The dynamic architectural and epigenetic nuclear landscape: Developing the genomic almanac of biology and disease

Journal of Cellular Physiology

Volumn 229, Issue 6, 2014, Pages 711-727

  Tai, Phillip W L ^a   Zaidi, Sayyed K ^a   Wu, Hai ^a   Grandy, Rodrigo A ^a   Montecino, Martin ^b   Van Wijnen, André J ^c   Lian, Jane B ^a   Stein, Gary S ^a   Stein, Janet L ^a  

^a UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

^b UNIVERSIDAD ANDRÉS BELLO   (Chile)

^c MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SCAFFOLD PROTEIN;

ARTICLE; CANCER MODEL; CELL COMPARTMENTALIZATION; CELL DIFFERENTIATION; CELL FUNCTION; CELL NUCLEUS; CHROMOSOME TRANSLOCATION; DE LANGE SYNDROME; EMBRYO DEVELOPMENT; EPIGENETICS; FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY; GENE CONTROL; GENE EXPRESSION; GENE THERAPY; GENETIC DISORDER; GENETIC STABILITY; GENETIC TRANSCRIPTION; GENOME; HUMAN; INHERITANCE; MICROENVIRONMENT; MITOSIS; NONHUMAN; NUCLEAR LAMINA; PRIORITY JOURNAL; PROGERIA; SILENT GENE; ULTRASTRUCTURE;

ANIMALS; EPIGENESIS, GENETIC; EUKARYOTA; GENOMICS;

EID: 84894273898     PISSN: 00219541     EISSN: 10974652     Source Type: Journal    
DOI: 10.1002/jcp.24508     Document Type: Article

References (256)

1. Adessi C, Matton G, Ayala G, Turcatti G, Mermod JJ, Mayer P, Kawashima E. 2000. Solid phase DNA amplification: Characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res 28:E87.
2. Anderson DM, Smith LD. 1978. Patterns of synthesis and accumulation of heterogeneous RNA in lampbrush stage oocytes of Xenopus laevis (Daudin). Dev Biol 67:274-285.
3. Apostolou E, Thanos D. 2008. Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell 134:85-96.
4. Augello MA, Hickey TE, Knudsen KE. 2011. FOXA1: Master of steroid receptor function in cancer. EMBO J 30:3885-3894.
5. Avery OT, Macleod CM, McCarty M. 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type Iii. J Exp Med 79:137-158.
6. Barr ML, Bertram EG. 1949. A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis. Nature 163:676.
7. Barrack ER. 1987. Steroid hormone receptor localization in the nuclear matrix: Interaction with acceptor sites. J Steroid Biochem 27:115-121.
8. Barseguian K, Lutterbach B, Hiebert SW, Nickerson J, Lian JB, Stein JL, van Wijnen AJ, Stein GS. 2002. Multiple subnuclear targeting signals of the leukemia-related AML1/ETO and ETO repressor proteins. Proc Natl Acad Sci U S A 99:15434-15439.
9. Bartova E, Krejci J, Harnicarova A, Kozubek S. 2008. Differentiation of human embryonic stem cells induces condensation of chromosome territories and formation of heterochromatin protein 1 foci. Differentiation 76:24-32.
10. Bau D, Marti-Renom MA. 2011. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res 19:25-35.
11. Bender MA, Ragoczy T, Lee J, Byron R, Telling A, Dean A, Groudine M. 2012. The hypersensitive sites of the murine beta-globin locus control region act independently to affect nuclear localization and transcriptional elongation. Blood 119:3820-3827.
12. Berezney R, Coffey DS. 1974. Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410-1417.
13. Berezney R, Coffey DS. 1975. Nuclear protein matrix: Association with newly synthesized DNA. Science 189:291-293.
14. Berezney R, Wei X. 1998. The new paradigm: Integrating genomic function and nuclear architecture. J Cell Biochem Suppl. 30-31:238-242.
15. Berezney R, Mortillaro MJ, Ma H, Wei X, Samarabandu J. 1995. The nuclear matrix: A structural milieu for genomic function. Int Rev Cytol 162A:1-65.
16. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315-326.
17. Bickmore WA, Teague P. 2002. Influences of chromosome size, gene density and nuclear position on the frequency of constitutional translocations in the human population. Chromosome Res 10:707-715.
18. Bilican B, Goding CR. 2006. Cell cycle regulation of the T-box transcription factor tbx2. Exp Cell Res 312:2358-2366.
19. Billett MA, Barry JM. 1974. Role of histones in chromatin condensation. Eur J Biochem 49:477-484.
20. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermuller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaoz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrimsdottir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
21. Bogdanove AJ, Voytas DF. 2011. TAL effectors: Customizable proteins for DNA targeting. Science 333:1843-1846.
22. Boisvert FM, van Koningsbruggen S, Navascues J, Lamond AI. 2007. The multifunctional nucleolus. Nat Rev Mol Cell Biol 8:574-585.
23. 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.
24. Bonnefoy E, Orsi GA, Couble P, Loppin B. 2007. The essential role of Drosophila HIRA for de novo assembly of paternal chromatin at fertilization. PLoS Genet 3:1991-2006.
