Cell-by-cell dissection of gene expression and chromosomal interactions reveals consequences of nuclear reorganization

PLoS Biology

Volumn 3, Issue 3, 2005, Pages 0450-0462

  Harmon, Brian ^a   Sedat, John ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PIGMENT;

ANIMAL TISSUE; AUTOFLUORESCENCE; CELL CYCLE; CELL NUCLEUS; CELL TYPE; CHROMOSOME 2; CHROMOSOME 3; CHROMOSOME STRUCTURE; CONFERENCE PAPER; CONTROLLED STUDY; CORRELATION ANALYSIS; DROSOPHILA; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE SILENCING; HETEROCHROMATIN; IMMUNOFLUORESCENCE; MALE; MOLECULAR INTERACTION; NONHUMAN; OPTIC DISK; STOCHASTIC MODEL; X CHROMOSOME; ANIMAL; ARTICLE; CELL FUNCTION; CHROMOSOME; EYE; GENE EXPRESSION REGULATION; GENETICS; PHYSIOLOGY; ULTRASTRUCTURE;

ANIMALS; CELL NUCLEUS; CELL PHYSIOLOGY; CHROMOSOMES; DROSOPHILA; EYE; GENE EXPRESSION REGULATION; HETEROCHROMATIN;

EID: 18044364584     PISSN: 15449173     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030067     Document Type: Conference Paper

References (66)

