Chromatin-driven behavior of topologically associating domains

Journal of Molecular Biology

Volumn 427, Issue 3, 2015, Pages 608-625

  Ciabrelli, Filippo ^a   Cavalli, Giacomo ^a  

^a INSTITUTE OF HUMAN GENETICS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; CHROMATIN; CHROMATIN CONDENSATION; CONSTITUTIVE HETEROCHROMATIN; DNA REPLICATION; DNA REPLICATION TIMING; DROSOPHILA MELANOGASTER; ENHANCER REGION; GENE ACTIVATION; GENE EXPRESSION; GENETIC ASSOCIATION; GENOME ANALYSIS; HISTONE MODIFICATION; HOUSEKEEPING GENE; INTRON; NONHUMAN; NUCLEAR LAMINA; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; TOPOLOGICALLY ASSOCIATING DOMAIN; TRANSCRIPTION INITIATION; CELL NUCLEUS; EPIGENETICS; GENETICS; GENOME; HUMAN;

METAZOA;

CHROMATIN;

ANIMALS; CELL NUCLEUS; CHROMATIN; EPIGENOMICS; GENOME; HUMANS;

EID: 84925636391     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2014.09.013     Document Type: Review

References (191)

1. T. Cremer, and M. Cremer Chromosome territories Cold Spring Harb Perspect Biol 2 2010 a003889
2. E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, and Telling Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
3. T. Sexton, E. Yaffe, E. Kenigsberg, F. Bantignies, B. Leblanc, and M. Hoichman Three-dimensional folding and functional organization principles of the Drosophila genome Cell 148 2012 458 472
4. E.P. Nora, B.R. Lajoie, E.G. Schulz, L. Giorgetti, I. Okamoto, and N. Servant Spatial partitioning of the regulatory landscape of the X-inactivation centre Nature 485 2012 381 385
5. J.R. Dixon, S. Selvaraj, F. Yue, A. Kim, and Y. Li Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 485 2012 376 380
6. D. Cmarko, P.J. Verschure, T.E. Martin, M.E. Dahmus, S. Krause, and X.D. Fu Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection Mol Biol Cell 10 1999 211 223
7. S. Feng, S.J. Cokus, V. Schubert, J. Zhai, M. Pellegrini, and S.E. Jacobsen Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis Mol Cell 55 2014 694 707
8. S. Grob, M.W. Schmid, and U. Grossniklaus Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila Mol Cell 55 2014 678 693
9. G. Moissiard, S.J. Cokus, J. Cary, S. Feng, A.C. Billi, and H. Stroud MORC family ATPases required for heterochromatin condensation and gene silencing Science 336 2012 1448 1451
10. H. Tanizawa, O. Iwasaki, A. Tanaka, J.R. Capizzi, P. Wickramasinghe, and M. Lee Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation Nucleic Acids Res 38 2010 8164 8177
11. H. Tjong, K. Gong, L. Chen, and F. Alber Physical tethering and volume exclusion determine higher-order genome organization in budding yeast Genome Res 22 2012 1295 1305
12. L.D. Hurst, C. Pal, and M.J. Lercher The evolutionary dynamics of eukaryotic gene order Nat Rev Genet 5 2004 299 310
13. H. Caron, B. van Schaik, M. van der Mee, F. Baas, G. Riggins, and P. van Sluis The human transcriptome map: clustering of highly expressed genes in chromosomal domains Science 291 2001 1289 1292
14. H.J. Gierman, M.H. Indemans, J. Koster, S. Goetze, J. Seppen, and D. Geerts Domain-wide regulation of gene expression in the human genome Genome Res 17 2007 1286 1295
15. P.T. Spellman, and G.M. Rubin Evidence for large domains of similarly expressed genes in the Drosophila genome J Biol 1 2002 5
16. J. Ernst, and M. Kellis Discovery and characterization of chromatin states for systematic annotation of the human genome Nat Biotechnol 28 2010 817 825
17. P.V. Kharchenko, A.A. Alekseyenko, Y.B. Schwartz, A. Minoda, N.C. Riddle, and J. Ernst Comprehensive analysis of the chromatin landscape in Drosophila melanogaster Nature 471 2011 480 485
18. J. Ernst, P. Kheradpour, T.S. Mikkelsen, N. Shoresh, L.D. Ward, and C.B. Epstein Mapping and analysis of chromatin state dynamics in nine human cell types Nature 473 2011 43 49
19. O. Ram, A. Goren, I. Amit, N. Shoresh, N. Yosef, and J. Ernst Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells Cell 147 2011 1628 1639
20. J. Zhu, M. Adli, J.Y. Zou, G. Verstappen, M. Coyne, and X. Zhang Genome-wide chromatin state transitions associated with developmental and environmental cues Cell 152 2013 642 654