25. Bornfleth H, Edelmann P, Zink D, Cremer T, Cremer C. 1999. Quantitative motion analysis of subchromosomal foci in living cells using four-dimensional microscopy. Biophys J 77:2871-2886.
26. Boveri T. 1909. Die Blastomerenkerne von Ascaris megalocephala und die Theorie der Chromosomenindividualitat. Arch Zellforsch 3:181-268.
27. Brasch K, Ochs RL. 1992. Nuclear bodies (NBs): A newly "rediscovered" organelle. Exp Cell Res 202:211-223.
28. Brickner DG, Ahmed S, Meldi L, Thompson A, Light W, Young M, Hickman TL, Chu F, Fabre E, Brickner JH. 2012. Transcription factor binding to a DNA zip code controls interchromosomal clustering at the nuclear periphery. Dev Cell 22:1234-1246.
29. Brooks AR, Nagy BP, Taylor S, Simonet WS, Taylor JM, Levy-Wilson B. 1994. Sequences containing the second-intron enhancer are essential for transcription of the human apolipoprotein B gene in the livers of transgenic mice. Mol Cell Biol 14:2243-2256.
30. Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, Beisel C, Schubeler D, Stadler MB, Peters AH. 2010. Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat Struct Mol Biol 17:679-687.
31. Burgess-Beusse B, Farrell C, Gaszner M, Litt M, Mutskov V, Recillas-Targa F, Simpson M, West A, Felsenfeld G. 2002. The insulation of genes from external enhancers and silencing chromatin. Proc Natl Acad Sci U S A 99:16433-16437.
32. Cabianca DS, Gabellini D. 2010. The cell biology of disease: FSHD: Copy number variations on the theme of muscular dystrophy. J Cell Biol 191:1049-1060.
33. Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D. 2012. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149:819-831.
34. Caiulo A, Nicolis S, Bianchi P, Zuffardi O, Bardoni B, Maraschio P, Ottolenghi S, Camerino G, Giglioni B. 1991. Mapping the gene encoding the human erythroid transcriptional factor NFE1-GF1 to Xp11.23. Hum Genet 86:388-390.
35. Cajal S. 1903. Un sencillo metodo de coloracion selectiva del reticulo protoplasmico y sus efectos en los diversos organos nerviosos de vertebrados e invertebrados. Trab Lab Investig Biol Univ Madr 2:129-221.
36. Capell BC, Collins FS. 2006. Human laminopathies: Nuclei gone genetically awry. Nat Rev Genet 7:940-952.
37. Caravaca JM, Donahue G, Becker JS, He X, Vinson C, Zaret KS. 2013. Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. Genes Dev 27:251-260.
38. Carone BR, Fauquier L, Habib N, Shea JM, Hart CE, Li R, Bock C, Li C, Gu H, Zamore PD, Meissner A, Weng Z, Hofmann HA, Friedman N, Rando OJ. 2010. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell 143:1084-1096.
39. Carvajal JJ, Keith A, Rigby PW. 2008. Global transcriptional regulation of the locus encoding the skeletal muscle determination genes Mrf4 and Myf5. Genes Dev 22:265-276.
40. Cavalli G, Misteli T. 2013. Functional implications of genome topology. Nat Struct Mol Biol 20:290-299.
41. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH. 2009. Unlocking the secrets of the genome. Nature 459:927-930.
42. Chaly N, Munro SB, Swallow MA. 1996. Remodelling of the nuclear periphery during muscle cell differentiation in vitro. J Cell Biochem 62:76-89.
43. Chen J, Young F, Bottaro A, Stewart V, Smith RK, Alt FW. 1993. Mutations of the intronic IgH enhancer and its flanking sequences differentially affect accessibility of the JH locus. EMBO J 12:4635-4645.
44. Cheung SW, Tishler PV, Atkins L, Sengupta SK, Modest EJ, Forget BG. 1977. Gene mapping by fluorescent in situ hybridization. Cell Biol Int Rep 1:255-262.
45. Chiarle R, Zhang Y, Frock RL, Lewis SM, Molinie B, Ho YJ, Myers DR, Choi VW, Compagno M, Malkin DJ, Neuberg D, Monti S, Giallourakis CC, Gostissa M, Alt FW. 2011. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147:107-119.
46. Chiolo I, Minoda A, Colmenares SU, Polyzos A, Costes SV, Karpen GH. 2011. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 144:732-744.
47. Chow JC, Yen Z, Ziesche SM, Brown CJ. 2005. Silencing of the mammalian X chromosome. Annu Rev Genomics Hum Genet 6:69-92.
48. Chubb JR, Boyle S, Perry P, Bickmore WA. 2002. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12:439-445.
49. Chubb JR, Trcek T, Shenoy SM, Singer RH. 2006. Transcriptional pulsing of a developmental gene. Curr Biol 16:1018-1025.
50. Cirillo LA, Lin FR, Cuesta I, Friedman D, Jarnik M, Zaret KS. 2002. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol Cell 9:279-289.
