Chromatin remodelling and the interaction between enhancers and promoters in the β-globin locus

Briefings in Functional Genomics and Proteomics

Volumn 2, Issue 4, 2004, Pages 344-354

  Dean, Ann ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

Chromatin remodelling; Enhancers; Globin genes; Locus control regions

Indexed keywords

GLOBIN; HISTONE;

ANIMAL; BIOLOGICAL MODEL; CELL NUCLEUS; CHEMISTRY; CHICKEN; CHROMATIN; ENHANCER REGION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; MOUSE; PROMOTER REGION; REVIEW; SERODIAGNOSIS; TRANSACTIVATION;

ANIMALS; CELL NUCLEUS; CHICKENS; CHROMATIN; ENHANCER ELEMENTS (GENETICS); GLOBINS; HISTONES; HUMANS; MICE; MODELS, GENETIC; PRECIPITIN TESTS; PROMOTER REGIONS (GENETICS); TRANS-ACTIVATION (GENETICS); TRANSCRIPTION, GENETIC;

EID: 3042809986     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/2.4.344     Document Type: Article

References (75)

1. Stamatoyannopoulos, G. and Grosveld, F. (2001), 'Hemoglobin Switching', in Stamatoyannopoulos, G., Majerus, P. W., Perlmutter, R. M. and Vamus, H. (Eds), 'The Molecular Basis of Blood Diseases', W. B. Saunders, Philadelphia, PA, pp. 135-182.
2. Goodman, M., Koop, B. F., Czelusniak, J. and Weiss, M. L. (1984), 'The eta-globin gene. Its long evolutionary history in the beta-globin gene family of mammals', J. Mol. Bid., Vol. 180, pp. 803-823.
3. Hardison, R. C. (1984), 'Comparison of the beta-like globin gene families of rabbits and humans indicates that the gene cluster 5'-epsilon-gamma-delta- beta-3' predates the mammalian radiation', Mol. Biol. Evol, Vol. 1, pp. 390-410.
4. Wheeler, D., Hope, R., Cooper, S. B. et al. (2001), 'An orphaned mammalian beta-globin gene of ancient evolutionary origin', Proc. Natl. Acad. Sci. USA, Vol. 98, pp. 1101-1106.
5. Harciison, R. C. (2001), 'New views of evolution and regulation of vertebrate betalike globin gene clusters from an orphaned gene in marsupials', Proc. Natl. Acad. Sci. USA, Vol. 98, pp. 1327-1329.
6. Forrester, W. C, Epner, E., Driscoll, M. C. et al. (1990), '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., Vol. 4, pp. 1637-1649.
7. Schubeler, D., Francastel, C, Cimbora, D. M. et al. (2000), 'Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus', Genes Dev., Vol. 14, pp. 940-950.
8. Schubeler, D., Groudine, M. and Bender, M. A. (2001), 'The murine beta-globin locus control region regulates the rate of transcription but not the hyperacetylation of histones at the active genes', Proc. Natl. Acad. Sci. USA, Vol. 98, pp. 11432-11437.
9. Li, Q., Peterson, K. R., Fang, X. and Stamatoyannopoulos, G. (2002), 'Locus control regions', Blood, Vol. 100, pp. 3077-3086.
10. Efstratiadis, A., Posakony, J. W., Maniatis, T. et al. (1980), 'The structure and evolution of the human beta-globin gene family', Cell, Vol. 21, pp. 653-668.
11. Dierks, P., van Ooyen, A., Cochran, M. D. et al. (1983), 'Three regions upstream from the cap site are required for efficient and accurate transcription of the rabbit β-globin gene in mouse 3T6 cells', Cell, Vol. 32, pp. 695-706.
12. Evans, T. and Felsenfeld, G. (1989), 'The erythroid-specific transcription factor Eryf1: a new finger protein', Cell, Vol. 58, pp. 877-885.
13. Andrews, N. C, Erdjument-Bromage, H., Davidson, M. B. et al. (1993), 'Erythroid transcription factor NF-E2 is a haematopoietic-specific basic-leucine zipper protein', Nature, Vol. 362, pp. 722-728.
14. Miller, I.J. and Bieker, J. J. (1993), 'A novel, erythroid cell-specific murine transcription factor that binds to the CACCC element and is related to the Kruppel family of nuclear proteins', Mol. Cell Biol, Vol. 13, pp. 2776-2786.
