From silencing to gene expression: Real-time analysis in single cells

Cell

Volumn 116, Issue 5, 2004, Pages 683-698

  Janicki, Susan M ^a   Tsukamoto, Toshiro ^b   Salghetti, Simone E ^a   Tansey, William P ^a   Sachidanandam, Ravi ^a   Prasanth, Kannanganattu V ^a   Ried, Thomas ^c   Shav Tal, Yaron ^d   Bertrand, Edouard ^e   Singer, Robert H ^d   Spector, David L ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b UTSUNOMIYA UNIVERSITY   (Japan)

^c NATIONAL CANCER INSTITUTE   (United States)

^d ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^e CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 1; CONTROLLED STUDY; CORRELATION ANALYSIS; EUCHROMATIN; GENE EXPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; METHYLATION; PRIORITY JOURNAL; SYNTHESIS; TRANSGENE;

EID: 12144289862     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(04)00171-0     Document Type: Article

References (83)

1. Ahmad K., Henikoff S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell. 9:2002;1191-1200.
2. Archer T.K., Lee H.L., Cordingley M.G., Mymryk J.S., Fragoso G., Berard D.S., Hager G.L. Differential steroid hormone induction of transcription from the mouse mammary tumor virus promoter. Mol. Endocrinol. 8:1994;568-576.
3. Ayyanathan K., Lechner M.S., Bell P., Maul G.G., Schultz D.C., Yamada Y., Tanaka K., Torigoe K., Rauscher F.J. 3rd. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing. a mammalian cell culture model of gene variegation Genes Dev. 17:2003;1855-1869.
4. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature. 410:2001;120-124.
5. Bannister A.J., Schneider R., Kouzarides T. Histone methylation. dynamic or static? Cell. 109:2002;801-806.
6. Beckett D., Uhlenbeck O.C. Ribonucleoprotein complexes of R17 coat protein and a translational operator analog. J. Mol. Biol. 204:1988;927-938.
7. Belmont A.S. Visualizing chromosome dynamics with GFP. Trends Cell Biol. 11:2001;250-257.
8. Bertrand E., Chartrand P., Schaefer M., Shenoy S.M., Singer R.H., Long R.M. Localization of ASH1 mRNA particles in living yeast. Mol. Cell. 2:1998;437-445.
9. Bickmore W.A., Van Der Maarel S.M. Perturbations of chromatin structure in human genetic disease. recent advances Hum. Mol. Genet. 12(Suppl 2):2003;R207-R213.
10. Calapez A., Pereira H.M., Calado A., Braga J., Rino J., Carvalho C., Tavanez J.P., Wahle E., Rosa A.C., Carmo-Fonseca M. The intranuclear mobility of messenger RNA binding proteins is ATP dependent and temperature sensitive. J. Cell Biol. 159:2002;795-805.
11. Chen C., Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Mol. Cell. Biol. 7:1987;2745-2752.
12. Cheutin T., McNairn A.J., Jenuwein T., Gilbert D.M., Singh P.B., Misteli T. Maintenance of Stable Heterochromatin Domains by Dynamic HP1 Binding. Science. 299:2003;721-725.
13. Clegg N.J., Honda B.M., Whitehead I.P., Grigliatti T.A., Wakimoto B., Brock H.W., Lloyd V.K., Sinclair D.A. Suppressors of position-effect variegation in Drosophila melanogaster affect expression of the heterochromatic gene light in the absence of a chromosome rearrangement. Genome. 41:1998;495-503.
14. Dietzel S., Belmont A.S. Reproducible but dynamic positioning of DNA in chromosomes during mitosis. Nat. Cell Biol. 3:2001;767-770.
15. Dorer D.R., Henikoff S. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell. 77:1994;993-1002.
16. Emerson B.M. Specificity of gene regulation. Cell. 109:2002;267-270.
17. Fanti L., Dorer D.R., Berloco M., Henikoff S., Pimpinelli S. Heterochromatin protein 1 binds transgene arrays. Chromosoma. 107:1998;286-292.
18. Femino A.M., Fay F.S., Fogarty K., Singer R.H. Visualization of single RNA transcripts in situ. Science. 280:1998;585-590.
19. Festenstein R., Pagakis S.N., Hiragami K., Lyon D., Verreault A., Sekkali B., Kioussis D. Modulation of heterochromatin protein 1 dynamics in primary Mammalian cells. Science. 299:2003;719-721.
20. Fischle W., Wang Y., Allis C.D. Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15:2003;172-183.
21. Forrest K.M., Gavis E.R. Live imaging of endogenous RNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in Drosophila. Curr. Biol. 13:2003;1159-1168.
22. Fusco D., Accornero N., Lavoie B., Shenoy S.M., Blanchard J.M., Singer R.H., Bertrand E. Single mRNA molecules demonstrate probabilistic movement in living Mammalian cells. Curr. Biol. 13:2003;161-167.
23. Gottesman S. Stealth regulation. biological circuits with small RNA switches Genes Dev. 16:2002;2829-2842.