51. Cockerill PN, Yuen MH, Garrard WT. 1987. The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J Biol Chem 262:5394-5397.
52. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819-823.
53. Cook P. 1998. Duplicating a tangled genome. Science 281:1466-1467.
54. Cremer M, Kupper K, Wagler B, Wizelman L, von Hase J, Weiland Y, Kreja L, Diebold J, Speicher MR, Cremer T. 2003. Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol 162:809-820.
55. Cremer M, Grasser F, Lanctot C, Muller S, Neusser M, Zinner R, Solovei I, Cremer T. 2008. Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. Methods Mol Biol 463:205-239.
56. Crick FH. 1958. On protein synthesis. Symp Soc Exp Biol 12:138-163.
57. 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.
58. Daujat S, Bauer UM, Shah V, Turner B, Berger S, Kouzarides T. 2002. Crosstalk between CARM1 methylation and CBP acetylation on histone H3. Curr Biol 12:2090-2097.
59. Davies HG. 1967. Fine structure of heterochromatin in certain cell nuclei. Nature 214:208-210.
60. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. 2010. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8:e1000384.
61. Degner SC, Verma-Gaur J, Wong TP, Bossen C, Iverson GM, Torkamani A, Vettermann C, Lin YC, Ju Z, Schulz D, Murre CS, Birshtein BK, Schork NJ, Schlissel MS, Riblet R, Murre C, Feeney AJ. 2011. 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 108:9566-9571.
62. Dekker J, Rippe K, Dekker M, Kleckner N. 2002. Capturing chromosome conformation. Science 295:1306-1311.
63. Dekker J, Marti-Renom MA, Mirny LA. 2013. Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data. Nat Rev Genet 14:390-403.
64. Delcuve GP, He S, Davie JR. 2008. Mitotic partitioning of transcription factors. J Cell Biochem 105:1-8.
65. Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. 2012. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149:1233-1244.
66. Dennis E, Berg P. 1985. Transcription from a plant gene promoter in animal cells. Nucleic Acids Res 13:7945-7957.
67. Dickinson LA, Joh T, Kohwi Y, Kohwi-Shigematsu T. 1992. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70:631-645.
68. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376-380.
69. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Roder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigo R, Gingeras TR. 2012a. Landscape of transcription in human cells. Nature 489:101-108.
70. Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpi JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigo R, Gingeras TR. 2012b. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS ONE 7:e28213.
71. Dobie KW, Lee M, Fantes JA, Graham E, Clark AJ, Springbett A, Lathe R, McClenaghan M. 1996. Variegated transgene expression in mouse mammary gland is determined by the transgene integration locus. Proc Natl Acad Sci U S A 93:6659-6664.
72. Drissen R, Palstra RJ, Gillemans N, Splinter E, Grosveld F, Philipsen S, de Laat W. 2004. The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev 18:2485-2490.
73. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. 2010. A three-dimensional model of the yeast genome. Nature 465:363-367.
74. Dunaway M, Droge P. 1989. Transactivation of the Xenopus rRNA gene promoter by its enhancer. Nature 341:657-659.
75. Dworetzky SI, Wright KL, Fey EG, Penman S, Lian JB, Stein JL, Stein GS. 1992. Sequence-specific DNA-binding proteins are components of a nuclear matrix-attachment site. Proc Natl Acad Sci U S A 89:4178-4182.
76. Edelmann P, Bornfleth H, Zink D, Cremer T, Cremer C. 2001. Morphology and dynamics of chromosome territories in living cells. Biochim Biophys Acta 1551:M29-M39.
77. Eils R, Dietzel S, Bertin E, Schrock E, Speicher MR, Ried T, Robert-Nicoud M, Cremer C, Cremer T. 1996. Three-dimensional reconstruction of painted human interphase chromosomes: Active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. J Cell Biol 135:1427-1440.
78. Erickson P, Gao J, Chang KS, Look T, Whisenant E, Raimondi S, Lasher R, Trujillo J, Rowley J, Drabkin H. 1992. Identification of breakpoints in t(8;21) acute myelogenous leukemia and isolation of a fusion transcript, AML1/ETO, with similarity to Drosophila segmentation gene, runt. Blood 80:1825-1831.
79. Faro-Trindade I, Cook PR. 2006a. A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. Mol Biol Cell 17:2910-2920.
80. Faro-Trindade I, Cook PR. 2006b. Transcription factories: Structures conserved during differentiation and evolution. Biochem Soc Trans 34:1133-1137.
81. Finlan LE, Sproul D, Thomson I, Boyle S, Kerr E, Perry P, Ylstra B, Chubb JR, Bickmore WA. 2008. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4:e1000039.
82. Fischer AH, Bardarov S, Jr., Jiang Z. 2004. Molecular aspects of diagnostic nucleolar and nuclear envelope changes in prostate cancer. J Cell Biochem 91:170-184.
83. Flemming W. 1882. Zellsubstanz, Kern und Zelltheilung. Vogel, F.C.W.
84. Fox AH, Lam YW, Leung AK, Lyon CE, Andersen J, Mann M, Lamond AI. 2002. Paraspeckles: A novel nuclear domain. Curr Biol 12:13-25.
