Interphase chromatin organisation in Arabidopsis nuclei: Constraints versus randomness

Chromosoma

Volumn 121, Issue 4, 2012, Pages 369-387

  Schubert, Veit ^a   Berr, Alexandre ^a,b   Meister, Armin ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE;

ARABIDOPSIS; ARTICLE; CELL DIFFERENTIATION; CELL INTERACTION; CELL NUCLEUS; CENTROMERE; CHROMATIN STRUCTURE; CHROMOSOME ARM; CHROMOSOME REARRANGEMENT; DNA BINDING; ENDOREDUPLICATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LOCATION; HETEROCHROMATIN; INTERPHASE; NONHUMAN; PLANT LEAF; STRUCTURAL HOMOLOGY; TELOMERE;

ARABIDOPSIS; CELL NUCLEUS; CENTROMERE; CHROMATIN; CHROMOSOMES, PLANT; GENE ORDER; IMAGE PROCESSING, COMPUTER-ASSISTED; INTERPHASE; POLYPLOIDY; TELOMERE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; HEXAPODA;

EID: 84864871898     PISSN: 00095915     EISSN: 14320886     Source Type: Journal    
DOI: 10.1007/s00412-012-0367-8     Document Type: Article

References (141)

1. Andrey P, Kieu K, Kress C, Lehmann G, Tirichine L, Liu ZC, Biot E, Adenot PG, Hue-Beauvais C, Houba-Herin N, Duranthon V, Devinoy E, Beaujean N, Gaudin V, Maurin Y, Debey P (2010) Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol 6(7):e1000853. doi:10.1371/journal.pcbi.1000853
2. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
3. Aragon-Alcaide L, Reader S, Beven A, Shaw P, Miller T, Moore G (1997) Association of homologous chromosomes during floral development. Curr Biol 7:905-908
4. Armstrong SJ, Franklin FC, Jones GH (2001) Nucleolus-Associated telomere clustering and pairing precede meiotic chromosome synapsis in Arabidopsis thaliana. J Cell Sci 114:4207-4217
5. Barow M (2006) Endopolyploidy in seed plants. Bioessays 28:271-281
6. Berchtold D, Fesser S, Bachmann G, Kaiser A, Eilert JC, Frohns F, Sadoni N, Muck J, Kremmer E, Eick D, Layer PG, Zink D (2011) Nuclei of chicken neurons in tissues and three-dimensional cell cultures are organized into distinct radial zones. Chromosome Res 19:165-182
7. Berr A, Schubert I (2007) Interphase chromosome arrangement in Arabidopsis thaliana is similar in differentiated and meristematic tissues and shows a transientmirror symmetry after nuclear division. Genetics 176:853-863
8. Berr A, Pecinka A, Meister A, Kreth G, Fuchs J, Blattner FR, Lysak MA, Schubert I (2006) Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata. Plant Journal 48:771-783
9. Blower MD, Sullivan BA, Karpen GH (2002) Conserved organization of centromeric chromatin in flies and humans. Dev Cell 2:319-330
10. Bourdon M et al (2010) Endoreduplication and growth of fleshy fruits. Prog Bot 71:101-132
11. Bourdon M, Coriton O, Pirrello J, Cheniclet C, Brown SC, Poujol C, Chevalier C, Renaudin JP, Frangne N (2011) In planta quantification of endoreduplication using fluorescent in situ hybridization (FISH). Plant J 66:1089-1099
12. Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA (2001) The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10:211-219
13. Branco MR, Pombo A (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcriptiondependent associations. PLoS Biol 4:e138
14. 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
15. Bystricky K, Laroche T, van Houwe G, Blaszczyk M, Gasser SM (2005) Chromosome looping in yeast: telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization. J Cell Biol 168:375-387
16. Chakalova L, Fraser P (2010) Organization of transcription. Cold Spring Harb Perspect Biol. doi:10.1101/cshperspect.a000729
17. Chakalova L, Carter D, Debrand E, Goyenechea B, Horton A, Miles J, Osborne C, Fraser P (2005) Developmental regulation of the betaglobin gene locus. Prog Mol Subcell Biol 38:183-206
18. Chandley AC, Speed RM, Leitch AR (1996) Different distributions of homologous chromosomes in adult human Sertoli cells and in lymphocytes signify nuclear differentiation. J Cell Sci 109:773-776