21. H. Julienne, A. Zoufir, B. Audit, and A. Arneodo Human genome replication proceeds through four chromatin states PLoS Comput Biol 9 2013 e1003233
22. T. Liu, A. Rechtsteiner, T.A. Egelhofer, A. Vielle, I. Latorre, and M.S. Cheung Broad chromosomal domains of histone modification patterns in C. elegans Genome Res 21 2011 227 236
23. G.J. Filion, J.G. van Bemmel, U. Braunschweig, W. Talhout, J. Kind, and L.D. Ward Systematic protein location mapping reveals five principal chromatin types in Drosophila cells Cell 143 2010 212 224
24. Y. Shen, F. Yue, D.F. McCleary, Z. Ye, L. Edsall, and S. Kuan A map of the cis-regulatory sequences in the mouse genome Nature 488 2012 116 120
25. X. Lan, H. Witt, K. Katsumura, Z. Ye, Q. Wang, and E.H. Bresnick Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages Nucleic Acids Res 40 2012 7690 7704
26. M.B. Gerstein, A. Kundaje, M. Hariharan, S.G. Landt, K.K. Yan, and C. Cheng Architecture of the human regulatory network derived from ENCODE data Nature 489 2012 91 100
27. E. de Wit, and W. de Laat A decade of 3C technologies: insights into nuclear organization Genes Dev 26 2012 11 24
28. J. Dekker, M.A. Marti-Renom, and L.A. Mirny Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data Nat Rev Genet 14 2013 390 403
29. J. Rouquette, C. Cremer, T. Cremer, and S. Fakan Functional nuclear architecture studied by microscopy: present and future Int Rev Cell Mol Biol 282 2010 1 90
30. N. Harmston, and B. Lenhard Chromatin and epigenetic features of long-range gene regulation Nucleic Acids Res 41 2013 7185 7199
31. R.E. Thurman, E. Rynes, R. Humbert, J. Vierstra, M.T. Maurano, and E. Haugen The accessible chromatin landscape of the human genome Nature 489 2012 75 82
32. M.A. Nobrega, I. Ovcharenko, V. Afzal, and E.M. Rubin Scanning human gene deserts for long-range enhancers Science 302 2003 413
33. H. Kikuta, M. Laplante, P. Navratilova, A.Z. Komisarczuk, P.G. Engstrom, and D. Fredman Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates Genome Res 17 2007 545 555
34. D. Noordermeer, M. Leleu, E. Splinter, J. Rougemont, W. De Laat, and D. Duboule The dynamic architecture of Hox gene clusters Science 334 2011 222 225
35. G. Andrey, T. Montavon, B. Mascrez, F. Gonzalez, D. Noordermeer, and M. Leleu A switch between topological domains underlies HoxD genes collinearity in mouse limbs Science 340 2013 1234167
36. T. Nagano, Y. Lubling, T.J. Stevens, S. Schoenfelder, E. Yaffe, and W. Dean Single-cell Hi-C reveals cell-to-cell variability in chromosome structure Nature 502 2013 59 64
37. F. Jin, Y. Li, J.R. Dixon, S. Selvaraj, Z. Ye, and A.Y. Lee A high-resolution map of the three-dimensional chromatin interactome in human cells Nature 503 2013 290 294
38. K.R. Kieffer-Kwon, Z. Tang, E. Mathe, J. Qian, M.H. Sung, and G. Li Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation Cell 155 2013 1507 1520
39. G. Li, X. Ruan, R.K. Auerbach, K.S. Sandhu, M. Zheng, and P. Wang Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation Cell 148 2012 84 98
40. S.M. Tan-Wong, J.D. French, N.J. Proudfoot, and M.A. Brown Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene Proc Natl Acad Sci U S A 105 2008 5160 5165
41. D. O'Reilly, and D.R. Greaves Cell-type-specific expression of the human CD68 gene is associated with changes in Pol II phosphorylation and short-range intrachromosomal gene looping Genomics 90 2007 407 415
42. K.E. Cullen, M.P. Kladde, and M.A. Seyfred Interaction between transcription regulatory regions of prolactin chromatin Science 261 1993 203 206
43. C.S. Osborne, L. Chakalova, K.E. Brown, D. Carter, A. Horton, and E. Debrand Active genes dynamically colocalize to shared sites of ongoing transcription Nat Genet 36 2004 1065 1071
44. B. Tolhuis, R.J. Palstra, E. Splinter, F. Grosveld, and W. de Laat Looping and interaction between hypersensitive sites in the active beta-globin locus Mol Cell 10 2002 1453 1465
45. G.A. Maston, S.K. Evans, and M.R. Green Transcriptional regulatory elements in the human genome Annu Rev Genomics Hum Genet 7 2006 29 59
