3713-3722.
47. Xu M, Hammer RE, Blasquez VC, Jones SL, Garrard WT (1989): Immunoglobulin kappa gene expression after stable integration. II. Role of intronic MAR and enhancer in transgenic mice. J Biol Chem 264:21190-21195.
48. Zhao K, Käs E, Gonzalez E, Laemmli UK (1993) SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J 12:3237-3247.