19. Chevalier C, Nafati M, Mathieu-Rivet E, Bourdon M, Frangne N, Cheniclet C, Renaudin JP, Gevaudant F, Hernould M (2011) Elucidating the functional role of endoreduplication in tomato fruit development. Ann Bot 107:1159-1169
20. Cope NF, Fraser P, Eskiw CH (2010) The yin and yang of chromatin spatial organization. Genome Biol 11:204
21. Corredor E, Diez M, Shepherd K, Naranjo T (2005) The positioning of rye homologous chromosomes added to wheat through the cell cycle in somatic cells untreated and treated with colchicine. Cytogenet Genome Res 109:112-119
22. Coulthard AB, Nolan N, Bell JB, Hilliker AJ (2005) Transvection at the vestigial locus of Drosophila melanogaster. Genetics 170:1711-1721
23. Cremer T, Cremer M (2010) Chromosome territories. Cold Spring Harb Perspect Biol 2:a003889
24. Cremer M, von Hase J, Volm T, Brero A, Kreth G, Walter J, Fischer C, Solovei I, Cremer C, Cremer T (2001) Non-random radial higherorder chromatin arrangements in nuclei of diploid human cells. Chromosome Res 9:541-567
25. 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
26. Csink AK, Henikoff S (1998) Large-scale chromosomal movements during interphase progression in Drosophila. J Cell Biol 143:13-22
27. de Nooijer S, Wellink J, Mulder B, Bisseling T (2009) Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei. Nucleic Acids Res 37:3558-3568
28. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306-1311
29. Dong F, Jiang J (1998) Non-Rabl patterns of centromere and telomere distribution in the interphase nuclei of plant cells. Chromosome Res 6:551-558
30. Dostie J, Zhan Y, Dekker J (2007) Chromosome conformation capture carbon copy technology. Curr Protoc Mol Biol 80:21.14.1-21.14.13
31. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS (2010) A threedimensional model of the yeast genome. Nature 465:363-367
32. Duncan IW (2002) Transvection effects in Drosophila. Ann Rev Genet 36:521-556
33. Eskiw CH, Cope NF, Clay I, Schoenfelder S, Nagano T, Fraser P (2011) Transcription factories and nuclear organization of the genome. Cold Spring Harb Symp Quant Biol 75:501-506
34. Essers J, van Cappellen WA, Theil AF, van Drunen E, Jaspers NG, Hoeijmakers JH, Wyman C, Vermeulen W, Kanaar R (2005) Dynamics of relative chromosome position during the cell cycle. Mol Biol Cell 16:769-775
35. Fang Y, Spector DL (2005) Centromere positioning and dynamics in living Arabidopsis plants. Mol Biol Cell 16:5710-5718
36. Ferrai C, de Castro IJ, Lavitas L, Chotalia M, Pombo A (2010) Gene positioning. Cold Spring Harb Perspect Biol 2:a000588
37. Fransz P (2004) The interphase nucleus. In: Goodman RM (ed) Encyclopedia of plant and crop science. Marcel Dekker, New York, pp 568-571
38. Fransz P, De Jong JH (2011) From nucleosome to chromosome: A dynamic organization of genetic information. Plant J 66:4-17
39. Fransz P, Armstrong S, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G (1998) Cytogenetics for the model system Arabidopsis thaliana. Plant J 13:867-876
40. Fransz P, De Jong JH, Lysak M, Castiglione MR, Schubert I (2002) Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc Natl Acad Sci USA 99:14584-14589
41. Fritsch CC, Langowski J (2011) Chromosome dynamics, molecular crowding, and diffusion in the interphase cell nucleus: A Monte Carlo lattice simulation study. Chromosome Res 19:63-81
42. 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
43. Galbraith DW, Harkins KR, Knapp S (1991) Systemic endopolyploidy in Arabidopsis thaliana. Plant Physiol 96:985-989
44. Galitski T, Saldanha AJ, Styles CA, Lander ES, Fink GR (1999) Ploidy regulation of gene expression. Science 285:251-254
45. Gerlich D, Beaudouin J, Kalbfuss B, Daigle N, Eils R, Ellenberg J (2003) Global chromosome positions are transmitted through mitosis in mammalian cells. Cell 112:751-764
46. Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL (2004) Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. Plos Biology 2:1325-1339
47. Gotta M, Laroche T, Formenton A, Maillet L, Scherthan H, Gasser SM (1996) The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-Type Saccharomyces cerevisiae. J Cell Biol 134:1349-1363
