title: Cell-by-cell dissection of gene expression and chromosomal interactions reveals consequences of nuclear reorganization.
abstract: The functional consequences of long-range nuclear reorganization were studied in a cell-by-cell analysis of gene expression and long-range chromosomal interactions in the Drosophila eye and eye imaginal disk. Position-effect variegation was used to stochastically perturb gene expression and probe nuclear reorganization. Variegating genes on rearrangements of Chromosomes X, 2, and 3 were probed for long-range interactions with heterochromatin. Studies were conducted only in tissues known to express the variegating genes. Nuclear structure was revealed by fluorescence in situ hybridization with probes to the variegating gene and heterochromatin. Gene expression was determined alternately by immunofluorescence against specific proteins and by eye pigment autofluorescence. This allowed cell-by-cell comparisons of nuclear architecture between cells in which the variegating gene was either expressed or silenced. Very strong correlations between heterochromatic association and silencing were found. Expressing cells showed a broad distribution of distances between variegating genes and their own centromeric heterochromatin, while silenced cells showed a very tight distribution centered around very short distances, consistent with interaction between the silenced genes and heterochromatin. Spatial and temporal analysis of interactions with heterochromatin indicated that variegating genes primarily associate with heterochromatin in cells that have exited the cell cycle. Differentiation was not a requirement for association, and no differences in association were observed between cell types. Thus, long-range interactions between distal chromosome regions and their own heterochromatin have functional consequences for the organism.
authors.affiliation: University of California, San Francisco, California, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Harmon
authors.forename: John
authors.initials: J
authors.lastname: Sedat
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000502:physiology* / Q000648:ultrastructure*; D002468:Cell Physiological Phenomena; D002875:Chromosomes; D004330:Drosophila / Q000235:genetics; D005123:Eye; D005786:Gene Expression Regulation; D006570:Heterochromatin / Q000235:genetics
chemical_list: D006570:Heterochromatin
references.citation: Cell. 2001 Mar 9;104(5):699-708
references.pmid: 11257224
references.citation: Genetics. 1994 Feb;136(2):559-71
references.pmid: 8150283
references.citation: J Cell Biol. 1998 Mar 9;140(5):975-89
references.pmid: 9490713
references.citation: Genetics. 1993 Aug;134(4):1149-74
references.pmid: 8375654
references.citation: Biophys J. 1990 Feb;57(2):325-33
references.pmid: 2317554
references.citation: Genetics. 1999 Nov;153(3):1333-56
references.pmid: 10545463
references.citation: Proc Natl Acad Sci U S A. 1989 Sep;86(17):6704-8
references.pmid: 2505257
references.citation: Cell. 2001 Mar 9;104(5):639-42
references.pmid: 11257217
references.citation: Nucleic Acids Res. 1999 Aug 15;27(16):3364-70
references.pmid: 10454645
references.citation: Development. 2003 May;130(9):1817-24
references.pmid: 12642487
references.citation: Cell. 1996 May 31;85(5):745-59
references.pmid: 8646782
references.citation: Genetics. 1995 Jul;140(3):1007-17
references.pmid: 7672573
references.citation: J Cell Biol. 1998 Apr 6;141(1):5-20
references.pmid: 9531544
references.citation: Semin Cell Biol. 1991 Jun;2(3):153-65
references.pmid: 1720334
references.citation: Curr Opin Genet Dev. 1996 Apr;6(2):193-202
references.pmid: 8722176
references.citation: Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6824-9