46. R. Drissen, R.J. Palstra, N. Gillemans, E. Splinter, F. Grosveld, and S. Philipsen The active spatial organization of the beta-globin locus requires the transcription factor EKLF Genes Dev 18 2004 2485 2490
47. M.H. Kagey, J.J. Newman, S. Bilodeau, Y. Zhan, D.A. Orlando, and N.L. van Berkum Mediator and cohesin connect gene expression and chromatin architecture Nature 467 2010 430 435
48. S.C. Degner, J. Verma-Gaur, T.P. Wong, C. Bossen, G.M. Iverson, and A. Torkamani CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells Proc Natl Acad Sci U S A 108 2011 9566 9571
49. I. Chepelev, G. Wei, D. Wangsa, Q. Tang, and K. Zhao Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization Cell Res 22 2012 490 503
50. H.G. Roider, B. Lenhard, A. Kanhere, S.A. Haas, and M. Vingron CpG-depleted promoters harbor tissue-specific transcription factor binding signals-implications for motif overrepresentation analyses Nucleic Acids Res 37 2009 6305 6315
51. T. Montavon, N. Soshnikova, B. Mascrez, E. Joye, L. Thevenet, and E. Splinter A regulatory archipelago controls Hox genes transcription in digits Cell 147 2011 1132 1145
52. Y. Zhang, C.H. Wong, R.Y. Birnbaum, G. Li, R. Favaro, and C.Y. Ngan Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations Nature 504 2013 306 310
53. K.M. Lower, J.R. Hughes, M. De Gobbi, S. Henderson, V. Viprakasit, and C. Fisher Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition Proc Natl Acad Sci U S A 106 2009 21771 21776
54. J. Yang, and V.G. Corces Insulators, long-range interactions, and genome function Curr Opin Genet Dev 22 2012 86 92
55. Y. Ghavi-Helm, F.A. Klein, T. Pakozdl, L. Ciglar, D. Noordermeer, and W. Huber Enhancer loops appear stable during development and are associated with paused polymerase 2014 Nature
56. D. Noordermeer, E. de Wit, P. Klous, H. van de Werken, M. Simonis, and M. Lopez-Jones Variegated gene expression caused by cell-specific long-range DNA interactions Nat Cell Biol 13 2011 944 951
57. H.B. Li, K. Ohno, H. Gui, and V. Pirrotta Insulators target active genes to transcription factories and polycomb-repressed genes to polycomb bodies PLoS Genet 9 2013 e1003436
58. D.A. Jackson, A.B. Hassan, R.J. Errington, and P.R. Cook Visualization of focal sites of transcription within human nuclei EMBO J 12 1993 1059 1065
59. E. Apostolou, and D. Thanos Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression Cell 134 2008 85 96
60. E. de Wit, B.A. Bouwman, Y. Zhu, P. Klous, E. Splinter, and M.J. Verstegen The pluripotent genome in three dimensions is shaped around pluripotency factors Nature 501 2013 227 231
61. Q. Hu, Y.S. Kwon, E. Nunez, M.D. Cardamone, K.R. Hutt, and K.A. Ohgi Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules Proc Natl Acad Sci U S A 105 2008 19199 19204
62. S. Schoenfelder, T. Sexton, L. Chakalova, N.F. Cope, A. Horton, and S. Andrews Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells Nat Genet 42 2010 53 61
63. C.H. Eskiw, and P. Fraser Ultrastructural study of transcription factories in mouse erythroblasts J Cell Sci 124 2011 3676 3683
64. C.H. Eskiw, A. Rapp, D.R. Carter, and P.R. Cook RNA polymerase II activity is located on the surface of protein-rich transcription factories J Cell Sci 121 2008 1999 2007
65. J.A. Mitchell, and P. Fraser Transcription factories are nuclear subcompartments that remain in the absence of transcription Genes Dev 22 2008 20 25
66. F. Bantignies, V. Roure, I. Comet, B. Leblanc, B. Schuettengruber, and J. Bonnet Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila Cell 144 2011 214 226
67. B. Tolhuis, M. Blom, R.M. Kerkhoven, L. Pagie, H. Teunissen, and M. Nieuwland Interactions among Polycomb domains are guided by chromosome architecture PLoS Genet 7 2011 e1001343
68. A. Nemeth, and G. Langst Genome organization in and around the nucleolus Trends Genet 27 2011 149 156
69. M. Kalmarova, E. Smirnov, M. Masata, K. Koberna, A. Ligasova, and A. Popov Positioning of NORs and NOR-bearing chromosomes in relation to nucleoli J Struct Biol 160 2007 49 56