48. Guacci V, Hogan E, Koshland D (1994) Chromosome condensation and sister chromatid pairing in budding yeast. J Cell Biol 125:517-530
49. HaseY, TrungKH, Matsunaga T, TanakaA (2006)Amutation in the uvi4 gene promotes progression of endo-reduplication and confers increased tolerance towards ultraviolet B light. Plant J 46:317-326
50. Heride C, Ricoul M, Kieu K, von Hase J, Guillemot V, Cremer C, Dubrana K, Sabatier L (2010) Distance between homologous chromosomes results from chromosome positioning constraints. J Cell Sci 123:4063-4075
51. Hiraoka Y, Dernburg AF, Parmelee SJ, Rykowski MC, Agard DA, Sedat JW (1993) The onset of homologous chromosome pairing during Drosophila melanogaster embryogenesis. J Cell Biol 120:591-600
52. Hochstrasser M, Mathog D, Gruenbaum Y, Saumweber H, Sedat JW (1986) Spatial organization of chromosomes in the salivary gland nuclei of Drosophila melanogaster. J Cell Biol 102:112-123
53. Ijdo JW, Wells RA, Baldini A, Reeders ST (1991) Improved telomere detection using a telomere repeat probe (TTAGGG)n generated by PCR. Nucleic Acids Res 19:4780
54. Jasencakova Z, Meister A, Walter J, Turner BM, Schubert I (2000) Histone H4 acetylation of euchromatin and heterochromatin is cell cycle dependent and correlated with replication rather than with transcription. Plant Cell 12:2087-2100
55. Jin QW, Fuchs J, Loidl J (2000) Centromere clustering is a major determinant of yeast interphase nuclear organization. J Cell Sci 113:1903-1912
56. Jovtchev G, Schubert V, Meister A, Barow M, Schubert I (2006) Nuclear DNA content and nuclear and cell volume are positively correlated in angiosperms. Cytogenet Genome Res 114:77-82
57. Jovtchev G, Watanabe K, Pecinka A, Rosin FM, Mette MF, Lam E, Schubert I (2008) Size and number of tandem repeat arrays can determine somatic homologous pairing of transgene loci mediated by epigenetic modifications in Arabidopsis thaliana nuclei. Chromosoma 117:267-276
58. Jovtchev G, Borisova BE, Kuhlmann M, Fuchs J, Watanabe K, Schubert I, Mette MF (2011) Pairing of lacO tandem repeats in Arabidopsis thaliana nuclei requires the presence of hypermethylated, large arrays at two chromosomal positions, but does not depend on H3-lysine-9-dimethylation. Chromosoma 120:609-619
59. Kato N, Lam E (2003) Chromatin of endoreduplicated pavement cells has greater range of movement than that of diploid guard cells in Arabidopsis thaliana. J Cell Sci 116:2195-2201
60. Kawabe A, Nasuda S (2005) Structure and genomic organization of centromeric repeats in Arabidopsis species. Mol Genet Genomics 272:593-602
61. Koehler D, Zakhartchenko V, Froenicke L, Stone G, Stanyon R, Wolf E, Cremer T, Brero A (2009) Changes of higher order chromatin arrangements during major genome activation in bovine preimplantation embryos. Exp Cell Res 315:2053-2063
62. Kondorosi E, Kondorosi A (2004) Endoreduplication and activation of the anaphase-promoting complex during symbiotic cell development. FEBS Lett 567:152-157
63. Kozubek S, Lukasova E, Jirsova P, Koutna I, Kozubek M, Ganova A, Bartova E, Falk M, Pasekova R (2002) 3D structure of the human genome: order in randomness. Chromosoma 111:321-331
64. Küpper K, Kolbl A, Biener D, Dittrich S, von Hase J, Thormeyer T, Fiegler H, Carter NP, Speicher MR, Cremer T, Cremer M (2007) Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116:285-306
65. Laloraya S, Guacci V, Koshland D (2000) Chromosomal addresses of the cohesin component Mcd1p. J Cell Biol 151:1047-1056
66. Lanctot C, Cheutin T, Cremer M, Cavalli G, Cremer T (2007) Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 8:104-115
67. Leiva-Neto JT, Grafi G, Sabelli PA, Dante RA, Woo YM, Maddock S, Gordon-Kamm WJ, Larkins BA (2004) A dominant negative mutant of cyclin-dependent kinase A reduces endoreduplication but not cell size or gene expression in maize endosperm. Plant Cell 16:1854-1869
