A hypothesis for chromatin domain opening

BioEssays

Volumn 25, Issue 5, 2003, Pages 507-514

  Xin, Li ^a   Liu, De Pei ^a,b   Ling, Chih chuan ^a  

^a INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

^b INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

ACETYLATION; ARTICLE; CELL CYCLE G1 PHASE; CHROMATIN; CHROMATIN CONDENSATION; DNA STRAND BREAKAGE; HYPOTHESIS; PREDICTION; PROMOTER REGION; REGULATOR GENE; TRANSCRIPTION INITIATION;

CHROMATIN; NUCLEIC ACID CONFORMATION; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 0038218003     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.10267     Document Type: Article

References (61)

1. Li Q, Harju S, Peterson KR. Locus control regions: coming of age at a decade plus. Trends Genet 1999;15:403-408.
2. Blackwood EM, Kadonaga JT. Going the distance: a current view of enhancer action. Science 1998;281:61-63.
3. Bulger M, Groudine M. Looping versus linking: toward a model for longdistance gene activation. Genes Dev 1999;13:2465-2477.
4. Bell AC, West AG, Felsenfeld G. Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. Science 2001;291:447-450
5. Gerasimova TI, Byrd K, Corces VG. A chromatin insulator determines the nuclear localization of DNA. Mol Cell 2000;6:1025-1035.
6. Cai HN, Shen P. Effects of cis arrangement of chromatin insulators on enhancer-blocking activity. Science 2001;291:493-495.
7. Muravyova E, Golovnin A, Gracheva E, Parshikov A, Belenkaya T, Pirrotta V, Georgiev P. Loss of insulator activity by paired Su(Hw) chromatin insulators. Science 2001;291:495-498.
8. Parnell TJ, Geyer PK. Differences in insulator properties revealed by enhancer blocking assays on episomes. EMBO J 2000;19:5864-5874.
9. West AG, Gaszner M, Felsenfeld G. Insulators: many functions, many mechanisms. Genes Dev 2002;16:271-288
10. Villemure JF, Savard N, Belmaaza A. Promoter suppression in cultured mammalian cells can be blocked by the chicken beta-globin chromatin insulator 5′HS4 and matrix/scaffold attachment regions. J Mol Biol 2001;312:963-974.
11. Litt MD, Simpson M, Recillas-Targa F, Prioleau MN, Felsenfeld G. Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci. EMBO J 2001;20:2224-2235.
12. Forsberg EC, Downs KM, Christensen HM, Im H, Nuzzi PA, Bresnick EH. Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain. Proc Natl Acad Sci USA 2000;97:14494-14499.
13. Schubeler D, Groudine M, Bender MA. 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 2001;98:11432-11437
14. Woodcock CL, Dimitrov S. Higher-order structure of chromatin and chromosomes. Curr Opin Genet Dev 2001;11:130-135
15. Fry CJ, Peterson CL. Chromatin remodeling enzymes: who's on first? Curr Biol 2001;11:R185-R197
16. Fry CJ, Peterson CL. TRANSCRIPTION: Unlocking the Gates to Gene Expression. Science 2002;295:1847-1848.
17. Soutoglou E, Talianidis I. Coordination of PIC Assembly and Chromatin Remodeling During Differentiation-Induced Gene Activation. Science 2002;295:1901-1904.
18. Liu R, Liu H, Chen X, Kirby M, Brown PO, Zhao K. Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell 2001;106:309-318.
19. Kruhlak MJ, Hendzel MJ, Fischle W, Bertos NR, Hameed S, Yang XJ, Verdin E, Bazett-Jones DP. Regulation of global acetylation in mitosis through loss of histone acetyltransferases and deacetylases from chromatin. J Biol Chem 2001;276:38307-38319
20. Narlikar GJ, Fan HY, Kingston RE. Cooperation between Complexes that Regulate Chromatin Structure and Transcription. Cell 2002;108:475-487
21. Holmes VF, Cozzarelli NR. Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling. Proc Natl Acad Sci USA 2000;97:1322-1324.
22. Guyon JR, Narlikar GJ, Sullivan EK, Kingston RE. Stability of a human SWI-SNF remodeled nucleosomal array. Mol Cell Biol 2001;21:1132-1144.
23. Varga-Weisz PD, Wilm M, Bonte E, Dumas K, Mann M, Becker PB. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 1997;388:598-602
24. Lupo R, Breiling A, Bianchi ME, Orlando V. Drosophila chromosome condensation proteins Topoisomerase II and Barren colocalize with Polycomb and maintain Fab-7 PRE silencing. Mol Cell 2001;7:127-136.
25. Cavalli G, Paro R. The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell 1998;93:505-518.
26. Cavalli G, Paro R. Epigenetic inheritance of active chromatin after removal of the main transactivator. Science 1999;286:955-958.
27. Cirillo LA, Zaret KS. An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA. Mol Cell 1999;4:961-969.
28. Tsutsui K, Tsutsui K, Sano K, Kikuchi A, Tokunaga A. Involvement of DNA topoisomerase II beta in neuronal differentiation. J Biol Chem 2001;276:5769-5778.
29. Walia H, Chen HY, Sun JM, Holth LT, Davie JR. Histone acetylation is required to maintain the unfolded nucleosome structure associated with transcribing DNA. J Biol Chem 1998;273:14516-14522.
30. Vassetzky Y, Lemaitre JM, Mechali M. Specification of chromatin domains and regulation of replication and transcription during development. Crit Rev Eukaryot Gene Expr 2000;10:31-38.
31. Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, KohwiShigematsu T. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 1992;255:195-197.
32. Fernandez LA, Winkler M, Grosschedl R. Matrix attachment region-dependent function of the immunoglobulin mu enhancer involves histone acetylation at a distance without changes in enhancer occupancy. Mol Cell Biol 2001;21:196-208.
33. Forsberg EC, Downs KM, Bresnick EH Direct interaction of NF-E2 with hypersensitive site 2 of the beta-globin locus control region in living cells. Blood 2000;96:334-339.
34. Sawado T, Igarashi K, Groudine M. Activation of beta-major globin gene transcription is associated with ecruitment of NF-E2 to the beta-globin LCR and gene promoter. Proc Natl Acad Sci USA 2001;98:10226-10231.
35. Butler JE, Kadonaga JT. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 2001;15:2515-2519
36. Ohtsuki S, Levine M, Cai HN. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev 1998;12:547-556.
37. Gui CY, Dean A. Acetylation of a specific promoter nucleosome accompanies activation of the epsilon-globin gene by beta-globin locus control region HS2. Mol Cell Biol 2001;21:1155-1163.
38. Johnson KD, Christensen HM, Zhao B, Bresnick EH. Distinct mechanisms control RNA polymerase II recruitment to a tissue-specific locus control region and a downstream promoter. Mol Cell 2001;8:465-471.
39. Zannis VI, Kan HY, Kritis A, Zanni EE, Kardassis D. Transcriptional regulatory mechanisms of the human apolipoprotein genes in vitro and in vivo. Curr Opin Lipidol 2001;12:181-207.
40. Zannis VI, Kan HY, Kritis A, Zanni E, Kardassis D. Transcriptional regulation of the human apolipoprotein genes. Front Biosci 2001;6:D456-D504.
41. Vyas P, Vickers MA, Simmons DL, Ayyub H, Craddock CF, Higgs DR. Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. Cell 1992;69:781-793.
42. Dillon N, Sabbattini P. Functional gene expression domains: defining the functional unit of eukaryotic gene regulation. Bioessays 2000;22:657-665.
43. Wang JC. DNA topoisomerases. Annu Rev Biochem 1996;65:635-692.
44. Austin CA, Marsh KL. Eukaryotic DNA topoisomerase II beta. Bioessays 1998;20:215-226.
45. Burden DA, Osheroff N. Mechanism of action of eukaryotic topoisometase II and drugs targeted to the enzyme. Biochim Biophys Acta 1998;1400:139-154.
46. Jenkins JR, Ayton P, Jones T, Davies SL, Simmons DL, Harris AL, Sheer D, Hickson ID. Isolation of cDNA clones encoding the beta isozyme of human DNA topoisomerase II and localisation of the gene to chromosome 3p24. Nucleic Acids Res 1992;20:5587-5592.
47. Tan KB, Dorman TE, Falls KM, Chung TD, Mirabelli CK, Crooke ST, Mao J. Topoisomerase II alpha and topoisomerase II beta genes: characterization and mapping to human chromosomes 17 and 3, respectively. Cancer Res 1992;52:231-234.
48. Mondal N, Parvin JD. DNA topoisomerase II alpha is required for RNA polymerase II transcription on chromatin templates. Nature 2001;413:435-438.
49. Cockerill PN, Garrard WT. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 1986;44:273-282.
50. Ura K, Hirose S. Possible role of DNA topoisomerase II on transcription of the homeobox gene Hox-2.1 in F9 embryonal carcinoma cells. Nucleic Acids Res 1991;19:6087-6092.
51. Ishii K, Arib G, Lin C, Van Houwe G, Laemmli UK. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 2002;109:551-562.
52. Recillas-Targa F, Pikaart MJ, Burgess-Beusse B, Bell AC, Litt MD, West AG, Gaszner M, Felsenfeld G. Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities. Proc Natl Acad Sci USA 2002;99:6883-6888.
53. Holm C, Goto T, Wang JC, Botstein D. DNA topoisomerase II is required at the time of mitosis in yeast. Cell 1985;41:553-563.
54. DiNardo S, Voelkel K, Sternglanz R. DNA topoisomerase II mutant of Saccharomyces cerevisiae: topoisomerase II is required for segregation of daughter molecules at the termination of DNA replication. Proc Natl Acad Sci USA 1984;81:2616-2620.
55. Uemura T, Yanagida M. Isolation of type I and II DNA topoisomerase mutants from fission yeast: single and double mutants show different phenotypes in cell growth and chromatin organization. EMBO J 1984;3:1737-1744.
56. Holm C, Goto T, Wang JC, Botstein D. DNA topoisomerase II is required at the time of mitosis in yeast. Cell 1985;41:553-563
57. Uemura T, Ohkura H, Adachi Y, Morino K, Shiozaki K, Yanagida M. DNA topoisomerase II is required for condensation and separation of mitotic chromosomes in S. pombe. Cell 1987;50:917-925.
58. Tanabe H, Muller S, Neusser M, von Hase J, Calcagno E, Cremer M, Solovei I, Cremer C, Cremer T. Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci USA 2002;99:4424-4429.
59. Tyler JK, Kadonaga TJ. The "dark side" of chromatin remodeling: repressive effects on transcription. Cell 1999;99:443-446.
60. Escargueil AE, Plisov SY, Skladanowski A, Borgne A, Meijer L, Gorbsky GJ, Larsen AK. Recruitment of cdc2 kinase by DNA topoisomerase II is coupled to chromatin remodeling. FASEB J 2001;15:2288-2290.
61. Orphanides G, Reinberg D. A unified theory of gene expression. Cell 2002;108:439-451.