references.pmid: 8041703
references.citation: J Neurobiol. 1995 Nov;28(3):363-80
references.pmid: 8568517
references.citation: Development. 1998 Jun;125(12):2223-34
references.pmid: 9584122
references.citation: J Cell Biol. 1996 Dec;135(6 Pt 2):1685-700
references.pmid: 8991083
references.citation: Genes Dev. 1992 Jul;6(7):1241-54
references.pmid: 1628830
references.citation: Genetics. 1999 Jun;152(2):595-604
references.pmid: 10353902
references.citation: Cell. 1997 Dec 12;91(6):845-54
references.pmid: 9413993
references.citation: Development. 1998 Dec;125(24):5069-78
references.pmid: 9811590
references.citation: EMBO J. 1996 Mar 15;15(6):1323-32
references.pmid: 8635465
references.citation: Methods Cell Biol. 1989;30:353-77
references.pmid: 2494418
references.citation: J Cell Biol. 1997 Apr 7;137(1):5-18
references.pmid: 9105032
references.citation: Exp Cell Res. 2002 May 15;276(1):10-23
references.pmid: 11978004
references.citation: Genetics. 2000 Apr;154(4):1611-26
references.pmid: 10747057
references.citation: Nature. 1996 Jun 6;381(6582):529-31
references.pmid: 8632827
references.citation: Cell. 1989 Mar 24;56(6):957-68
references.pmid: 2564316
references.citation: Genes Dev. 1995 May 15;9(10):1263-77
references.pmid: 7758950
references.citation: Curr Biol. 2002 Mar 19;12(6):439-45
references.pmid: 11909528
references.citation: Curr Biol. 2004 Jan 20;14(2):166-72
references.pmid: 14738741
references.citation: Curr Biol. 1997 Dec 1;7(12):930-9
references.pmid: 9382846
references.citation: Methods Cell Biol. 1998;53:187-233
references.pmid: 9348510
references.citation: J Struct Biol. 1996 Jan-Feb;116(1):56-60
references.pmid: 8742723
references.citation: Mol Cell Biol. 1988 Dec;8(12):5206-15
references.pmid: 3149712
references.citation: Chromosoma. 1989 Aug;98(2):129-43
references.pmid: 2476279
references.citation: Mol Cell. 1999 Feb;3(2):207-17
references.pmid: 10078203
references.citation: J Cell Biol. 2002 May 13;157(4):579-89
references.pmid: 11994314
references.citation: Immunity. 2001 Mar;14(3):205-15
references.pmid: 11290331
references.citation: Chromosoma. 1998 Nov;107(5):286-92
references.pmid: 9880761
references.citation: J Cell Biol. 2003 Mar 3;160(5):685-97
references.pmid: 12604593
references.citation: Curr Biol. 2001 Aug 21;11(16):1227-39
references.pmid: 11525737
references.citation: Cell. 1998 May 1;93(3):321-4
references.pmid: 9590165
references.citation: Cell. 2001 Mar 23;104(6):839-47
references.pmid: 11290322
references.citation: J Cell Sci. 1999 Jun;112 ( Pt 11):1655-69
references.pmid: 10318759
references.citation: Cell. 1990 Jul 13;62(1):89-106
references.pmid: 2194675
references.citation: Curr Biol. 2002 Mar 5;12(5):R185-92
references.pmid: 11882311
references.citation: Curr Opin Genet Dev. 2002 Apr;12(2):178-87
references.pmid: 11893491
references.citation: Chromosoma. 1993 Sep;102(8):583-90
references.pmid: 8243169
references.citation: Curr Opin Genet Dev. 1999 Apr;9(2):199-205
references.pmid: 10322139
references.citation: Mol Biol Cell. 1996 May;7(5):825-42
references.pmid: 8744953
references.citation: Genetics. 2000 Jan;154(1):259-72
references.pmid: 10628986
references.citation: Genetics. 2002 Jan;160(1):257-69
references.pmid: 11805061
references.citation: Science. 1997 Jul 25;277(5325):574-8
references.pmid: 9228009
references.citation: J Cell Biol. 1998 Oct 5;143(1):13-22
references.pmid: 9763417
references.citation: Chromosome Res. 1995 Sep;3(6):351-60
references.pmid: 7551550
references.citation: Genetics. 2003 Nov;165(3):1183-93
references.pmid: 14668374
references.citation: Mol Cell. 2000 Nov;6(5):1025-35
references.pmid: 11106742
references.citation: J Cell Biol. 1993 Feb;120(3):591-600
references.pmid: 8425892