24. Grewal S.I., Moazed D. Heterochromatin and epigenetic control of gene expression. Science. 301:2003;798-802.
25. Hall I.M., Shankaranarayana G.D., Noma K., Ayoub N., Cohen A., Grewal S.I. Establishment and maintenance of a heterochromatin domain. Science. 297:2002;2232-2237.
26. Hannon G.J. RNA interference. Nature. 418:2002;244-251.
27. Heard E., Rougeulle C., Arnaud D., Avner P., Allis C.D., Spector D.L. Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell. 107:2001;727-738.
28. Hearn M.G., Hedrick A., Grigliatti T.A., Wakimoto B.T. The effect of modifiers of position-effect variegation on the variegation of heterochromatic genes of Drosophila melanogaster. Genetics. 128:1991;785-797.
29. Hsieh J., Fire A. Recognition and silencing of repeated DNA. Annu. Rev. Genet. 34:2000;187-204.
30. Huang, S., and Spector, D.L. (1997). Pre-mRNA splicing: nuclear organization of factors and substrates. In Eukaryotic Messenger RNA Processing, A.R. Krainer, ed. (Oxford, IRL Press), pp. 33-67.
31. Jacobs S.A., Khorasanizadeh S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science. 295:2002;2080-2083.
32. Jacobs S.A., Taverna S.D., Zhang Y., Briggs S.D., Li J., Eissenberg J.C., Allis C.D., Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20:2001;5232-5241.
33. Janicki S.M., Spector D.L. Nuclear choreography. interpretations from living cells Curr. Opin. Cell Biol. 15:2003;149-157.
34. Jenuwein T., Allis C.D. Translating the histone code. Science. 293:2001;1074-1080.
35. Jiang G., Yang F., van Overveld P.G., Vedanarayanan V., van der Maarel S., Ehrlich M. Testing the position-effect variegation hypothesis for facioscapulohumeral muscular dystrophy by analysis of histone modification and gene expression in subtelomeric 4q. Hum. Mol. Genet. 12:2003;2909-2921.
36. Kimura H., Cook P.R. Kinetics of core histones in living human cells. little exchange of H3 and H4 and some rapid exchange of H2B J. Cell Biol. 153:2001;1341-1353.
37. Krogan N.J., Keogh M.C., Datta N., Sawa C., Ryan O.W., Ding H., Haw R.A., Pootoolal J., Tong A., Canadien V.et al. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell. 12:2003;1565-1576.
38. Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature. 410:2001;116-120.
39. Lau S., Jardine K., McBurney M.W. DNA methylation pattern of a tandemly repeated LacZ transgene indicates that most copies are silent. Dev. Dyn. 215:1999;126-138.
40. Lemon B., Tjian R. Orchestrated response. a symphony of transcription factors for gene control Genes Dev. 14:2000;2551-2569.
41. Lever M.A., Th'ng J.P., Sun X., Hendzel M.J. Rapid exchange of histone H1.1 on chromatin in living human cells. Nature. 408:2000;873-876.
42. Li W.H., Gu Z., Wang H., Nekrutenko A. Evolutionary analyses of the human genome. Nature. 409:2001;847-849.
43. Li Y., Kirschmann D.A., Wallrath L.L. Does heterochromatin protein 1 always follow code? Proc. Natl. Acad. Sci. USA. 99(Suppl. 4):2002;16462-16469.
44. Lu B.Y., Emtage P.C., Duyf B.J., Hilliker A.J., Eissenberg J.C. Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila. Genetics. 155:2000;699-708.
45. Maniatis T., Reed R. An extensive network of coupling among gene expression machines. Nature. 416:2002;499-506.
46. Marmorstein R. Structure of SET domain proteins. a new twist on histone methylation Trends Biochem. Sci. 28:2003;59-62.
47. McNally J.G., Muller W.G., Walker D., Wolford R., Hager G.L. The glucocorticoid receptor. rapid exchange with regulatory sites in living cells Science. 287:2000;1262-1265.
48. Misteli T., Caceres J.F., Spector D.L. The dynamics of a pre-mRNA splicing factor in living cells. Nature. 387:1997;523-527.
49. Mizuguchi G., Shen X., Landry J., Wu W.H., Sen S., Wu C. ATP-Driven Exchange of Histone H2AZ Variant Catalyzed by SWR1 Chromatin Remodeling Complex. Science. 303:2003;343-348.
50. Muller W.G., Walker D., Hager G.L., McNally J.G. Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter. J. Cell Biol. 154:2001;33-48.
51. Nelson P., Kiriakidou M., Sharma A., Maniataki E., Mourelatos Z. The microRNA world. small is mighty Trends Biochem. Sci. 28:2003;534-540.
52. Ogawa H., Ishiguro K., Gaubatz S., Livingston D.M., Nakatani Y. A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. Science. 296:2002;1132-1136.
53. Orphanides G., Reinberg D. A unified theory of gene expression. Cell. 108:2002;439-451.
54. Pal-Bhadra M., Bhadra U., Birchler J.A. Cosuppression in Drosophila. gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent Cell. 90:1997;479-490.