1. Marshall WF(2002)Order and disorder in the nucleus. Curr Biol 12: 185-192.
2. Gerasimova TI, Byrd K, Corces VG (2000) A chromatin insulator determines the nuclear localization of DNA. Mol Cell 6: 1025-1035.
3. Muller M, Hagstrom K, Gyurkovics H, Pirrotta V, Schedl P (1999) The mcp element from the Drosophila melanogaster bithorax complex mediates longdistance regulatory interactions. Genetics 153: 1333-1356.
4. Messmer S, Franke A, Paro R (1992) Analysis of the functional role of the Polycomb chromodomain in Drosophila melanogaster. Genes Dev 6: 1241-1254.
5. Franke A, Messmer S, Paro R (1995) Mapping functional domains of the Polycomb protein of Drosophila melanogaster. Chromosome Res 3: 351-360.
6. Gasser SM (2001) Positions of potential: Nuclear organization and gene expression. Cell 104: 639-642.
7. Cockell M, Gasser SM (1999) Nuclear compartments and gene regulation. Curr Opin Genet Dev 9: 199-205.
8. Hiraoka Y, Dernburg AF, Parmelee SJ, Rykowski MC, Agard DA, et al. (1993) The onset of homologous chromosome pairing during Drosophila melanogaster embryogenesis. J Cell Biol 120: 591-600.
9. Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J, et al. (1996) Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85: 745-759.
10. Marshall WF, Dernburg AF, Harmon B, Agard DA, Sedat JW (1996) Specific interactions of chromatin with the nuclear envelope: Positional determination within the nucleus in Drosophila melanogaster. Mol Biol Cell 7: 825-842.
11. Fung JC, Marshall WF, Dernburg A, Agard DA, Sedat JW (1998) Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations. J Cell Biol 141: 5-20.
12. Brown KE, Baxter J, Graf D, Merkenschlager M, Fisher AG (1999) Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol Cell 3: 207-217.
13. Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, et al. (1997) Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91: 845-854.
14. Grogan JL, Mohrs M, Harmon B, Lacy DA, Sedat JW, et al. (2001) Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity 14: 205-215.
15. Robinett CC, Straight A, Li G, Willhelm C, Sudlow G, et al. (1996) In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J Cell Biol 135:1685-1700.
16. Straight AF, Marshall WF, Sedat JW, Murray AW (1997) Mitosis in living budding yeast: Anaphase A but no metaphase plate. Science 277: 574-578.
17. Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, et al. (1997) Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7: 930-939.
18. Li G, Sudlow G, Belmont AS (1998) Interphase cell cycle dynamics of a late-replicating, heterochromatic homogeneously staining region: Precise choreography of condensation/decondensation and nuclear positioning. J Cell Biol 140: 975-989.
19. Vazquez J, Belmont AS, Sedat JW (2001) Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr Biol 11: 1227-1239.
20. Elgin SC (1996) Heterochromatin and gene regulation in Drosophila. Curr Opin Genet Dev 6: 193-202.
21. Wakimoto BT (1998) Beyond the nucleosome: Epigenetic aspects of position-effect variegation in Drosophila. Cell 93: 321-324.
22. Csink AK, Henikoff S (1996) Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381: 529-531.
23. Talbert PB, Henikoff S (2000) A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster. Genetics 154: 259-272.
24. Sass GL, Henikoff S (1999) Pairing-dependent mislocalization of a Drosophila brown gene reporter to a heterochromatic environment. Genetics 152: 595-604.
25. Henikoff S, Jackson JM, Talbert PB (1995) Distance and pairing effects on the brownDominant heterochromatic element in Drosophila. Genetics 140:1007-1017.
26. Talbert PB, LeCiel CD, Henikoff S (1994) Modification of the Drosophila heterochromatic mutation brownDominant by linkage alterations. Genetics 136: 559-571.
27. Dreesen TD, Johnson DH, Henikoff S (1988) The brown protein of Drosophila melanogaster is similar to the white protein and to components of active transport complexes. Mol Cell Biol 8: 5206-5215.
28. Lu BY, Bishop CP, Eissenberg JC (1996) Developmental timing and tissue specificity of heterochromatin-mediated silencing. EMBO J 15: 1323-1332.
29. Lu BY, Ma J, Eissenberg JC (1998) Developmental regulation of heterochromatin-mediated gene silencing in Drosophila. Development 125: 2223-2234.
30. Csink AK, Henikoff S (1998) Large-scale chromosomal movements during interphase progression in Drosophila. J Cell Biol 143: 13-22.
31. Wolff T, Ready DF (1993) Pattern formation in the Drosophila retina. In: Bate MA, editor. The development of Drosophila melanogaster. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press. pp. 1277-1325.
32. Baker NE, Yu SY (2001) The Egf receptor defines domains of cell cycle progression and survival to regulate cell number in the developing Drosophila eye. Cell 104: 699-708.
33. Horsfield J, Penton A, Secombe J, Hoffman FM, Richardson H (1998) decapentaplegic is required for arrest in G1 phase during Drosophila eye development. Development 125: 5069-5078.