70. C.N. Shiue, R.G. Berkson, and A.P. Wright c-Myc induces changes in higher order rDNA structure on stimulation of quiescent cells Oncogene 28 2009 1833 1842
71. H.A. Foster, and J.M. Bridger The genome and the nucleus: a marriage made by evolution Genome organisation and nuclear architecture Chromosoma 114 2005 212 229
72. S.T. Kosak, D. Scalzo, S.V. Alworth, F. Li, S. Palmer, and T. Enver Coordinate gene regulation during hematopoiesis is related to genomic organization PLoS Biol 5 2007 e309
73. J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague, and W.A. Bickmore Differences in the localization and morphology of chromosomes in the human nucleus J Cell Biol 145 1999 1119 1131
74. E.B. Lewis A gene complex controlling segmentation in Drosophila Nature 276 1978 565 570
75. Z. Shao, F. Raible, R. Mollaaghababa, J.R. Guyon, C.T. Wu, and W. Bender Stabilization of chromatin structure by PRC1, a Polycomb complex Cell 98 1999 37 46
76. J. Muller, C.M. Hart, N.J. Francis, M.L. Vargas, A. Sengupta, and B. Wild Histone methyltransferase activity of a Drosophila Polycomb group repressor complex Cell 111 2002 197 208
77. B. Tolhuis, E. de Wit, I. Muijrers, H. Teunissen, W. Talhout, and B. van Steensel Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster Nat Genet 38 2006 694 699
78. N. Negre, J. Hennetin, L.V. Sun, S. Lavrov, M. Bellis, and K.P. White Chromosomal distribution of PcG proteins during Drosophila development PLoS Biol 4 2006 e170
79. B. Schuettengruber, M. Ganapathi, B. Leblanc, M. Portoso, R. Jaschek, and B. Tolhuis Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos PLoS Biol 7 2009 e13
80. B. Schuettengruber, and G. Cavalli Recruitment of polycomb group complexes and their role in the dynamic regulation of cell fate choice Development 136 2009 3531 3542
81. J.A. Kassis, and J.L. Brown Polycomb group response elements in Drosophila and vertebrates Adv Genet 81 2013 83 118
82. Y.B. Schwartz, and V. Pirrotta A new world of Polycombs: unexpected partnerships and emerging functions Nat Rev Genet 14 2013 853 864
83. W.A. Bickmore, and B. van Steensel Genome architecture: domain organization of interphase chromosomes Cell 152 2013 1270 1284
84. J. Schlossherr, H. Eggert, R. Paro, S. Cremer, and R.S. Jack Gene inactivation in Drosophila mediated by the Polycomb gene product or by position-effect variegation does not involve major changes in the accessibility of the chromatin fibre Mol Gen Genet 243 1994 453 462
85. A. Boivin, and J.M. Dura In vivo chromatin accessibility correlates with gene silencing in Drosophila Genetics 150 1998 1539 1549
86. M. Marchetti, L. Fanti, M. Berloco, and S. Pimpinelli Differential expression of the Drosophila BX-C in polytene chromosomes in cells of larval fat bodies: a cytological approach to identifying in vivo targets of the homeotic Ubx, Abd-A and Abd-B proteins Development 130 2003 3683 3689
87. D. Zink, and R. Paro Drosophila Polycomb-group regulated chromatin inhibits the accessibility of a trans-activator to its target DNA EMBO J 14 1995 5660 5671
88. D.P. Fitzgerald, and W. Bender Polycomb group repression reduces DNA accessibility Mol Cell Biol 21 2001 6585 6597
89. N.J. Francis, R.E. Kingston, and C.L. Woodcock Chromatin compaction by a polycomb group protein complex Science 306 2004 1574 1577
90. I.F. King, R.B. Emmons, N.J. Francis, B. Wild, J. Muller, and R.E. Kingston Analysis of a polycomb group protein defines regions that link repressive activity on nucleosomal templates to in vivo function Mol Cell Biol 25 2005 6578 6591
91. D.J. Grau, B.A. Chapman, J.D. Garlick, M. Borowsky, N.J. Francis, and R.E. Kingston Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge Genes Dev 25 2011 2210 2221
92. K. Isono, T.A. Endo, M. Ku, D. Yamada, R. Suzuki, and J. Sharif SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing Dev Cell 26 2013 565 577
93. R. Eskeland, M. Leeb, G.R. Grimes, C. Kress, S. Boyle, and D. Sproul Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination Mol Cell 38 2010 452 464