68. Lermontova I, Schubert V, Fuchs J, Klatte S, Macas J, Schubert I (2006) Loading of Arabidopsis centromeric histone CENH3 occurs mainly during G2 and requires the presence of the histone fold domain. Plant Cell 18:2443-2451
69. Lermontova I, Fuchs J, Schubert V, Schubert I (2007) Loading time of the centromeric histone H3 variant differs between plants and animals. Chromosoma 116:507-510
70. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289-293
71. Louwers M, Bader R, Haring M, van Driel R, de Laat W, Stam M (2009) Tissue-And expression level-specific chromatin looping at maize b1 epialleles. Plant Cell 21:832-842
72. Lukasova E, Kozubek S, Kozubek M, Falk M, Amrichova J (2002) The 3D structure of human chromosomes in cell nuclei. Chromosome Res 10:535-548
73. Maestra B, De Jong JH, Shepherd K, Naranjo T (2002) Chromosome arrangement and behaviour of two rye homologous telosomes at the onset of meiosis in disomic wheat-5RL addition lines with and without the Ph1 locus. Chromosome Res 10:655-667
74. Maguire MP (1990) Sister chromatid cohesiveness: vital function, obscure mechanism. Biochem Cell Biol 68:1231-1242
75. Martinez-Perez E, Shaw P, Reader S, Aragon-Alcaide L, Miller T, Moore G (1999) Homologous chromosome pairing in wheat. J Cell Sci 112(Pt 11):1761-1769
76. Martinez-Perez E, Shaw PJ, Moore G (2000) Polyploidy induces centromere association. J Cell Biol 148:233-238
77. Martinez-Zapater JM, Estelle AM, Sommerville CR (1986) A highly repeated DNA sequence in Arabidopsis thaliana. Mol Gen Genet 204:4417-4423
78. Mateos-Langerak J, Bohn M, de Leeuw W, Giromus O, Manders EM, Verschure PJ, Indemans MH, Gierman HJ, Heermann DW, van Driel R, Goetze S (2009) Spatially confined folding of chromatin in the interphase nucleus. Proc Natl Acad Sci USA 106:3812-3817
79. Mathieu O, Jasencakova Z, Vaillant I, Gendrel AV, Colot V, Schubert I, Tourmente S (2003) Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell 15:2929-2939
80. McNally JG, Mazza D (2010) Fractal geometry in the nucleus. EMBO J 29:2-3
81. Melaragno JE, Mehrotra B, Coleman AW (1993) Relationship between endopolyploidy and cell size in epidermal tissue of Arabidopsis. Plant Cell 5:1661-1668
82. Meshorer E, Misteli T (2006) Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol 7:540-546
83. Mirny LA (2011) The fractal globule as a model of chromatin architecture in the cell. Chromosome Res 19:37-51
84. Misteli T (2007) Beyond the sequence: cellular organization of genome function. Cell 128:787-800
85. Misteli T (2009) Self-organization in the genome. Proc Natl Acad Sci USA 106:6885-6886
86. Misteli T, Soutoglou E (2009) The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat Rev Mol Cell Biol 10:243-254
87. Miyazaki WY, Orr-Weaver TL (1994) Sister-chromatid cohesion in mitosis and meiosis. Annu Rev Genet 28:167-187
88. Munkel C, Eils R, Dietzel S, Zink D, Mehring C, Wedemann G, Cremer T, Langowski J (1999) Compartmentalization of interphase chromosomes observed in simulation and experiment. J Mol Biol 285:1053-1065
89. Nafati M, Cheniclet C, Hernould M, Do PT, Fernie AR, Chevalier C, Gevaudant F (2011) The specific overexpression of a cyclindependent kinase inhibitor in tomato fruit mesocarp cells uncouples endoreduplication and cell growth. Plant J 65:543-556
90. Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, Jiang J (2003) Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163:1221-1225
91. Nagele RG, Freeman T, McMorrow L, Thomson Z, Kitson-Wind K, Lee H (1999) Chromosomes exhibit preferential positioning in nuclei of quiescent human cells. J Cell Sci 112:525-535
92. Nagele RG, Velasco AQ, Anderson WJ, McMahon DJ, Thomson Z, Fazekas J, Wind K, Lee H (2001) Telomere associations in interphase nuclei: possible role in maintenance of interphase chromosome topology. J Cell Sci 114:377-388
93. Nagl W (1976) DNA endoreduplication and polyteny understood as evolutionary strategies. Nature 261:614-615