34. Lehner CF, O'Farrell PH (1989) Expression and function of Drosophila cyclin A during embryonic cell cycle progression. Cell 56: 957-968.
35. Sage BT, Csink AK (2003) Heterochromatic self-association, a determinant of nuclear organization, does not require sequence homology in Drosophila. Genetics 165: 1183-1193.
36. Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157: 579-589.
37. Solovei I, Cavallo A, Schermelleh L, Jaunin F, Scasselati C, et al. (2002) Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp Cell Res 276: 10-23.
38. Tolchkov EV, Rasheva VI, Bonaccorsi S, Westphal T, Gvozdev VA (2000) The size and internal structure of a heterochromatic block determine its ability to induce position effect variegation in Drosophila melanogaster. Genetics 154: 1611-1626.
39. Ahmad K, Henikoff S (2001) Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila. Cell 104: 839-847.
40. Csink AK, Bounoutas A, Griffith ML, Sabl JF, Sage BT (2002) Differential gene silencing by trans-heterochromatin in Drosophila melanogaster. Genetics 160: 257-269.
41. Li Y, Danzer JR, Alvarez P, Belmont AS, Wallrath LL (2003) Effects of tethering HP1 to euchromatic regions of the Drosophila genome. Development 130: 1817-1824.
42. Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12: 439-445.
43. Thomson I, Gilchrist S, Bickmore WA, Chubb JR (2004) The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol 14: 166-172.
44. Walter J, Schermelleh L, Cremer M, Tashiro S, Cremer T (2003) Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J Cell Biol 160: 685-697.
45. Grewal SIS, Elgin SCR (2002) Heterochromatin: New possibilities for the inheritance of structure. Curr Opin Genet Dev 12: 178-187.
46. Wallrath LL, Elgin SC (1995) Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev 9: 1263-1277.
47. Belyaeva ES, Demakova OV, Umbetova GH, Zhimulev IF (1993) Cytogenetic and molecular aspects of position-effect variegation in Drosophila melanogaster. V Heterochromatin-associated protein HP1 appears in euchromatic chromosomal regions that are inactivated as a result of position-effect variegation. Chromosoma 102: 583-590.
48. Fanti L, Dorer DR, Berloco M, Henikoff S, Pimpinelli S (1998) Heterochromatin protein 1 binds transgene arrays. Chromosoma 107: 286-292.
49. Cryderman DE, Tang H, Bell C, Gilmour DS, Wallrath LL (1999) Heterochromatic silencing of Drosophila heat shock genes acts at the level of promoter potentiation. Nucleic Acids Res 27: 3364-3370.
50. 3 Drosoph Inf Serv 37: 81.
51. Henikoff S, Dreesen TD (1989) Trans-inactivation of the Drosophila brown gene: Evidence for transcriptional repression and somatic pairing dependence. Proc Natl Acad Sci U S A 86: 6704-6708.
52. Dernburg AF, Sedat JW (1998) Mapping three-dimensional chromosome architecture in situ. Methods Cell Biol 53: 187-233.
53. Hartl DL, Nurminsky DI, Jones RW, Lozovskaya ER (1994) Genome structure and evolution in Drosophila: Applications of the framework P1 map. Proc Natl Acad Sci U S A 91: 6824-6829.
54. Hartl DL, Lozovskaya ER (1995) The Drosophila genome map: A practical guide. Georgetown (Texas): R.G. Landes Company. 120 p.
55. Li C, Meinertzhagen IA (1995) Conditions for the primary culture of eye imaginal discs from Drosophila melanogaster. J Neurobiol 28: 363-380.
56. Belmont AS, Braunfeld MB, Sedat JW, Agard DA (1989) Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro. Chromosoma 98: 129-143.
57. Paddy MR, Belmont AS, Saumweber H, Agard DA, Sedat JW (1990) Interphase nuclear envelope lamins form a discontinuous network that interacts with only a fraction of the chromatin in the nuclear periphery. Cell 62: 89-106.
58. Bass HW, Marshall WF, Sedat JW, Agard DA, Cande WZ (1997) Telomeres cluster de novo before the initiation of synapsis: A three-dimensional spatial analysis of telomere positions before and during meiotic prophase. J Cell Biol 137: 5-18.
59. Hiraoka Y, Swedlow JR, Paddy MR, Agard DA, Sedat JW (1991) Three-dimensional multiple-wavelength fluorescence microscopy for the structural analysis of biological phenomena. Semin Cell Biol 2: 153-165.
60. Hiraoka Y, Sedat JW, Agard DA (1990) Determination of three-dimensional imaging properties of a light microscope system. Partial confocal behavior in epifluorescence microscopy. Biophys J 57: 325-333.
61. Agard DA, Hiraoka Y, Shaw P, Sedat JW (1989) Fluorescence microscopy in three dimensions. Methods Cell Biol 30: 353-377.
62. Chen H, Hughes DD, Chan TA, Sedat JW, Agard DA (1996) IVE (Image Visualization Environment): A software platform for all three-dimensional microscopy applications. J Struct Biol 116: 56-60.
63. Zamir E, Katz BZ, Aota S, Yamada KM, Geiger B, et al. (1999) Molecular diversity of cell-matrix adhesions. J Cell Sci 112: 1655-1669.
64. Sokal RR, Rohlf FJ (1981) Biometry, 2nd ed. New York: W.H. Freeman and Company. 859 p.
65. Lindsley DL, Zimm GG (1992) The genome of Drosophila melanogaster. San Diego: Academic Press. 1,133 p.
66. Lohe AR, Hilliker AJ, Roberts PA (1993) Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster. Genetics 134: 1149-1174.