94. R. Terranova, S. Yokobayashi, M.B. Stadler, A.P. Otte, M. van Lohuizen, and S.H. Orkin Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos Dev Cell 15 2008 668 679
95. R. Margueron, G. Li, K. Sarma, A. Blais, J. Zavadil, and C.L. Woodcock Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms Mol Cell 32 2008 503 518
96. W. Yuan, T. Wu, H. Fu, C. Dai, H. Wu, and N. Liu Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation Science 337 2012 971 975
97. F. Cleard, Y. Moshkin, F. Karch, and R.K. Maeda Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification Nat Genet 38 2006 931 935
98. C. Lanzuolo, V. Roure, J. Dekker, F. Bantignies, and V. Orlando Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex Nat Cell Biol 9 2007 1167 1174
99. M. Ronshaugen, and M. Levine Visualization of trans-homolog enhancer-promoter interactions at the Abd-B Hox locus in the Drosophila embryo Dev Cell 7 2004 925 932
100. I. Comet, B. Schuettengruber, T. Sexton, and G. Cavalli A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber Proc Natl Acad Sci U S A 108 2011 2294 2299
101. P.W. Holland Evolution of homeobox genes Wiley Interdiscip Rev Dev Biol 2 2013 31 45
102. M.A. Ferraiuolo, M. Rousseau, C. Miyamoto, S. Shenker, X.Q. Wang, and M.B. Nadler The three-dimensional architecture of Hox cluster silencing Nucleic Acids Res 38 2010 7472 7484
103. J. Fraser, M. Rousseau, S. Shenker, M.A. Ferraiuolo, Y. Hayashizaki, and M. Blanchette Chromatin conformation signatures of cellular differentiation Genome Biol 10 2009 R37
104. M. Rousseau, J.L. Crutchley, H. Miura, M. Suderman, M. Blanchette, and J. Dostie Hox in motion: tracking HoxA cluster conformation during differentiation Nucleic Acids Res 42 2014 1524 1540
105. V.K. Tiwari, K.M. McGarvey, J.D. Licchesi, J.E. Ohm, J.G. Herman, and D. Schubeler PcG proteins, DNA methylation, and gene repression by chromatin looping PLoS Biol 6 2008 2911 2927
106. S. Kheradmand Kia, P. Solaimani Kartalaei, E. Farahbakhshian, and F. Pourfarzad EZH2-dependent chromatin looping controls INK4a and INK4b, but not ARF, during human progenitor cell differentiation and cellular senescence Epigenetics Chromatin 2 2009 16
107. T. Kondo, K. Isono, K. Kondo, T.A. Endo, S. Itohara, and M. Vidal Polycomb Potentiates Meis2 Activation in Midbrain by Mediating Interaction of the Promoter with a Tissue-Specific Enhancer Dev Cell 2013
108. J. Vazquez, M. Muller, V. Pirrotta, and J.W. Sedat The Mcp element mediates stable long-range chromosome-chromosome interactions in Drosophila Mol Biol Cell 17 2006 2158 2165
109. F. Bantignies, C. Grimaud, S. Lavrov, M. Gabut, and G. Cavalli Inheritance of Polycomb-dependent chromosomal interactions in Drosophila Genes Dev 17 2003 2406 2420
110. H.B. Li, M. Muller, I.A. Bahechar, O. Kyrchanova, K. Ohno, and P. Georgiev Insulators, not Polycomb response elements, are required for long-range interactions between Polycomb targets in Drosophila melanogaster Mol Cell Biol 31 2011 616 625
111. V.K. Tiwari, L. Cope, K.M. McGarvey, J.E. Ohm, and S.B. Baylin A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations Genome Res 18 2008 1171 1179
112. C. Grimaud, F. Bantignies, M. Pal-Bhadra, P. Ghana, U. Bhadra, and G. Cavalli RNAi components are required for nuclear clustering of Polycomb group response elements Cell 124 2006 957 971
113. T. Cheutin, and G. Cavalli Progressive polycomb assembly on H3K27me3 compartments generates polycomb bodies with developmentally regulated motion PLoS Genet 8 2012 e1002465
114. T. Cheutin, and G. Cavalli Polycomb silencing: from linear chromatin domains to 3D chromosome folding Curr Opin Genet Dev 25C 2014 30 37
115. A.J. Saurin, C. Shiels, J. Williamson, D.P. Satijn, A.P. Otte, and D. Sheer The human polycomb group complex associates with pericentromeric heterochromatin to form a novel nuclear domain J Cell Biol 142 1998 887 898
116. M. Denholtz, G. Bonora, C. Chronis, E. Splinter, W. de Laat, and J. Ernst Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization Cell Stem Cell 13 2013 602 616
