Interchromosomal associations between alternatively expressed loci

Nature

Volumn 435, Issue 7042, 2005, Pages 637-645

  Spilianakis, Charalampos G ^a   Lalioti, Maria D ^a   Town, Terrence ^a   Lee, Gap Ryol ^a   Flavell, Richard A ^a,b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; IMMUNOLOGY; NATURAL SCIENCES;

CHROMATIN; GENE EXPRESSIONS; INTERCHROMOSOMAL INTERACTIONS; LOCUS CONTROL REGION (LCR);

CHROMOSOMES;

CD4 ANTIGEN; DEOXYRIBONUCLEASE I; GAMMA INTERFERON; INTERLEUKIN 4; CYTOKINE; INTERLEUKIN DERIVATIVE; MESSENGER RNA;

BIOLOGY;

ADOLESCENT; ALTERNATIVELY EXPRESSED LOCUS; ANIMAL CELL; ARTICLE; CELL FATE; CELL NUCLEUS; CELL SPECIFICITY; CHROMATIN STRUCTURE; CHROMOSOME; CHROMOSOME 10; CHROMOSOME 11; CYTOKINE GENE; DEVELOPMENT; DEVELOPMENTAL REGULATION; EUKARYOTE; GAMMA INTERFERON GENE; GENE; GENE ACTIVATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE LOCUS; HOST; IMMUNE SYSTEM; INTERCHROMOSOMAL ASSOCIATION; INTRACHROMOSOME INTERACTION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULATOR GENE; T LYMPHOCYTE SUBPOPULATION; TH1 CELL; TH2 CELL; ALLELE; ANIMAL; C57BL MOUSE; CELL CULTURE; CHROMATIN; CHROMOSOME POSITIONING; CYTOLOGY; ENHANCER REGION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; METABOLISM; POLYMERASE CHAIN REACTION;

ANIMALIA; EUKARYOTA;

ALLELES; ANIMALS; CELL NUCLEUS; CELLS, CULTURED; CHROMATIN; CHROMOSOME POSITIONING; CHROMOSOMES, MAMMALIAN; CYTOKINES; DEOXYRIBONUCLEASE I; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION; IN SITU HYBRIDIZATION, FLUORESCENCE; INTERFERON TYPE II; INTERLEUKINS; LOCUS CONTROL REGION; MICE; MICE, INBRED C57BL; POLYMERASE CHAIN REACTION; PROMOTER REGIONS (GENETICS); RNA, MESSENGER; TH1 CELLS; TH2 CELLS;

EID: 20444494936     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03574     Document Type: Article

References (38)

