Where shall we meet? A role for genome organisation and nuclear sub-compartments in mediating interchromosomal interactions

Journal of Cellular Biochemistry

Volumn 104, Issue 5, 2008, Pages 1553-1561

  Osborne, Cameron S ^a,b   Eskiw, Christopher H ^a  

^a BABRAHAM INSTITUTE   (United Kingdom)

^b Babraham Research Campus ^*  (United Kingdom)

Author keywords

Genome organisation; Interchromosomal interactions; Nuclear sub compartments

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; PROMYELOCYTIC LEUKEMIA PROTEIN; RNA POLYMERASE II;

CELL COMPARTMENTALIZATION; CELL NUCLEUS INCLUSION BODY; GENE INTERACTION; GENE LOCUS; GENETIC ORGANIZATION; GENETIC TRANSCRIPTION; HUMAN; NUCLEOLUS; PRIORITY JOURNAL; REVIEW;

ANIMALS; CELL NUCLEOLUS; CELL NUCLEUS; CHROMOSOME POSITIONING; CHROMOSOMES; GENOME; HUMANS; TRANSCRIPTION, GENETIC;

MAMMALIA;

EID: 50249168718     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.21750     Document Type: Review

References (64)

1. Bacher CP, Guggiari M, Brors B, Augui S, Clerc P, Avner P, Eils R, Heard E. 2006. Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol 8:293-299.
2. Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, Muller S, Eils R, Cremer C, Speicher MR, Cremer T. 2005. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3:e157.
3. Branco MR, Pombo A. 2006. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 4: e138.
4. Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, Wood WG, Higgs DR, Iborra FJ, Buckle VJ. 2006. Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172:177-187.
5. Cai L, Friedman N, Xie XS. 2006. Stochastic protein expression in individual cells at the single molecule level. Nature 440:358-362.
6. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P. 2002. Long-range chromatin regulatory interactions in vivo. Nat Genet 32:623-626.
7. Chambeyron S, Bickmore WA. 2004. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18:1119-1130.
8. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149-1154.
9. Chubb JR, Trcek T, Shenoy SM, Singer RH. 2006. Transcriptional pulsing of a developmental gene. Curr Biol 16:1018-1025.
10. Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA. 1999. Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145: 1119-1131.
11. de Laat W, Grosveld F. 2007. Inter-chromosomal gene regulation in the mammalian cell nucleus. Curr Opin Genet Dev 17:456-464.
12. Dousset T, Wang C, Verheggen C, Chen D, Hernandez-Verdun D, Huang S. 2000. Initiation of nucleolar assembly is independent of RNA polymerase I transcription. Mol Biol Cell 11:2705-2717.
13. Dundr M, Ospina JK, Sung MH, John S, Upender M, Ried T, Hager GL, Matera AG. 2007. Actin-dependent intranuclear repositioning of an active gene locus in vivo. J Cell Biol 179:1095-1103.
14. Elbi C, Misteli T, Hager GL. 2002. Recruitment of dioxin receptor to active transcription sites. Mol Biol Cell 13: 2001-2015.
15. Eskiw CH, Dellaire G, Mymryk JS, Bazett-Jones DP. 2003. Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supra-molecular trafficking and assembly. J Cell Sci 116:4455-4466.
16. Eskiw CH, Dellaire G, Bazett-Jones DP. 2004. Chromatin contributes to structural integrity of promyelocytic leukemia bodies through a SUMO-1-independent mechanism. J Biol Chem 279:9577-9585.
17. Faro-Trindade I, Cook PR. 2006. A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. Mol Biol Cell 17: 2910-2920.
18. Foster HA, Abeydeera LR, Griffin DK, Bridger JM. 2005. Non-random chromosome positioning in mammalian sperm nuclei, with migration of the sex chromosomes during late spermatogenesis. J Cell Sci 118:1811-1820.
19. Frey MR, Bailey AD, Weiner AM, Matera AG. 1999. Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts. Curr Biol 9: 126-135.
20. Gerasimova TI, Lei EP, Bushey AM, Corces VG. 2007. Coordinated control of dCTCF and gypsy chromatin insulators in Drosophila. Mol Cell 28:761-772.
21. Grande MA, van der Kraan I, de Jong L, van Driel R. 1997. Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J Cell Sci 110(Pt 15):1781-1791.
22. He S, Sun JM, Li L, Davie JR. 2005. Differential intranuclear organization of transcription factors Sp1 and Sp3. Mol Biol Cell 16:4073-4083.
23. Iborra FJ, Pombo A, Jackson DA, Cook PR. 1996. Active RNA polymerases are localized within discrete transcription 'factories' in human nuclei. J Cell Sci 109(Pt 6): 1427-1436.
24. Jackson DA, Cook PR. 1985. Transcription occurs at a nucleoskeleton. EMBO J 4:919-925.
25. Ju BG, Lunyak W, Perissi V, Garcia-Bassets I, Rose DW, Glass CK, Rosenfeld MG. 2006. A topoisomerase Ilbeta-mediated dsDNA break required for regulated transcription. Science 312:1798-1802.
26. Kaufmann BB, Yang Q, Mettetal JT, van Oudenaarden A. 2007. Heritable stochastic switching revealed by single-cell genealogy. PLoS Biol 5:e239.
27. Kimura H, Tao Y, Roeder RG, Cook PR. 1999. Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: Little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol Cell Biol 19:5383-5392.
28. Kruhlak MJ, Lever MA, Fischle W, Verdin E, Bazett-Jones DP, Hendzel MJ. 2000. Reduced mobility of the alternate splicing factor (ASF) through the nucleoplasm and steady state speckle compartments. J Cell Biol 150:41-51.
29. Kumar PP, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S. 2007. Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat Cell Biol 9:45-56.