85. Fraser J, Rousseau M, Shenker S, Ferraiuolo MA, Hayashizaki Y, Blanchette M, Dostie J. 2009. Chromatin conformation signatures of cellular differentiation. Genome Biol 10:R37.
86. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y. 2009. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58-64.
87. Gall JG, Murphy C, Callan HG, Wu ZA. 1991. Lampbrush chromosomes. Methods Cell Biol 36:149-166.
88. Gao F, Wei Z, An W, Wang K, Lu W. 2013. The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells. Sci Rep 3:1588.
89. Getzenberg RH. 1994. Nuclear matrix and the regulation of gene expression: Tissue specificity. J Cell Biochem 55:22-2231.
90. Getzenberg RH, Coffey DS. 1990. Tissue specificity of the hormonal response in sex accessory tissues is associated with nuclear matrix protein patterns. Mol Endocrinol 4:1336-1342.
91. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:442-451.
92. Gingeras TR. 2009. Implications of chimaeric non-co-linear transcripts. Nature 461:206-211.
93. Girst S, Hable V, Drexler GA, Greubel C, Siebenwirth C, Haum M, Friedl AA, Dollinger G. 2013. Subdiffusion supports joining of correct ends during repair of DNA double-strand breaks. Sci Rep 3:2511.
94. Gluch A, Vidakovic M, Bode J. 2008. Scaffold/matrix attachment regions (S/MARs): Relevance for disease and therapy. Handb Exp Pharmacol 67-6103.
95. Goodman RH, Spiro D. 1962. Electron microscopic studies of giant salivary gland chromosomes. Exp Cell Res 27:359-363.
96. Grosveld F, van Assendelft GB, Greaves DR, Kollias G. 1987. Position-independent, high-level expression of the human beta-globin gene in transgenic mice. Cell 51:975-985.
97. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B. 2008. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453:948-951.
98. Guo B, Odgren PR, van Wijnen AJ, Last TJ, Nickerson J, Penman S, Lian JB, Stein JL, Stein GS. 1995. The nuclear matrix protein NMP-1 is the transcription factor YY1. Proc Natl Acad Sci U S A 92:10526-10530.
99. Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q. 2012. CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice. Proc Natl Acad Sci U S A 109:21081-21086.
100. Hadchouel J, Carvajal JJ, Daubas P, Bajard L, Chang T, Rocancourt D, Cox D, Summerbell D, Tajbakhsh S, Rigby PW, Buckingham M. 2003. Analysis of a key regulatory region upstream of the Myf5 gene reveals multiple phases of myogenesis, orchestrated at each site by a combination of elements dispersed throughout the locus. Development 130:3415-3426.
101. Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR. 2009. Distinctive chromatin in human sperm packages genes for embryo development. Nature 460:473-478.
102. Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL. 2011. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 43:630-638.
103. Hanna J, Saha K, Pando B, van Zon J, Lengner CJ, Creyghton MP, van Oudenaarden A, Jaenisch R. 2009. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462:595-601.
104. Hay ED, Revel JP. 1963. The fine structure of the DNP component of the nucleus. An electron microscopic study utilizing autoradiography to localize DNA synthesis. J Cell Biol 16:29-51.
105. He DC, Martin T, Penman S. 1991. Localization of heterogeneous nuclear ribonucleoprotein in the interphase nuclear matrix core filaments and on perichromosomal filaments at mitosis. Proc Natl Acad Sci U S A 88:7469-7473.
106. Heisterkamp N, Stam K, Groffen J, de Klein A, Grosveld G. 1985. Structural organization of the bcr gene and its role in the Ph' translocation. Nature 315:758-761.
107. Heitz E. 1928. Das heterochromatin der Moose. Jehrb Wiss Botanik 69:762-818.
108. Hepperger C, Mannes A, Merz J, Peters J, Dietzel S. 2008. Three-dimensional positioning of genes in mouse cell nuclei. Chromosoma 117:535-551.
109. Hertwig O, Campbell HJ. 1895. The cell; Outlines of general anatomy and physiology. London: Sonnenschein. xvi, 368, pp.
110. Hou C, Li L, Qin ZS, Corces VG. 2012. Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol Cell 48:471-484.
111. Hutchison N, Weintraub H. 1985. Localization of DNAase I-sensitive sequences to specific regions of interphase nuclei. Cell 43:471-482.
112. Iborra FJ, Pombo A, Jackson DA, Cook PR. 1996a. Active RNA polymerases are localized within discrete transcription "factories" in human nuclei. J Cell Sci 109:1427-1436.
113. Iborra FJ, Pombo A, McManus J, Jackson DA, Cook PR. 1996b. The topology of transcription by immobilized polymerases. Exp Cell Res 229:167-173.
114. Jackson DA, Pombo A. 1998. Replicon clusters are stable units of chromosome structure: Evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J Cell Biol 140:1285-1295.
115. Jacob F, Brenner S. 1963. [On the regulation of DNA synthesis in bacteria: The hypothesis of the replicon]. C R Hebd Seances Acad Sci 256:298-300.