117. J.G. van Bemmel, G.J. Filion, A. Rosado, W. Talhout, M. de Haas, and T. van Welsem A network model of the molecular organization of chromatin in Drosophila Mol Cell 49 2013 759 771
118. D.T. Brown Histone H1 and the dynamic regulation of chromatin function Biochem Cell Biol 81 2003 221 227
119. C. Hou, L. Li, Z.S. Qin, and V.G. Corces Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains Mol Cell 48 2012 471 484
120. P. Pascual-Garcia, and M. Capelson Nuclear pores as versatile platforms for gene regulation Curr Opin Genet Dev 25C 2014 110 117
121. A. Mattout-Drubezki, and Y. Gruenbaum Dynamic interactions of nuclear lamina proteins with chromatin and transcriptional machinery Cell Mol Life Sci 60 2003 2053 2063
122. A. Munoz-Alarcon, M. Pavlovic, J. Wismar, B. Schmitt, M. Eriksson, and P. Kylsten Characterization of lamin mutation phenotypes in Drosophila and comparison to human laminopathies PLoS One 2 2007 e532
123. H.J. Worman Nuclear lamins and laminopathies J Pathol 226 2012 316 325
124. M. Prokocimer, R. Barkan, and Y. Gruenbaum Hutchinson-Gilford progeria syndrome through the lens of transcription Aging Cell 12 2013 533 543
125. J.G. van Bemmel, L. Pagie, U. Braunschweig, W. Brugman, W. Meuleman, and R.M. Kerkhoven The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome PLoS One 5 2010 e15013
126. L. Guelen, L. Pagie, E. Brasset, W. Meuleman, M.B. Faza, and W. Talhout Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions Nature 453 2008 948 951
127. D. Peric-Hupkes, W. Meuleman, L. Pagie, S.W. Bruggeman, I. Solovei, and W. Brugman Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation Mol Cell 38 2010 603 613
128. H. Pickersgill, B. Kalverda, E. de Wit, W. Talhout, M. Fornerod, and B. van Steensel Characterization of the Drosophila melanogaster genome at the nuclear lamina Nat Genet 38 2006 1005 1014
129. J. Kind, L. Pagie, H. Ortabozkoyun, S. Boyle, S.S. de Vries, and H. Janssen Single-cell dynamics of genome-nuclear lamina interactions Cell 153 2013 178 192
130. J. Kind, and B. van Steensel Genome-nuclear lamina interactions and gene regulation Curr Opin Cell Biol 22 2010 320 325
131. Y.Y. Shevelyov, S.A. Lavrov, L.M. Mikhaylova, I.D. Nurminsky, R.J. Kulathinal, and K.S. Egorova The B-type lamin is required for somatic repression of testis-specific gene clusters Proc Natl Acad Sci U S A 106 2009 3282 3287
132. M. Kohwi, J.R. Lupton, S.L. Lai, M.R. Miller, and C.Q. Doe Developmentally regulated subnuclear genome reorganization restricts neural progenitor competence in Drosophila Cell 152 2013 97 108
133. P. Meister, B.D. Towbin, B.L. Pike, A. Ponti, and S.M. Gasser The spatial dynamics of tissue-specific promoters during C. elegans development Genes Dev 24 2010 766 782
134. W. Meuleman, D. Peric-Hupkes, J. Kind, J.B. Beaudry, L. Pagie, and M. Kellis Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence Genome Res 23 2013 270 280
135. B.C. Milon, H. Cheng, M.V. Tselebrovsky, S.A. Lavrov, V.V. Nenasheva, and E.A. Mikhaleva Role of histone deacetylases in gene regulation at nuclear lamina PLoS One 7 2012 e49692
136. R. Somech, S. Shaklai, O. Geller, N. Amariglio, A.J. Simon, and G. Rechavi The nuclear-envelope protein and transcriptional repressor LAP2beta interacts with HDAC3 at the nuclear periphery, and induces histone H4 deacetylation J Cell Sci 118 2005 4017 4025
137. J.M. Zullo, I.A. Demarco, R. Pique-Regi, D.J. Gaffney, C.B. Epstein, and C.J. Spooner DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina Cell 149 2012 1474 1487
138. J. Demmerle, A.J. Koch, and J.M. Holaska The nuclear envelope protein emerin binds directly to histone deacetylase 3 (HDAC3) and activates HDAC3 activity J Biol Chem 287 2012 22080 22088
139. S. Bhaskara, B.J. Chyla, J.M. Amann, S.K. Knutson, D. Cortez, and Z.W. Sun Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control Mol Cell 30 2008 61 72
140. B. Wen, H. Wu, Y. Shinkai, R.A. Irizarry, and A.P. Feinberg Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells Nat Genet 41 2009 246 250