1. Cremer, T. & Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Rev. Genet. 2, 292-301 (2001).
2. Spector, D. L. The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem. 72, 573-608 (2003).
3. Brown, K. E. et al. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91, 845-854 (1997).
4. Brown, K. E., Baxter, J., Graf, D., Merkenschlager, M. & Fisher, A. G. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell 3, 207-217 (1999).
5. Grogan, J. L. et al. Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity 14, 205-215 (2001).
6. Ragoczy, T., Telling, A., Sawado, T., Groudine, M. & Koxak, S. T. A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res. 11, 513-525 (2003).
7. Francastel, C., Walters, M. C., Groudine, M. & Martin, D. I. A functional enhancer suppresses silencing of a transgene and prevents its localization close to centromeric heterochromatin. Cell 99, 259-269 (1999).
8. Schubeler, D. et al. Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human β-globin locus. Genes Dev. 14, 940-950 (2000).
9. Gerasimova, T. I., Byrd, K. & Corces, V. A chromatin insulator determines the nuclear localization of DNA. Mol. Cell 6, 1025-1035 (2000).
10. Cobb, B. S. et al. Targeting Ikaros to pericentromeric heterochromatin by direct DNA binding. Genes Dev. 14, 2146-2160 (2000).
11. Carmo-Fonseca, M., Platani, M. & Swedlow, J. R. Macromolecular mobility inside the cell nucleus. Trends Cell Biol. 12, 491-495 (2002).
12. Carmo-Fonseca, M. The contribution of nuclear compartmentalization to gene regulation. Cell 108, 513-521 (2002).
13. Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074-1080 (2001).
14. Mahy, N. L., Perry, P. E., Goilchrist, S., Baldock, R. A. & Bickmore, W. A. Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J. Cell Biol. 157, 579-589 (2004).
15. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306-1311 (2002).
16. Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between Hypersensitive sites in the active β-globin locus. Mol. Cell 10, 1453-1465 (2002).
17. Palstra, R.-J. et al The β-globin nuclear compartment in development and erythroid differentiation. Nature Genet. 35, 190-194 (2003).
18. Spilianakis, C. & Flavell, R. A. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nature Immunol. 5, 1017-1027 (2004).
19. Takemoto, N. et al. TH2-specific DNase I-hypersensitive sites in the murine IL-13 and IL-4 intergenic region. Int. Immunol. 10, 1981-1985 (1998).
20. Agarwal, S. & Rao, A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity 9, 765-775 (1998).
21. Loots, G. G. et al. Identification of a coordinate regulator of interleukins-4, 13 and 5 by cross-species sequence comparisons. Science 288, 136-140 (2000).
22. Agarwal, S., Avni, O. & Rao, A. Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo. Immunity 12, 643-652 (2000).
23. Lee, G. R., Fields, P. E., Griffin, T. J. IV & Flavell, R. A. Regulation of the Th2 cytokine locus by a Locus Control Region. Immunity 19, 145-153 (2003).
24. Fields, P. E., Lee, G. R., Kim, S. T., Bartsevich, V. & Flavell, R. A. Th2-specific chromatin remodeling and enhancer activity in the Th2 cytokine locus control region. Immunity 21, 865-876 (2004).
25. Lee, D. U., Avni, O., Chen, L. & Rao, A. A distal enhancer in the IFN-γ locus revealed by genome sequence comparison. J. Biol. Chem. 279, 4802-4810 (2004).
26. Shnyreva, M. et al. Evolutionary conserved sequence elements that positively regulate IFN-γ expression in T cells. Proc. Natl Acad. Sci. USA 101, 12622-12627 (2004).
27. Lee, G. R., Spilianakis, C. & Flavell, R. A. Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions. Nature Immunol. 6, 42-48 (2005).
28. Eivazova, E. R. & Aune, T. M. Dynamic alterations in the conformation of the lfng gene region during T helper cell differentiation. Proc. Natl Acad. Sci. USA 101, 251-256 (2004).
29. Taddei, A., Maison, C., Roche, D. & Almouzni, G. Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases. Nature Cell Biol. 3, 114-120 (2001).
30. Schmiedeberg, L., Weisshart, K., Diekmann, S., Meyerzu Hoerste, G. & Hemmerich, P. High- and low-mobility populations of HP1 in heterochromatin of mammalian cells. Mol. Biol. Cell 15, 2819-2833 (2004).
31. Eggenschwiler, J. et al. Mouse mutant embryos overexpressing IGF-II exhibit phenotypic features of the Beckwith-Wiedemann and Simpson-Golabi-Behmel syndromes. Genes Dev. 11, 3128-3142 (1997).
32. Dong, C. & Flavell, R. A. Cell fate decision: T-helper 1 and 2 subsets in immune responses. Arthritis Res. 2, 179-188 (2000).
33. Guo, L. et al. In TH2 cells the II4 gene has a series of accessibility states associated with distinctive probabilities of IL-4 production, Proc. Natl Acad Sci. USA 99, 10623-10628 (2002).
34. Kosak, S. T. & Groudine, M. Form follows function: the genomic organization of cellular differentiation. Genes Dev. 18, 1371-1384 (2004).
35. Guo, L. et al. In TH2 cells the IL-4 gene has a series of accessibility states associated with distinctive probabilities of IL-4 production. Proc. Natl Acad. Sci USA 99, 10623-10628 (2002).
36. Parada, L. A., Sotiriou, S. & Misteli, T. Spatial genome organization. Exp. Cell Res. 296, 64-70 (2004).
37. Roix, J. J., McQueen, P. G., Munson, P. J., Parada, L. A. & Misteli, T. Spatial proximity of translocation-prone gene loci in human lymphomas. Nature Genet 34, 287-291 (2003).
38. Avni, O. et al. TH cell differentiation is accompanied by dynamic changes in histone acetylation of cytokine genes. Nature Immunol. 3, 643-651 (2002).