94. Nemeth A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Peterfia B, Solovei I, Cremer T, Dopazo J, Langst G (2010) Initial genomics of the human nucleolus. PLoS Genet 6:e1000889
95. Neusser M, Schubel V, Koch A, Cremer T, Muller S (2007) Evolutionarily conserved, cell type and species-specific higher order chromatin arrangements in interphase nuclei of primates. Chromosoma 116:307-320
96. Onn I, Heidinger-Pauli JM, Guacci V, Ünal E, Koshland DE (2008) Sister chromatid cohesion: A simple concept with a complex reality. Annu Rev Cell Dev Biol 24:105-129
97. Papantonis A, Cook PR (2010) Genome architecture and the role of transcription. Curr Opin Cell Biol 22:271-276
98. Parada LA, Sotiriou S, Misteli T (2004) Spatial genome organization. Exp Cell Res 296:64-70
99. Pavet V, Quintero C, Cecchini NM, Rosa AL, Alvarez ME (2006) Arabidopsis displays centromeric DNA hypomethylation and cytological alterations of heterochromatin upon attack by Pseudomonas syringae. Mol Plant Microbe Interact 19:577-587
100. Pecinka A, Schubert V, Meister A, Kreth G, Klatte M, Lysak MA, Fuchs J, Schubert I (2004) Chromosome territory arrangement and homologous pairing in nuclei of Arabidopsis thaliana are predominantly random except for NOR-bearing chromosomes. Chromosoma 113:258-269
101. Pecinka A, Kato N, Meister A, Probst AV, Schubert I, Lam E (2005) Tandem repetitive transgenes and fluorescent chromatin tags alter local interphase chromosome arrangement in Arabidopsis thaliana. J Cell Sci 118:3751-3758
102. Pecinka A, Dinh HQ, Baubec T, RosaM, Lettner N,Mittelsten Scheid O (2010) Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 22:3118-3129
103. Prieto P, Santos AP, Moore G, Shaw P (2004) Chromosomes associate premeiotically and in xylem vessel cells via their telomeres and centromeres in diploid rice (Oryza sativa). Chromosoma 112:300-307
104. Rabl C (1885) Über Zelltheilung. Morph Jb 10:214-330
105. Radziejwoski A, Vlieghe K, Lammens T, Berckmans B, Maes S, Jansen MA, Knappe C, Albert A, Seidlitz HK, Bahnweg G, Inze D, De Veylder L (2011) Atypical E2F activity coordinates PHR1 photolyase gene transcription with endoreduplication onset. EMBO J 30:355-363
106. Rajapakse I, Perlman MD, Scalzo D, Kooperberg C, Groudine M, Kosak ST (2009) The emergence of lineage-specific chromosomal topologies from coordinate gene regulation. Proc Natl Acad Sci USA 106:6679-6684
107. Saez-Vasquez J, Gadal O (2010) Genome organization and function: A view from yeast and Arabidopsis. Molecular Plant 3:678-690
108. Santaguida S, Musacchio A (2009) The life and miracles of kinetochores. EMBO J 28:2511-2531
109. Scheuermann MO, Tajbakhsh J, Kurz A, Saracoglu K, Eils R, Lichter P (2004) Topology of genes and nontranscribed sequences in human interphase nuclei. Exp Cell Res 301:266-279
110. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei CL, Ruan Y, Bieker JJ, Fraser P (2010) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42:53-61
111. Schubert V (2011) No neocentric activity on Aegilops markgrafii chromosome E. Cytogenet Genome Res 132:100-104
112. Schubert I, Shaw P (2011) Organization and dynamics of plant interphase chromosomes. Trends Plant Sci 16:273-281
113. Schubert I, Fransz PF, Fuchs J, De Jong JH (2001) Chromosome painting in plants. Methods Cell Sci 23:57-69
114. Schubert V, Klatte M, Pecinka A, Meister A, Jasencakova Z, Schubert I (2006) Sister chromatids are often incompletely aligned in meristematic and endopolyploid interphase nuclei of Arabidopsis thaliana. Genetics 172:467-475
115. Schubert V, Kim YM, Berr A, Fuchs J, Meister A, Marschner S, Schubert I (2007) Random homologous pairing and incomplete sister chromatid alignment are common in angiosperm interphase nuclei. Mol Genet Genomics 278:167-176
116. Schubert V, Kim YM, Schubert I (2008) Arabidopsis sister chromatids often show complete alignment or separation along a 1.2-Mb euchromatic region but no cohesion "hot spots". Chromosoma 117:261-266
