Abstract
Considerable progress has been made in understanding the mechanism of gene regulation in eukaryotic cells. Protein-DNA and protein-protein interactions are believed to bridge specific promoter and enhancer elements, thereby creating a favorable environment for RNA polymerase to initiate transcription (Ptashne 1988). Over the next few years it is predictable that perhaps hundreds of genes which encode regulatory proteins will be cloned, sequenced, and functionally characterized. While this information will be fundamental, these studies do not address the next important problem, namely how nuclear organization might participate in gene expression.
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References
Akimenko M-A, Mariame B, Rougeon F (1986) Evolution of the immunoglobulin x light chain locus in the rabbit: Evidence for differential gene conversion events. Proc Natl Acad Sci USA 83: 5180–5183
Amati BV, Gasser SM (1988) Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54: 967–978
Anand R, Boehm CD, Kazazian HH Jr, Vanin EF (1988) Molecular characterization of a β-thalassemia resulting from a 1.4 kilobase deletion. Blood 72: 636–641
Avramova Z, Tsanev R (1987) Stable DNA-protein complexes in eukaryotic chromatin. J Mol Biol 196: 437–440
Bae Y-S, Kawasaki I, Ikeda H, Liu LF (1988) Illegitimate recombination mediated by calf thymus DNA topoisomerase II in vitro. Proc Natl Acad Sci USA 85: 2076–2080
Beggs AH, Migeon BR (1989) Chromatin loop structure of the human X chromosome: Relevance to X inactivation and CpG clusters. Mol Cell Biol 9: 2322–2331
Benyajati C, Worcel A (1976) Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell 9: 393–407
Berezney R, Coffey D (1974) Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60: 1410–1419
Blasquez VC, Xu M, Moses SC, Garrard WT (1989a) Immunoglobulin x gene expression after stable integration I: role of the intronic MAR and enhancer in plasmacytoma cells. J Biol Chem 264: 21183–21189
Blasquez VC, Sperry AO, Cockerill PN, Garrard WT (1989b) Protein: DNA interactions at chromosomal loop attachment sites. Genome 31: 503–509
Blasquez VC, Sperry AO, Garrard WT (1989c) Elements that organize chromosomal loops in the interphase nucleus. In: DNA protein interactions in transcription. UCLA Symp Molecular and Cellular Biology, vol 95, Liss, Inc. NY, pp 273–286
Blobel G (1985) Gene gating: A hypothesis. Proc Natl Acad Sci USA 82: 8527–8529
Bode J, Maass K (1988) Chromatin domain surrounding the human interferon-β gene as defined by scaffold-attached regions. Biochemistry 27: 4706–4711
Boy de la Tour E, Laemmli UK (1988) The metaphase scaffold is helically folded: Sister chromatids have predominantly opposite helical handedness. Cell 55: 937–944
Brill SJ, Sternglanz R (1988) Transcription-dependent DNA supercoiling in yeast DNA topoisomerase mutants. Cell 54: 403–411
Capco D, Penman S (1983) Mitotic architecture of the cell: the filament networks of the nucleus and cytoplasm. J Cell Biol 96: 896–906
Chimera JA, Musich PR (1985) The association of the interspersed repetitive KpnI sequences with the nuclear matrix. J Biol Chem 260: 9373–9379
Cockerill PN, Garrard WT (1986a) Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44: 273–282
Cockerill PN, Garrard WT (1986b) Chromosomal loop anchorage sites appear to be evolutionarily conserved. FEBS Lett 204: 5–7
Cockerill PN, Yuen M-H, Garrard WT (1987) The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J Biol Chem 262: 5394–5397
Cook PR, Brazell IA (1976) Conformational constraints in nuclear DNA. J Cell Sci 22: 297–302
Cremer T, Cremer C, Baumann H, Luedtke EK, Sperling K, Teuber V, Zorn C (1982) Rabl’s model of the interphase chromosome arrangement tested in Chinese Hamster cells by premature chromosome condensation and laser-UV-microbeam experiments. Hum Genet 60: 46–56