141. B.D. Towbin, C. Gonzalez-Aguilera, R. Sack, D. Gaidatzis, V. Kalck, and P. Meister Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery Cell 150 2012 934 947
142. A. Nemeth, A. Conesa, J. Santoyo-Lopez, I. Medina, D. Montaner, and B. Peterfia Initial genomics of the human nucleolus PLoS Genet 6 2010 e1000889
143. S. van Koningsbruggen, M. Gierlinski, P. Schofield, D. Martin, G.J. Barton, and Y. Ariyurek High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli Mol Biol Cell 21 2010 3735 3748
144. E.J. Clowney, M.A. LeGros, C.P. Mosley, F.G. Clowney, E.C. Markenskoff-Papadimitriou, and M. Myllys Nuclear aggregation of olfactory receptor genes governs their monogenic expression Cell 151 2012 724 737
145. J. Padeken, and P. Heun Nucleolus and nuclear periphery: Velcro for heterochromatin Curr Opin Cell Biol 28C 2014 54 60
146. E. Passarge Emil Heitz and the concept of heterochromatin: longitudinal chromosome differentiation was recognized fifty years ago Am J Hum Genet 31 1979 106 115
147. S.W. Brown Heterochromatin Science 151 1966 417 425
148. S.C. Elgin, and G. Reuter Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila Cold Spring Harb Perspect Biol 5 2013 a017780
149. P. Dimitri, R. Caizzi, E. Giordano, M. Carmela Accardo, G. Lattanzi, and G. Biamonti Constitutive heterochromatin: a surprising variety of expressed sequences Chromosoma 118 2009 419 435
150. K.B. Moritz, and G.E. Roth Complexity of germline and somatic DNA in Ascaris Nature 259 1976 55 57
151. C.D. Smith, S. Shu, C.J. Mungall, and G.H. Karpen The Release 5.1 annotation of Drosophila melanogaster heterochromatin Science 316 2007 1586 1591
152. B.T. Wakimoto, and M.G. Hearn The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster Genetics 125 1990 141 154
153. N.C. Riddle, A. Minoda, P.V. Kharchenko, A.A. Alekseyenko, Y.B. Schwartz, and M.Y. Tolstorukov Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin Genome Res 21 2011 147 163
154. A.A. Aravin, and G.J. Hannon Small RNA silencing pathways in germ and stem cells Cold Spring Harb Symp Quant Biol 73 2008 283 290
155. J. Lu, and D.M. Gilbert Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin J Cell Biol 179 2007 411 421
156. S. Schoeftner, and M.A. Blasco Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II Nat Cell Biol 10 2008 228 236
157. M. Lachner, D. O'Carroll, S. Rea, K. Mechtler, and T. Jenuwein Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins Nature 410 2001 116 120
158. M. Gatti, and S. Pimpinelli Functional elements in Drosophila melanogaster heterochromatin Annu Rev Genet 26 1992 239 275
159. F. Greil, I. van der Kraan, J. Delrow, J.F. Smothers, E. de Wit, and H.J. Bussemaker Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location Genes Dev 17 2003 2825 2838
160. E. de Wit, F. Greil, and B. van Steensel High-resolution mapping reveals links of HP1 with active and inactive chromatin components PLoS Genet 3 2007 e38
161. J.R. Girton, and K.M. Johansen Chromatin structure and the regulation of gene expression: the lessons of PEV in Drosophila Adv Genet 61 2008 1 43
162. P. Finelli, S.M. Sirchia, M. Masciadri, M. Crippa, M.P. Recalcati, and D. Rusconi Juxtaposition of heterochromatic and euchromatic regions by chromosomal translocation mediates a heterochromatic long-range position effect associated with a severe neurological phenotype Mol Cytogenet 5 2012 16
163. P.B. Talbert, and S. Henikoff A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster Genetics 154 2000 259 272
164. D.R. Wines, P.B. Talbert, D.V. Clark, and S. Henikoff Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo Chromosoma 104 1996 332 340
165. L.L. Wallrath, and S.C. Elgin Position effect variegation in Drosophila is associated with an altered chromatin structure Genes Dev 9 1995 1263 1277
166. D.E. Cryderman, E.J. Morris, H. Biessmann, S.C. Elgin, and L.L. Wallrath Silencing at Drosophila telomeres: nuclear organization and chromatin structure play critical roles EMBO J 18 1999 3724 3735
167. F.L. Sun, M.H. Cuaycong, and S.C. Elgin Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin Mol Cell Biol 21 2001 2867 2879