15. Orkin, S. H. (1995), 'Regulation of globin gene expression in erythroid cells', Eur. J. Biochem., Vol. 231, pp. 271-281.
16. Levings, P. P. and Bungert, J. (2002), 'The human beta-globin locus control region', Eur. J. Biochem., Vol. 269, pp. 1589-1599.
17. Gumucio, D. L., Shelton, D. A., Zhu, W. et al. (1996), 'Evolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the beta-like globin genes', Mol. Phylogenet. Evol., Vol. 5, pp. 18-32.
18. Hardison, R., Slightom, J. L., Gumucio, D. L. et al. (1997), 'Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights', Gene, Vol. 205, pp. 73-94.
19. Lam, L. T. and Bresnick, E. H. (1996), 'A novel DNA-binding protein, HS2NF5, interacts with a functionally important sequence of the human beta-globin locus control region', J. Biol. Chem., Vol. 271, pp. 32421-32429.
20. Elnitski, L., Miller, W. and Hardison, R. (1997), 'Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins', J. Biol. Chem., Vol. 272, pp. 369-378.
21. Chung, J. H., Whiteley, M. and Felsenfeld, G. (1993), 'A 5' element of the chicken β-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila', Cell, Vol. 74, pp. 505-514.
22. Bell, A. C, West, A. G. and Felsenfeld, G. (1999), 'The protein CTCF is required for the enhancer blocking activity of vertebrate insulators', Cell, Vol. 98, pp. 387-396.
23. Farrell, C. M., West, A. G. and Felsenfeld, G. (2002), 'Conserved CTCF insulator elements flank the mouse and human beta-globin loci', Mol. Cell Biol., Vol. 22, pp. 3820-3831.
24. Bulger, M., Schubeler, D., Bender, M. A. et al. (2003), 'A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus', Mol. Cell Biol., Vol. 23, pp. 5234-5244.
25. Tsang, A. P., Visvader, J. E., Turner, C. A. et al. (1997), 'FOG, a multitype zinc finger protein, acts as a cofactor for transcription factor GATA-1 in erythroid and megakaryocyte differentiation', Cell, Vol. 90, pp. 109-119.
26. Wadman, I. A., Osada, H., Grutz, G. G. et al. (1997), 'The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TALI, E47, GATA-1 and Ldb1/NLI proteins', EMBO J., Vol. 16, pp. 3145-3157.
27. Armstrong, J. A., Bieker, J. J. and Emerson, B. M. (1998), 'A SWI/SNF-related chromatin remodeling complex, E-RC1, is required for tissue-specific transcriptional regulation by EKLF in vitro. Cell, Vol. 95, pp. 93-104.
28. Vignali, M., Hassan, A. H., Neely, K. E. and Workman, J. L. (2000), 'ATP-dependent chromatin-remodeling complexes', Mol. Cell Biol., Vol. 20, pp. 1899-1910.
29. Berger, S. L. (2002), 'Histone modifications in transcriptional regulation', Curr. Opin. Genet. Dev., Vol. 12, pp. 142-148.
30. Narlikar, G. J., Fan, H. Y. and Kingston, R. E. (2002), 'Cooperation between complexes that regulate chromatin structure and transcription', Cell, Vol. 108, pp. 475-487.
31. Fry, C.J. and Peterson, C. L. (2001), 'Chromatin remodeling enzymes: who's on first?', Curr. Biol., Vol. 11, pp. R185-R197.
32. Cosma, M. P. (2002), 'Ordered recruitment: gene-specific mechanism of transcription activation', Mot. Cell, Vol. 10, pp. 227-236.
33. Gui, C. Y. and Dean, A. (2003), 'A major role for the TATA box in recruitment of chromatin modifying complexes to a globin gene promoter', Proc. Natl. Acad. Sci. USA, Vol. 100, pp. 7009-7014.
34. Ptashne, M. (1986), 'Gene regulation by proteins acting nearby and at a distance', Nature, Vol. 322, pp. 697-701.