Cress AE, Kurath KM (1988) Identification of attachment proteins for DNA in Chinese hamster ovary cells. J Biol Chem 263: 19678–19683
Dijkwel PA, Hamlin JL (1988) Matrix attachment regions are positioned near replication initiation sites, and an interamplicon junction in the amplied dihydrofolate reductase domain of Chinese hamster cells. Mol Cell Biol 8: 5398–5409
Earnshaw WC, Heck MMS (1985) Localization of topoisomerase II in mitotic chromosomes. J Cell Biol 100: 1716–1725
Emorine L, Max EE (1983) Structural analysis of a rabbit immunoglobulin x2 J-C locus reveals multiple deletions. Nucleic Acids Res 11: 8877–8890
Ericsson C, Mehlin H, Bjorkroth B, Lamb MM, Daneholt B (1989) The ultrastructure regions of an active Balbiani ring gene. Cell 56: 631–639
Fairman R, Brutlag DL (1988) Expression of Drosophila type II topoisomerase is developmentally regulated. Biochemistry 27: 560–565
Gasser SM, Laemmli UK (1986b) The organization of chromatin loops: characterization of a scaffold attachment site. EMBO J 5: 511–518
Gasser SM, Laemmli UK (1987) A glimpse at chromosomal order. Trends Genet 3: 16–22
Gasser SM, Laroche T, Falquet J, Boy de la Tour E, Laemmli UK (1986) Metaphase chromosome structure: involvement of topoisomerase II. J Mol Biol 188: 613–629
Greenstein RJ (1988) Constitutive attachment of murine erythroleukemia cell histone depleted DNA loops to nuclear scaffolding is found in the β-major but not the α-1 globin gene. DNA 7: 601–607
Grosveld F, Van Assendelft GB, Greaves DR, Kollias G (1987) Position-independent, high-level expression of the human β-globin gene in transgenic mice. Cell 51: 975–985
Handeli S, Klar A, Meuth M, Cedar H (1989) Mapping replication units in animal cells. Cell 57: 909–920
Heck MMS, Earnshaw WC (1986) Topoisomerase II: A specific marker for cell proliferation. J Cell Biol 103: 2569–2581
Heck MMS, Hittelman WN, Earnshaw WC (1988) Differential expression of topoisomerases I and II during the eukaryotic cell cycle. Proc Natl Acad Sci USA 85: 1086–1090
Hofmann JF-X, Laroche T, Brand AH, Gasser SM (1989) RAP-1 factor is necessary for DNA loop formation in vitro at the silent mating type locus HML. Cell 57: 725–737
Holm C, Goto T, Wang JC, Botstein D (1985) DNA topoisomerase II is required at the time of mitosis. Cell 41: 553–563
Hornberger HP (1989) Bent DNA is a structural feature of scaffold-attached regions in Drosophila melanogaster interphase nuclei. Chromosoma (Berl) 98: 99–104
Hutchison N, Weintraub H (1985) Localization of DNAase I-sensitive sequences to specific regions of interphase nuclei. Cell 43: 471–482
Hyrien O, Debatisse M, Buttin G, deSaint Vincent BR (1987) A hotspot for novel amplification joints in a mosaic of Alu-like repeats and palindromic A+T-rich DNA. EMBO J 6: 2401–2408
Imler J-L, Lemaire C, Wasylyk C, Wasylyk B (1987) Negative regulation contributes to tissue-specificity of the immunoglobulin heavy chains enhancers. Mol Cell Biol 7: 2558–2567
Izaurralde E, Mirkovitch J, Laemmli UK (1988) Interaction of DNA with nuclear scaffolds in vitro. J Mol Biol 200: 111–125
Jackson DA, Cook PR (1988) Visualization of a filamentous nucleoskeleton with a 23 nm axial repeat. EMBO J 7: 3667–3677
Jarman AP, Higgs DR (1988) Nuclear scaffold attachment sites in the human globin gene complexes. EMBO J 7: 3337–3344
Kakkis E, Prehn J, Calame K (1986) An active chromatin structure acquired by translocated c-myc genes. Mol Cell Biol 6: 1357–1361
Kas E, Chasin LA (1987) Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs in an intragenic region. J Mol Biol 198: 677–692
Lawrence JB, Singer RH, Marselle LM (1989) Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization. Cell 57: 493–502