116. Jacobs EY, Frey MR, Wu W, Ingledue TC, Gebuhr TC, Gao L, Marzluff WF, Matera AG. 1999. Coiled bodies preferentially associate with U4, U11, and U12 small nuclear RNA genes in interphase HeLa cells but not with U6 and U7 genes. Mol Biol Cell 10:1653-1663.
117. Jiang J, Jing Y, Cost GJ, Chiang JC, Kolpa HJ, Cotton AM, Carone DM, Carone BR, Shivak DA, Guschin DY, Pearl JR, Rebar EJ, Byron M, Gregory PD, Brown CJ, Urnov FD, Hall LL, Lawrence JB. 2013. Translating dosage compensation to trisomy 21. Nature 500:296-300.
118. Jing H, Vakoc CR, Ying L, Mandat S, Wang H, Zheng X, Blobel GA. 2008. Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. Mol Cell 29:232-242.
119. Junier I, Dale RK, Hou C, Kepes F, Dean A. 2012. CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the beta-globin locus. Nucleic Acids Res 40:7718-7727.
120. Kadauke S, Blobel GA. 2013. Mitotic bookmarking by transcription factors. Epigenetics Chromatin 6:6.
121. Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. 2012. Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell 150:725-737.
122. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12:996-1006.
123. Kim J, Chu J, Shen X, Wang J, Orkin SH. 2008. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132:1049-1061.
124. Kind J, van Steensel B. 2010. Genome-nuclear lamina interactions and gene regulation. Curr Opin Cell Biol 22:320-325.
125. Kmita M, Duboule D. 2003. Organizing axes in time and space; 25 years of colinear tinkering. Science 301:331-333.
126. Knoepfler PS. 2008. Why myc? An unexpected ingredient in the stem cell cocktail. Cell Stem Cell 2:18-21.
127. Knutsen T, Gobu V, Knaus R, Padilla-Nash H, Augustus M, Strausberg RL, Kirsch IR, Sirotkin K, Ried T. 2005. The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: Linkage of chromosomal aberrations with the genome sequence. Genes Chromosomes Cancer 44:52-64.
128. Krantz ID, McCallum J, DeScipio C, Kaur M, Gillis LA, Yaeger D, Jukofsky L, Wasserman N, Bottani A, Morris CA, Nowaczyk MJ, Toriello H, Bamshad MJ, Carey JC, Rappaport E, Kawauchi S, Lander AD, Calof AL, Li HH, Devoto M, Jackson LG. 2004. Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B. Nat Genet 36:631-635.
129. Kubben N, Adriaens M, Meuleman W, Voncken JW, van Steensel B, Misteli T. 2012. Mapping of lamin A- and progerin-interacting genome regions. Chromosoma 121:447-464.
130. Larkin JD, Cook PR, Papantonis A. 2012. Dynamic reconfiguration of long human genes during one transcription cycle. Mol Cell Biol 32:2738-2747.
131. Larkin JD, Papantonis A, Cook PR. 2013a. Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J Cell Sci 126:2052-2059.
132. Larkin JD, Papantonis A, Cook PR, Marenduzzo D. 2013b. Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res 41:2216-2227.
133. Larson DR, Singer RH, Zenklusen D. 2009. A single molecule view of gene expression. Trends Cell Biol 19:630-637.
134. LaSalle JM, Lalande M. 1996. Homologous association of oppositely imprinted chromosomal domains. Science 272:725-728.
135. Lee W, Mitchell P, Tjian R. 1987. Purified transcription factor AP-1 interacts with TPA-inducible enhancer elements. Cell 49:741-752.
136. Lemmers RJ, van der Vliet PJ, Klooster R, Sacconi S, Camano P, Dauwerse JG, Snider L, Straasheijm KR, van Ommen GJ, Padberg GW, Miller DG, Tapscott SJ, Tawil R, Frants RR, van der Maarel SM. 2010. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science 329:1650-1653.
137. Levy-Wilson B. 1981. ADP-ribosylation of trout testis chromosomal proteins: Distribution of ADP-ribosylated proteins among DNase I-sensitive and -resistant chromatin domains. Arch Biochem Biophys 208:528-534.
138. Lewis E. 1954. The theory and application of a new method of detecting chromosomal rearrangements in drosophila melanogaster. Am Nat 88:225-239.
139. Li S, Heermann DW. 2013. Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts. DNA Res 20:45-53.
140. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y. 2012. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148:84-98.
141. Lian JB, Javed A, Zaidi SK, Lengner C, Montecino M, van Wijnen AJ, Stein JL, Stein GS. 2004. Regulatory controls for osteoblast growth and differentiation: Role of Runx/Cbfa/AML factors. Crit Rev Eukaryot Gene Expr 14:1-41.
142. 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.
143. Littau VC, Burdick CJ, Allfrey VG, Mirsky SA. 1965. The role of histones in the maintenance of chromatin structure. Proc Natl Acad Sci U S A 54:1204-1212.
144. Liu J, Krantz ID. 2008. Cohesin and human disease. Annu Rev Genomics Hum Genet 9:303-320.
145. Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Clark D, Kaur M, Tandy S, Kondoh T, Rappaport E, Spinner NB, Vega H, Jackson LG, Shirahige K, Krantz ID. 2009. Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol 7:e1000119.
146. Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH. 1990. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene. Oncogene 5:1743-1753.
147. Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R. 2006. Interchromosomal interactions and olfactory receptor choice. Cell 126:403-413.
148. Lyon MF. 1962. Sex chromatin and gene action in the mammalian X-chromosome. Am J Hum Genet 14:135-148.
149. Ma H, Samarabandu J, Devdhar RS, Acharya R, Cheng PC, Meng C, Berezney R. 1998. Spatial and temporal dynamics of DNA replication sites in mammalian cells. J Cell Biol 143:1415-1425.
150. Mahmoudi T, Katsani KR, Verrijzer CP. 2002. GAGA can mediate enhancer function in trans by linking two separate DNA molecules. EMBO J 21:1775-1781.
151. Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW. 1997. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7:930-939.
152. McClintock B. 1934. The relation of a particular chromosomal element to the development of the nucleoli in Zea mays. Zeitschrift fur Zellforschung und mikroskopische Anatomie 2:294-328.
153. McGuffee SR, Smith DJ, Whitehouse I. 2013. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Mol Cell 50:123-135.
154. McKeown PC, Shaw PJ. 2009. Chromatin: Linking structure and function in the nucleolus. Chromosoma 118:11-23.
155. McNeil S, Zeng C, Harrington KS, Hiebert S, Lian JB, Stein JL, van Wijnen AJ, Stein GS. 1999. The t(8;21) chromosomal translocation in acute myelogenous leukemia modifies intranuclear targeting of the AML1/CBFalpha2 transcription factor. Proc Natl Acad Sci U S A 96:14882-14887.
156. Medina R, Ghule PN, Cruzat F, Barutcu AR, Montecino M, Stein JL, van Wijnen AJ, Stein GS. 2012. Epigenetic control of cell cycle-dependent histone gene expression is a principal component of the abbreviated pluripotent cell cycle. Mol Cell Biol 32:3860-3871.
157. Meister P, Poidevin M, Francesconi S, Tratner I, Zarzov P, Baldacci G. 2003. Nuclear factories for signalling and repairing DNA double strand breaks in living fission yeast. Nucleic Acids Res 31:5064-5073.
158. Melnik S, Deng B, Papantonis A, Baboo S, Carr IM, Cook PR. 2011. The proteomes of transcription factories containing RNA polymerases I, II or III. Nat Methods 8:963-968.
159. Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. 2013. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol (in press).
160. Metzker ML. 2010. Sequencing technologies-The next generation. Nat Rev Genet 11:31-46.
161. Miele A, Dekker J. 2008. Long-range chromosomal interactions and gene regulation. Mol Biosyst 4:1046-1057.
162. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-560.
163. Misteli T. 2013. The cell biology of genomes: Bringing the double helix to life. Cell 152:1209-1212.
164. Mitchell JA, Fraser P. 2008. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev 22:20-25.
165. Miyoshi H, Shimizu K, Kozu T, Maseki N, Kaneko Y, Ohki M. 1991. t(8;21) breakpoints on chromosome 21 in acute myeloid leukemia are clustered within a limited region of a single gene, AML1. Proc Natl Acad Sci U S A 88:10431-10434.
166. Monneron A, Bernhard W. 1969. Fine structural organization of the interphase nucleus in some mammalian cells. J Ultrastruct Res 27:266-288.
167. Morey C, Da Silva NR, Perry P, Bickmore WA. 2007. Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 134:909-919.
168. Morey C, Kress C, Bickmore WA. 2009. Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression. Genome Res 19:1184-1194.
169. Mousavi K, Zare H, Dell'orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V. 2013. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 51:606-617.
170. Mueller-Storm HP, Sogo JM, Schaffner W. 1989. An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge. Cell 58:767-777.
171. Nakamura H, Morita T, Sato C. 1986. Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp Cell Res 165:291-297.
172. 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.
173. Ng SF, Lin RC, Laybutt DR, Barres R, Owens JA, Morris MJ. 2010. Chronic high-fat diet in fathers programs beta-cell dysfunction in female rat offspring. Nature 467:963-966.
174. Nolen LD, Boyle S, Ansari M, Pritchard E, Bickmore WA. 2013. Regional chromatin decompaction in Cornelia de Lange syndrome associated with NIPBL disruption can be uncoupled from cohesin and CTCF. Hum Mol Genet 22:4180-4193.
175. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. 2011. The dynamic architecture of Hox gene clusters. Science 334:222-225.
176. Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Bluthgen N, Dekker J, Heard E. 2012. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485:381-385.
177. Nowell PC, Hungerford DA. 1960. Chromosome studies on normal and leukemic human leukocytes. J Natl Cancer Inst 25:85-109.
178. Ohlsson R, Bartkuhn M, Renkawitz R. 2010. CTCF shapes chromatin by multiple mechanisms: The impact of 20 years of CTCF research on understanding the workings of chromatin. Chromosoma 119:351-360.