168. A. Bulut-Karslioglu, V. Perrera, M. Scaranaro, I.A. de la Rosa-Velazquez, S. van de Nobelen, and N. Shukeir A transcription factor-based mechanism for mouse heterochromatin formation Nat Struct Mol Biol 19 2012 1023 1030
169. J. Padeken, M.J. Mendiburo, S. Chlamydas, H.J. Schwarz, E. Kremmer, and P. Heun The nucleoplasmin homolog NLP mediates centromere clustering and anchoring to the nucleolus Mol Cell 50 2013 236 249
170. R. Mayer, A. Brero, J. von Hase, T. Schroeder, T. Cremer, and S. Dietzel Common themes and cell type specific variations of higher order chromatin arrangements in the mouse BMC Cell Biol 6 2005 44
171. C. Weierich, A. Brero, S. Stein, J. von Hase, C. Cremer, and T. Cremer Three-dimensional arrangements of centromeres and telomeres in nuclei of human and murine lymphocytes Chromosome Res 11 2003 485 502
172. A. Brero, H.P. Easwaran, D. Nowak, I. Grunewald, T. Cremer, and H. Leonhardt Methyl CpG-binding proteins induce large-scale chromatin reorganization during terminal differentiation J Cell Biol 169 2005 733 743
173. L. Manuelidis Indications of centromere movement during interphase and differentiation Ann N Y Acad Sci 450 1985 205 221
174. G. Martou, and U. De Boni Nuclear topology of murine, cerebellar Purkinje neurons: changes as a function of development Exp Cell Res 256 2000 131 139
175. I. Solovei, L. Schermelleh, K. During, A. Engelhardt, S. Stein, and C. Cremer Differences in centromere positioning of cycling and postmitotic human cell types Chromosoma 112 2004 410 423
176. S. Henikoff, and T.D. Dreesen Trans-inactivation of the Drosophila brown gene: evidence for transcriptional repression and somatic pairing dependence Proc Natl Acad Sci U S A 86 1989 6704 6708
177. H.M. Slatis Position Effects at the Brown Locus in Drosophila Melanogaster Genetics 40 1955 5 23
178. A.K. Csink, and S. Henikoff Genetic modification of heterochromatic association and nuclear organization in Drosophila Nature 381 1996 529 531
179. E.S. Belyaeva, D.E. Koryakov, G.V. Pokholkova, O.V. Demakova, and I.F. Zhimulev Cytological study of the brown dominant position effect Chromosoma 106 1997 124 132
180. G.L. Sass, and S. Henikoff Pairing-dependent mislocalization of a Drosophila brown gene reporter to a heterochromatic environment Genetics 152 1999 595 604
181. D.R. Dorer, and S. Henikoff Transgene repeat arrays interact with distant heterochromatin and cause silencing in cis and trans Genetics 147 1997 1181 1190
182. L.E. Martin-Morris, A.K. Csink, D.R. Dorer, P.B. Talbert, and S. Henikoff Heterochromatic trans-inactivation of Drosophila white transgenes Genetics 147 1997 671 677
183. P. Dimitri Fluorescent in situ hybridization with transposable element probes to mitotic chromosomal heterochromatin of Drosophila Methods Mol Biol 260 2004 29 39
184. X. Sun, H.D. Le, J.M. Wahlstrom, and G.H. Karpen Sequence analysis of a functional Drosophila centromere Genome Res 13 2003 182 194
185. K.E. Brown, J. Baxter, D. Graf, M. Merkenschlager, and A.G. Fisher Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division Mol Cell 3 1999 207 217
186. L.A. Trinh, R. Ferrini, B.S. Cobb, A.S. Weinmann, K. Hahm, and P. Ernst Down-regulation of TDT transcription in CD4(+) CD8(+) thymocytes by Ikaros proteins in direct competition with an Ets activator Genes Dev 15 2001 1817 1832
187. R.C. Su, K.E. Brown, S. Saaber, A.G. Fisher, M. Merkenschlager, and S.T. Smale Dynamic assembly of silent chromatin during thymocyte maturation Nat Genet 36 2004 502 506
188. A. Groth Replicating chromatin: a tale of histones Biochem Cell Biol 87 2009 51 63
189. M. Radman-Livaja, K.F. Verzijlbergen, A. Weiner, T. van Welsem, N. Friedman, and O.J. Rando Patterns and mechanisms of ancestral histone protein inheritance in budding yeast PLoS Biol 9 2011 e1001075
190. N. Naumova, M. Imakaev, G. Fudenberg, Y. Zhan, B.R. Lajoie, and L.A. Mirny Organization of the mitotic chromosome Science 342 2013 948 953
191. I. Thomson, S. Gilchrist, W.A. Bickmore, and J.R. Chubb The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1 Curr Biol 14 2004 166 172