35. Elefant, F., Cooke, N. E. and Liebhaber, S. A. (2000), 'Targeted recruitment of histone acetyltransferase activity to a locus control region', J. Biol. Chem., Vol. 275, pp. 13827-13834.
36. Forsberg, E. C, Downs, K. M., Christensen, H. M. et al. (2000), 'Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain', Proc. Natl. Acad. Sci. USA, Vol. 97, pp. 14494-14499.
37. Gui, C. Y. and Dean, A. (2001), 'Acetylation of a specific promoter nucleosome accompanies activation of the epsilon-globin gene by beta-globin locus control region HS2', Mol. Cell Biol, Vol. 21, pp. 1155-1163.
38. Travers, A. (1999), 'Chromatin modification by DNA tracking', Proc. Natl. Acad. Sci. USA, Vol. 96, pp. 13634-13637.
39. Dorsett, D. (1999), 'Distant liaisons: long-range enhancer-promoter interactions in Drosophila', Curr. Opin. Genet. Dev., Vol. 9, pp. 505-514.
40. Bulger, M. and Groudine, M. (1999), 'Looping versus linking: toward a model for long-distance gene activation', Genes Dev., Vol. 13, pp. 2465-2477.
41. Blackwood, E. M. and Kadonaga, J. T. (1998), 'Going the distance: a current view of enhancer action', Science, Vol. 281, pp. 61-63.
42. Shang, Y., Myers, M. and Brown, M. (2002), 'Formation of the androgen receptor transcription complex', Mol. Cell, Vol. 9, pp. 601-610.
43. Spicuglia, S., Kumar, S., Yeh, J. H. et al. (2002), 'Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes', Mol Cell, Vol. 10, pp. 1479-1487.
44. Louie, M. C, Yang, H. Q., Ma, A. H. et al. (2003), 'Androgen-induced recruitment of RNA polymerase II to a nuclear receptor-p160 coactivator complex', Proc. Natl. Acad. Sci. USA, Vol. 100, pp. 2226-2230.
45. Hatzis, P. and Talianidis, I. (2002), 'Dynamics of enhancer-promoter communication during differentiation-induced gene activation', Mol. Cell, Vol. 10, pp. 1467-1477.
46. Ellis, J., Tan-Un, K. C, Harper, A. et al. (1996), 'A dominant chromatin-opening activity in 5' hypersensitive site 3 of the human β-globin locus control region', EMBO J., Vol. 15, pp. 562-568.
47. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002), 'Capturing chromosome conformation', Science, Vol. 295, pp. 1306-1311.
48. Tolhuis, B., Palstra, R. J., Splinter, E. et al. (2002), 'Looping and interaction between hypersensitive sites in the active beta-globin locus', Mol. Cell, Vol. 10, pp. 1453-1465.
49. Jackson, D. A., McDowell, J. C. and Dean, A. (2003), 'Beta-globin locus control region HS2 and HS3 interact structurally and functionally', Nucleic Acids Res., Vol. 31, pp. 1180-1190.
50. Carter, D., Chakalova, L., Osborne, C. S. et al. (2002), 'Long-range chromatin regulatory interactions in vivo', Nat. Genet., Vol. 32, pp. 623-626.
51. Palstra, R. J., Tolhuis, B., Splinter, E. et al. (2003), 'The beta-globin nuclear compartment in development and erythroid differentiation', Nat. Genet., Vol. 35, pp. 190-194.
52. McDowell, J. C. and Dean, A. (1999), 'Structural and functional cross-talk between a distant enhancer and the E-globin gene promoter shows interdependence of the two elements in chromatin', Mol. Cell Biol, Vol. 19, pp. 7600-7609.
53. Johnson, K. D., Christensen, H. M., Zhao, B. and Bresnick, E. H. (2001), 'Distinct mechanisms control RNA polymerase II recruitment to a tissue-specific locus control region and a downstream promoter', Mol. Cell, Vol. 8, pp. 465-471.
54. Sawado, T., Halow, J., Bender, M. A. and Groudine, M. (2003), 'The beta-globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation', Genes Dev., Vol. 17, pp. 1009-1018.
55. Jarman, A. P. and Higgs, D. R. (1989), 'Sites of attachment to the nuclear scaffold in the human a and β globin gene complexes', Prog. Clin. Biol. Res., Vol. 316B, pp. 33-45.