Lewis, CD, Laemmli UK (1982) Higher order metaphase chromosome structure: evidence for metalloprotein interactions. Cell 29: 171–181
Lyon MF (1974) Mechanisms and evolutionary origins of variable X-chromosome activity in mammals. Proc R Soc Lond B 187: 243–268
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
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
Mirkovitch J, Gasser SM, Laemmli UK (1988) Scaffold attachment of DNA loops in metaphase chromosomes. J Mol Biol 200: 101–109
Paulson JR, Laemmli UK (1977) The structure of histone-depleted metaphase chromosomes. Cell 12: 817–828
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
Pommier Y, Cockerill PN, Kohn KW, Garrard WT (1990) Identification of a chromosomal loop attachment site within the SV40 genome that contains topoisomerase II cleavage sites. J Virol 64: 419–423
Ptashne M (1988) How eukaryotic transcriptional activators work. Nature 335: 683–689
Roberge M, Dahmus ME, Bradbury EM (1988) Chromosomal loop/nuclear matrix organization of transcriptionally active and inactive RNA polymerase in HeLa nuclei. J Mol Biol 201: 545–555
Sander M, Hsieh T-S, Udvardy A, Schedl P (1987) Sequence dependence of Drosophila topoisomerase II in plasmid relaxation and DNA binding. J Mol Biol 194: 219–229
Scheuermann RH, Chen U (1989) A developmental-specific factor binds to suppressor sites flanking the immunoglobulin heavy-chain enhancer. Genes Develop 3: 1255–1266
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
Spitzner JR, Muller MT (1988) A consensus sequence for cleavage by vertebrate DNA topoisomerase II. Nucleic Acids Res 16: 5533–5556
Spofford JB (1976) Position effect variegation of Drosophila. In: Ashburnerand M, Novitski E (eds) Genetics and biology of Drosophila, vol 1C. Academic Press, New York, pp 955–1019
Spradling AC, Rubin GM (1983) The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene. Cell 34: 47–57
Stief A, Winter DM, Stratling WH, Sippel AE (1989) A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature 341: 343–345
Sykes RC, Lin D, Hwang SJ, Framson PE, Chinault AC (1988) Yeast ARS function and nuclear matrix association coincide in a short sequence from the human HPRT locus. Mol Gen Genet 212: 301–309
Vogelstein B, Pardoll DM, Coffey DS (1980) Supercoiled loops and eukaryotic DNA replication. Cell 22: 79–85
Worcel A, Burgi E (1972) On the structure of the folded chromosome of Escherichia coli. J Mol Biol 71: 127–147
Wu H-Y, Shyy S, Wang, Liu LF (1988) Transcription generates positively and negatively supercoiled domains in the template. Cell 53: 433–440
Xu M, Hammer RE, Blasquez VC, Jones SA, Garrard WT (1989) Immunoglobulin x gene expression after stable integration II: role of the intronic MAR and enhancer in transgenic mice. J Biol Chem 264: 21190–21195
Yang Y, Ames GF-L (1988) DNA gyrase binds to the family of prokaryotic repetitive extra-genic palindromic sequences. Proc Natl Acad Sci USA 85: 8850–8854
Zachar Z, Chapman CH, Bingham PM (1985) On the molecular basis of transvection effects and the regulation of transcription. Cold Spring Harbor Symp Quant Biol 50: 337–346
Zehnbauer BA, Vogelstein B (1985) Supercoiled loops and the organization of replication and transcription in eukaryotes. BioEssays 2: 52–54
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Garrard, W.T. (1990). Chromosomal Loop Organization in Eukaryotic Genomes. In: Eckstein, F., Lilley, D.M.J. (eds) Nucleic Acids and Molecular Biology 4. Nucleic Acids and Molecular Biology, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-84150-7_10
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DOI: https://doi.org/10.1007/978-3-642-84150-7_10
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