55. Pal-Bhadra M., Bhadra U., Birchler J.A. Cosuppression of nonhomologous transgenes in Drosophila involves mutually related endogenous sequences. Cell. 99:1999;35-46.
56. Pal-Bhadra M., Bhadra U., Birchler J.A. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell. 9:2002;315-327.
57. Peters A.H., O'Carroll D., Scherthan H., Mechtler K., Sauer S., Schofer C., Weipoltshammer K., Pagani M., Lachner M., Kohlmaier A.et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell. 107:2001;323-337.
58. Peters A.H., Kubicek S., Mechtler K., O'Sullivan R.J., Derijck A.A., Perez-Burgos L., Kohlmaier A., Opravil S., Tachibana M., Shinkai Y.et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell. 12:2003;1577-1589.
59. Phair R.D., Misteli T. High mobility of proteins in the mammalian cell nucleus. Nature. 404:2000;604-609.
60. Piacentini L., Fanti L., Berloco M., Perrini B., Pimpinelli S. Heterochromatin protein 1 (HP1) is associated with induced gene expression in Drosophila euchromatin. J. Cell Biol. 161:2003;707-714.
61. Politz J.C., Browne E.S., Wolf D.E., Pederson T. Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc. Natl. Acad. Sci. USA. 95:1998;6043-6048.
62. Politz J.C., Tuft R.A., Pederson T., Singer R.H. Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr. Biol. 9:1999;285-291.
63. Rappsilber J., Ryder U., Lamond A.I., Mann M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12:2002;1231-1245.
64. Rea S., Eisenhaber F., O'Carroll D., Strahl B.D., Sun Z.W., Schmid M., Opravil S., Mechtler K., Ponting C.P., Allis C.D., Jenuwein T. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature. 406:2000;593-599.
65. Ricci E., Galluzzi G., Deidda G., Cacurri S., Colantoni L., Merico B., Piazzo N., Servidei S., Vigneti E., Pasceri V.et al. Progress in the molecular diagnosis of facioscapulohumeral muscular dystrophy and correlation between the number of KpnI repeats at the 4q35 locus and clinical phenotype. Ann. Neurol. 45:1999;751-757.
66. Rice J.C., Briggs S.D., Ueberheide B., Barber C.M., Shabanowitz J., Hunt D.F., Shinkai Y., Allis C.D. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell. 12:2003;1591-1598.
67. Richards E.J., Elgin S.C. Epigenetic codes for heterochromatin formation and silencing. rounding up the usual suspects Cell. 108:2002;489-500.
68. Rook M.S., Lu M., Kosik K.S. CaMKIIalpha 3′ untranslated region-directed mRNA translocation in living neurons. visualization by GFP linkage J. Neurosci. 20:2000;6385-6393.
69. Sabl J.F., Henikoff S. Copy number and orientation determine the susceptibility of a gene to silencing by nearby heterochromatin in Drosophila. Genetics. 142:1996;447-458.
70. Spector D.L. Macromolecular domains within the cell nucleus. Annu. Rev. Cell Biol. 9:1993;265-315.
71. Spradling A.C., Rubin G.M. The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene. Cell. 34:1983;47-57.
72. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature. 403:2000;41-45.
73. Sugaya K., Vigneron M., Cook P.R. Mammalian cell lines expressing functional RNA polymerase II tagged with the green fluorescent protein. J. Cell Sci. 113:2000;2679-2683.
74. Tachibana M., Sugimoto K., Fukushima T., Shinkai Y. Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J. Biol. Chem. 276:2001;25309-25317.
75. Tachibana M., Sugimoto K., Nozaki M., Ueda J., Ohta T., Ohki M., Fukuda M., Takeda N., Niida H., Kato H., Shinkai Y. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 16:2002;1779-1791.
76. Tagami H., Ray-Gallet D., Almouzni G., Nakatani Y. Histone h3.1 and h3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell. 116:2004;51-61.
77. Takagaki Y., Manley J.L., MacDonald C.C., Wilusz J., Shenk T. A multisubunit factor, CstF, is required for polyadenylation of mammalian pre-mRNAs. Genes Dev. 4:1990;2112-2120.
78. Tsukamoto T., Hashiguchi N., Janicki S.M., Tumbar T., Belmont A.S., Spector D.L. Visualization of gene activity in living cells. Nat. Cell Biol. 2:2000;871-878.
79. Tumbar T., Sudlow G., Belmont A.S. Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J. Cell Biol. 145:1999;1341-1354.
80. Vasudevan S., Peltz S.W. Nuclear mRNA surveillance. Curr. Opin. Cell Biol. 15:2003;332-337.
81. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I., Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science. 297:2002;1833-1837.
82. Wilkinson M.F., Shyu A.B. RNA surveillance by nuclear scanning? Nat. Cell Biol. 4:2002;E144-E147.
83. Zhao T., Heyduk T., Allis C.D., Eissenberg J.C. Heterochromatin protein 1 binds to nucleosomes and DNA in vitro. J. Biol. Chem. 275:2000;28332-28338.