30. Kuroda M, Tanabe H, Yoshida K, Oikawa K, Saito A, Kiyuna T, Mizusawa H, Mukai K. 2004. Alteration of chromosome positioning during adipocyte differentiation. J Cell Sci 117:5897-5903.
31. Ling JQ, Li T, Hu JF, Vu TH, Chen HL, Qiu XW, Cherry AM, Hoffman AR. 2006. CTCF mediates interchromo-somal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312:269-272.
32. Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R. 2006. Interchromosomal interactions and olfactory receptor choice. Cell 126:403-413.
33. Mahy NL, Perry PE, Bickmore WA. 2002. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159:753-763.
34. Mais C, Wright JE, Prieto JL, Raggett SL, McStay B. 2005. UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery. Genes Dev 19:50-64.
35. Mitchell JA, Fraser P. 2008. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev 22:20-25.
36. Mo X, Dynan WS. 2002. Subnuclear localization of Ku protein: Functional association with RNA polymerase II elongation sites. Mol Cell Biol 22:8088-8099.
37. Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P. 2004. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36: 1065-1071.
38. Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, Corcoran AE, Fraser P. 2007. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol 5:e192.
39. Parada LA, McQueen PG, Munson PJ, Misteli T. 2002. Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol 12:1692-1697.
40. Parada LA, McQueen PG, Misteli T. 2004. Tissue-specific spatial organization of genomes. Genome Biol 5:R44.
41. Pombo A, Cuello P, Schul W, Yoon JB, Roeder RG, Cook PR, Murphy S. 1998. Regional and temporal specialization in the nucleus: A transcriptionally-active nuclear domain rich in PTF, Octl and PIKA antigens associates with specific chromosomes early in the cell cycle. EMBO J 17: 1768-1778.
42. Pombo A, Jackson DA, Hollinshead M, Wang Z, Roeder RG, Cook PR. 1999. Regional specialization in human nuclei: Visualization of discrete sites of transcription by RNA polymerase III. EMBO J 18:2241-2253.
43. Ragoczy T, Bender MA, Telling A, Byron R, Groudine M. 2006. The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 20:1447-1457.
44. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. 2006. Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4:e309.
45. Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T. 2003. Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet 34:287-291.
46. Rubbi CP, Milner J. 2000. Non-activated p53 co-localizes with sites of transcription within both the nucleoplasm and the nucleolus. Oncogene 19:85-96.
47. Schneider R, Grosschedl R. 2007. Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 21:3027-3043.
48. Schul W, van Der Kraan I, Matera AG, van Driel R, de Jong L. 1999. Nuclear domains enriched in RNA 3′-processing factors associate with coiled bodies and histone genes in a cell cycle-dependent manner. Mol Biol Cell 10:3815-3824.
49. Shiels C, Islam SA, Vatcheva R, Sasieni P, Sternberg MJ, Freemont PS, Sheer D. 2001. PML bodies associate specifically with the MHC gene cluster in interphase nuclei. J Cell Sci 114:3705-3716.
50. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W. 2006. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348-1354.
51. Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA. 2005. Interchromosomal associations between alternatively expressed loci. Nature 435:637-645.
52. Stenoien DL, Mancini MG, Patel K, Allegretto EA, Smith CL, Mancini MA. 2000. Subnuclear trafficking of estrogen receptor-alpha and steroid receptor coactivator-1. Mol Endocrinol 14:518-534.
53. Sun Y, Durrin LK, Krontiris TG. 2003. Specific interaction of PML bodies with the TP53 locus in Jurkat interphase nuclei. Genomics 82:250-252.
54. 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.
55. Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W. 2002. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 10:1453-1465.
56. Verschure PJ, van Der Kraan I, Manders EM, van Driel R. 1999. Spatial relationship between transcription sites and chromosome territories. J Cell Biol 147:13-24.
57. Volpi EV, Chevret E, Jones T, Vatcheva R, Williamson J, Beck S, Campbell RD, Goldsworthy M, Powis SH, Ragoussis J, Trowsdale J, Sheer D. 2000. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 113(Pt9):1565-1576.
58. Wang J, Shiels C, Sasieni P, Wu PJ, Islam SA, Freemont PS, Sheer D. 2004. Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions. J Cell Biol 164:515-526.
59. Wurtele H, Chartrand P. 2006. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res 14:477-495.
60. Xu N, Tsai CL, Lee JT. 2006. Transient homologous chromosome pairing marks the onset of X inactivation. Science 311:1149-1152.
61. Xu N, Donohoe ME, Silva SS, Lee JT. 2007. Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat Genet 39:1390-1396.
62. Yin H, Wang MD, Svoboda K, Landick R, Block SM, Gelles J. 1995. Transcription against an applied force. Science 270:1653-1657.
63. Zeng C, McNeil S, Pockwinse S, Nickerson J, Shopland L, Lawrence JB, Penman S, Hiebert S, Lian JB, van Wijnen AJ, Stein JL, Stein GS. 1998. Intranuclear targeting of AML/CBFalpha regulatory factors to nuclear matrix-associated transcriptional domains. Proc Natl Acad Sci USA 95:1585-1589.
64. Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38:1341-1347.