56. Ostermeier, G. C, Liu, Z., Martins, R. P. et al. (2003), 'Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR', Nucleic Acids Res., Vol. 31, pp. 3257-3266.
57. Francastel, C, Walters, M. C, Groudine, M. and Martin, D. I. (1999), 'A functional enhancer suppresses silencing of a transgene and prevents its localization close to centrometric heterochromatin', Cell, Vol. 99, pp. 259-269.
58. Hebbes, T. R., Clayton, A. L., Thorne, A. W. and Crane-Robinson, C. (1994), 'Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken β-globin chromosomal domain', EMBO J., Vol. 13, pp. 1823-1830.
59. Litt, M. D., Simpson, M., Gaszner, M. et al. (2001), 'Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus', Science, Vol. 293, pp. 2453-2455.
60. Litt, M. D., Simpson, M., Recillas-Targa, F. et al. (2001), 'Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci', EMBO J., Vol. 20, pp. 2224-2235.
61. Epner, E., Reik, A., Cimbora, D. et al. (1998), 'The β-globin LCR is not necessary for an open chromatin structure or developmentally regulated transcription of the native mouse β-globin locus', Mol. Cell, Vol. 2, pp. 447-55.
62. Bender, M. A., Reik, A., Close, J. et al. (1998), 'Description and targeted deletion of 5' hypersensitive site 5 and 6 of the mouse β-globin locus control region', Blood, Vol. 92, pp. 4394-4403.
63. Shannon, M., Hamilton, A. T., Gordon, L. et al. (2003), 'Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters', Genome Res., Vol. 13, pp. 1097-1110.
64. Kim, A. and Dean, A. (2003), 'A human globin enhancer causes both discrete and widespread alterations in chromatin structure', Mol. Cell Biol., Vol. 23, pp. 8099-8109
65. Pennacchio, L. A. and Rubin, E. M. (2001), 'Genomic strategies to identify mammalian regulatory sequences', Nat. Rev. Genet., Vol. 2, pp. 100-109.
66. Frazer, K. A., Elnitski, L., Church, D. M. et al. (2003), 'Cross-species sequence comparisons: a review of methods and available resources', Genome Res., Vol. 13, pp. 1-12.
67. Markstein, M., Markstein, P., Markstein, V. and Levine, M. S. (2002), 'Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo', Proc. Natl. Acad. Sci. USA, Vol. 99, pp. 763-768.
68. Berman, B. P., Nibu, Y., Pfeiffer, B. D. et al. (2002), 'Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome', Proc. Natl. Acad. Sci. USA, Vol. 99, pp. 757-762.
69. Carr, A. and Biggin, M. D. (1999), 'A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos', EMBO J., Vol. 18, pp. 1598-1608.
70. Horak, C. E., Mahajan, M. C., Luscombe, N. M. et al. (2002), 'GATA-1 binding sites mapped in the beta-globin locus by using mammalian ChIP-chip analysis', Proc. Natl. Acad. Sci. USA, Vol. 99, pp. 2924-2929.
71. Kadonaga, J. T. (1998), 'Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines', Cell, Vol. 92, pp. 307-313.
72. Drewes, G. and Bouwmeester, T. (2003), 'Global approaches to protein-protein interactions', Curr. Opin. Cell Biol., Vol. 15, pp. 199-205.
73. Singh, S. M., Zada, A. A., Hiddemann, W. et al. (2002), 'Proteomic analysis of transcription factor interactions in myeloid stem cell development and leukaemia', Expert. Opin. Ther. Targets, Vol. 6, pp. 491-495.
74. Gottgens, B., Barton, L. M., Gilbert, J. G. et al. (2000), 'Analysis of vertebrate SCL loci identifies conserved enhancers', Nat. Biotechnol., Vol. 18, pp. 181-186.
75. Ishii, K., Arib, G., Lin, C. et al. (2002), 'Chromatin boundaries in budding yeast: the nuclear pore connection', Cell, Vol. 109, pp. 551-562.