117. Schubert V, Meister A, Tsujimoto H, Endo TR, Houben A (2011) Similar rye A and B chromosome organization in meristematic and differentiated interphase nuclei. Chromosome Res 19:645-655
118. Selig S, Okumura K, Ward DC, Cedar H (1992) Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J 11:1217-1225
119. Shibata F, Murata M (2004) Differential localization of the centromerespecific proteins in the major centromeric satellite of Arabidopsis thaliana. J Cell Sci 117:2963-2970
120. Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21:6549-6559
121. Sugimoto-Shirasu K, Roberts K (2003) "Big it up": endoreduplication and cell-size control in plants. Curr Opin Plant Biol 6:544-553
122. Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S (2002) Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 14:1053-1066
123. Tessadori F, Chupeau MC, Chupeau Y, Knip M, Germann S, van Driel R, Fransz P, Gaudin V (2007a) Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. J Cell Sci 120:1200-1208
124. Tessadori F, Schulkes RK, van Driel R, Fransz P (2007b) Lightregulated large-scale reorganization of chromatin during the floral transition in Arabidopsis. Plant J 50:848-857
125. Tessadori F, van Zanten M, Pavlova P, Clifton R, Pontvianne F, Snoek LB, Millenaar FF, Schulkes RK, van Driel R, Voesenek LA, Spillane C, Pikaard CS, Fransz P, Peeters AJ (2009) Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet 5:e1000638
126. 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
127. Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, Nieuwland M, Simonis M, de Laat W, van Lohuizen M, van Steensel B (2011) Interactions among polycomb domains are guided by chromosome architecture. PLoS Genet 7:e1001343
128. Uhlmann F (2008) Molecular biology: cohesin branches out. Nature 451:777-778
129. van Zanten M, Tessadori F, McLoughlin F, Smith R, Millenaar FF, van Driel R, Voesenek LA, Peeters AJ, Fransz P (2010) Photoreceptors CRYTOCHROME2 and phytochrome B control chromatin compaction in Arabidopsis. Plant Physiol 154:1686-1696
130. van Zanten M, Koini MA, Geyer R, Liu Y, Brambilla V, Bartels D, Koornneef M, Fransz P, Soppe WJ (2011) Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation. Proc Natl Acad Sci USA 108:20219-20224
131. Verdaasdonk JS, Bloom K (2011) Centromeres: unique chromatin structures that drive chromosome segregation. Nat Rev Mol Cell Biol 12:320-332
132. Volpi EV, Sheer D, Uhlmann F (2001) Cohesion, but not too close. Curr Biol 11:R378
133. 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
134. Ward PB (2002) FISH probes and labelling techniques. In: Beatty BS, Mai J, Squire J (eds) FISH: A practical approach (practical approach series: 260). Oxford University Press, Oxford, pp 5-28
135. Watanabe K, Pacher M, Dukowic S, Schubert V, Puchta H, Schubert I (2009) The structural maintenance of chromosomes 5/6 complex promotes sister chromatid alignment and homologous recombination after DNA damage in Arabidopsis thaliana. Plant Cell 21:2688-2699
136. Wegel E, Shaw P (2005) Gene activation and deactivation related changes in the three-dimensional structure of chromatin. Chromosoma 114:331-337
137. Wegel E, Vallejos RH, Christou P, Stoger E, Shaw P (2005) Largescale chromatin decondensation induced in a developmentally activated transgene locus. J Cell Sci 118:1021-1031
138. Wegel E, Koumproglou R, Shaw P, Osbourn A (2009) Cell typespecific chromatin decondensation of a metabolic gene cluster in oats. Plant Cell 21:3926-3936
139. 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
140. Zhimulev IF, Belyaeva ES, Semeshin VF, Koryakov DE, Demakov SA, Demakova OV, Pokholkova GV, Andreyeva EN (2004) Polytene chromosomes: 70 years of genetic research. Intern Rev Cytol 241:203-275
141. Zink D, Amaral MD, Englmann A, Lang S, Clarke LA, Rudolph C, Alt F, Luther K, Braz C, Sadoni N, Rosenecker J, Schindelhauer D (2004) Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166:815-825