179. Okuda T, van Deursen J, Hiebert SW, Grosveld G, Downing JR. 1996. AML1, the target of multiple chromosomal translocations in human leukemia, is essential for normal fetal liver hematopoiesis. Cell 84:321-330.
180. Orsi GA, Algazeery A, Meyer RE, Capri M, Sapey-Triomphe LM, Horard B, Gruffat H, Couble P, Ait-Ahmed O, Loppin B. 2013. Drosophila yemanuclein and HIRA cooperate for de novo assembly of H3.3-containing nucleosomes in the male pronucleus. PLoS Genet 9:e1003285.
181. O'Sullivan JM, Tan-Wong SM, Morillon A, Lee B, Coles J, Mellor J, Proudfoot NJ. 2004. Gene loops juxtapose promoters and terminators in yeast. Nat Genet 36:1014-1018.
182. Palstra RJ, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, de Laat W. 2003. The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet 35:190-194.
183. Palstra RJ, Simonis M, Klous P, Brasset E, Eijkelkamp B, de Laat W. 2008. Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS ONE 3:e1661.
184. Papantonis A, Cook PR. 2013. Transcription factories: Genome organization and gene regulation. Chem Rev. 113:8683-8705.
185. Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR. 2010. Active RNA polymerases: Mobile or immobile molecular machines? PLoS Biol 8:e1000419.
186. Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, Li G, Poh HM, Ruan X, Aburatani H, Ruan Y, Kodama T, Wada Y, Cook PR. 2012. TNFalpha signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J 31:4404-4414.
187. Parada LA, McQueen PG, Munson PJ, Misteli T. 2002. Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol 12:1692-1697.
188. Parada LA, McQueen PG, Misteli T. 2004. Tissue-specific spatial organization of genomes. Genome Biol 5:R44.
189. Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C, Webster Z, Nesterova T, Cobb BS, Yokomori K, Dillon N, Aragon L, Fisher AG, Merkenschlager M. 2008. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132:422-433.
190. Paweletz N. 2001. Walther Flemming: Pioneer of mitosis research. Nat Rev Mol Cell Biol 2:72-75.
191. Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Graf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B. 2010. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 38:603-613.
192. Perry MW, Boettiger AN, Bothma JP, Levine M. 2010. Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol 20:1562-1567.
193. Perry MW, Boettiger AN, Levine M. 2011. Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A 108:13570-13575.
194. Phillips JE, Corces VG. 2009. CTCF: Master weaver of the genome. Cell 137:1194-1211.
195. Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG. 2013. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153:1281-1295.
196. Pombo A, Hollinshead M, Cook PR. 1999a. Bridging the resolution gap: Imaging the same transcription factories in cryosections by light and electron microscopy. J Histochem Cytochem 47:471-480.
197. Pombo A, Jackson DA, Hollinshead M, Wang Z, Roeder RG, Cook PR. 1999b. Regional specialization in human nuclei: Visualization of discrete sites of transcription by RNA polymerase III. EMBO J 18:2241-2253.
198. Rabl C. 1885. Uber Zelltheilung. Morph Jb 10:214-330.
199. Raj A, van Oudenaarden A. 2008. Nature, nurture, or chance: Stochastic gene expression and its consequences. Cell 135:216-226.
200. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. 2006. Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4:e309.
201. Rankin J, Ellard S. 2006. The laminopathies: A clinical review. Clin Genet 70:261-274.
202. Razin A, Cedar H. 1991. DNA methylation and gene expression. Microbiol Rev 55:451-458.
203. Reddy KL, Zullo JM, Bertolino E, Singh H. 2008. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452:243-247.
204. Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE. 2011. Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS ONE 6:e17634.
205. 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.
206. Ronneberger O, Baddeley D, Scheipl F, Verveer PJ, Burkhardt H, Cremer C, Fahrmeir L, Cremer T, Joffe B. 2008. Spatial quantitative analysis of fluorescently labeled nuclear structures: Problems, methods, pitfalls. Chromosome Res 16:523-562.
207. Roussel P, Andre C, Comai L, Hernandez-Verdun D. 1996. The rDNA transcription machinery is assembled during mitosis in active NORs and absent in inactive NORs. J Cell Biol 133:235-246.
208. Rowley JD. 1973a. Identificaton of a translocation with quinacrine fluorescence in a patient with acute leukemia. Ann Genet 16:109-112.
209. Rowley JD. 1973b. Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243:290-293.
210. Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A. 2008. CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A 105:8309-8314.
211. Schmutz J, Wheeler J, Grimwood J, Dickson M, Yang J, Caoile C, Bajorek E, Black S, Chan YM, Denys M, Escobar J, Flowers D, Fotopulos D, Garcia C, Gomez M, Gonzales E, Haydu L, Lopez F, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salazar A, Tsai M, Myers RM. 2004. Quality assessment of the human genome sequence. Nature 429:365-368.
212. Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G. 2007. Genome regulation by polycomb and trithorax proteins. Cell 128:735-745.
213. Schweiger MR, Barmeyer C, Timmermann B. 2013. Genomics and epigenomics: New promises of personalized medicine for cancer patients. Brief Funct Genomics 12:411-421.
214. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G. 2012. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148:458-472.
215. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y. 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941-953.
216. Simonis M, de Laat W. 2008. FISH-eyed and genome-wide views on the spatial organisation of gene expression. Biochim Biophys Acta 1783:2052-2060.
217. 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.
218. Solovei I, Kreysing M, Lanctot C, Kosem S, Peichl L, Cremer T, Guck J, Joffe B. 2009. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 137:356-368.
219. Soufi A, Donahue G, Zaret KS. 2012. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151:994-1004.
220. Soutoglou E, Dorn JF, Sengupta K, Jasin M, Nussenzweig A, Ried T, Danuser G, Misteli T. 2007. Positional stability of single double-strand breaks in mammalian cells. Nat Cell Biol 9:675-682.
221. Sridharan R, Tchieu J, Mason MJ, Yachechko R, Kuoy E, Horvath S, Zhou Q, Plath K. 2009. Role of the murine reprogramming factors in the induction of pluripotency. Cell 136:364-377.
222. Stack SM, Brown DB, Dewey WC. 1977. Visualization of interphase chromosomes. J Cell Sci 26:281-299.
223. Stein GS, van Wijnen AJ, Stein JL, Lian JB, Montecino M, Choi J, Zaidi K, Javed A. 2000. Intranuclear trafficking of transcription factors: Implications for biological control. J Cell Sci 113:2527-2533.
224. Stein GS, Zaidi SK, Stein JL, Lian JB, van Wijnen AJ, Montecino M, Young DW, Javed A, Pratap J, Choi JY, Ali SA, Pande S, Hassan MQ. 2009. Transcription-factor-mediated epigenetic control of cell fate and lineage commitment. Biochem Cell Biol 87:1-6.
225. Stief A, Winter DM, Stratling WH, Sippel AE. 1989. A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature 341:343-345.
226. Stuurman N, Meijne AM, van der Pol AJ, de Jong L, van Driel R, van Renswoude J. 1990. The nuclear matrix from cells of different origin. Evidence for a common set of matrix proteins. J Biol Chem 265:5460-5465.
227. Sutherland H, Bickmore WA. 2009. Transcription factories: Gene expression in unions? Nat Rev Genet 10:457-466.
228. Tai PW, Fisher-Aylor KI, Himeda CL, Smith CL, Mackenzie AP, Helterline DL, Angello JC, Welikson RE, Wold BJ, Hauschka SD. 2011. Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer. Skelet Muscle 1:25.
229. Takahashi K, Yamanaka S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663-676.
230. Tanabe H, Muller S, Neusser M, von Hase J, Calcagno E, Cremer M, Solovei I, Cremer C, Cremer T. 2002. Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci U S A 99:4424-4429.
231. Tan-Wong SM, French JD, Proudfoot NJ, Brown MA. 2008. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc Natl Acad Sci U S A 105:5160-5165.
232. Tan-Wong SM, Wijayatilake HD, Proudfoot NJ. 2009. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev 23:2610-2624.
233. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. 2007. How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers. Nat Struct Mol Biol 14:1025-1040.
234. Teller K, Solovei I, Buiting K, Horsthemke B, Cremer T. 2007. Maintenance of imprinting and nuclear architecture in cycling cells. Proc Natl Acad Sci U S A 104:14970-14975.
235. Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, Weiss MJ, Dekker J, Blobel GA. 2005. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell 17:453-462.
236. Van Driel R, Wansink DG, Van Steensel B, Grande MA, Schul W, De Jong L. 1995. Nuclear domains and the nuclear matrix. Int Rev Cytol 162A:151-189.
237. van Wijnen AJ, Bidwell JP, Fey EG, Penman S, Lian JB, Stein JL, Stein GS. 1993. Nuclear matrix association of multiple sequence-specific DNA binding activities related to SP-1, ATF, CCAAT, C/EBP, OCT-1, and AP-1. Biochemistry 32:8397-8402.
238. Vernimmen D, De Gobbi M, Sloane-Stanley JA, Wood WG, Higgs DR. 2007. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J 26:2041-2051.
239. Visser AE, Jaunin F, Fakan S, Aten JA. 2000. High resolution analysis of interphase chromosome domains. J Cell Sci 113:2585-2593.
240. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD. 2011. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474:390-394.
241. Ward WS, Coffey DS. 1991. DNA packaging and organization in mammalian spermatozoa: Comparison with somatic cells. Biol Reprod 44:569-574.
242. Ward WS, Zalensky AO. 1996. The unique, complex organization of the transcriptionally silent sperm chromatin. Crit Rev Eukaryot Gene Expr 6:139-147.
243. Watson JD, Crick FH. 1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737-738.
244. Wei X, Samarabandu J, Devdhar RS, Siegel AJ, Acharya R, Berezney R. 1998. Segregation of transcription and replication sites into higher order domains. Science 281:1502-1506.
245. Wischnitzer S. 1973. The submicroscopic morphology of the interphase nucleus. Int Rev Cytol 34:1-48.
246. Xu M, Cook PR. 2008. Similar active genes cluster in specialized transcription factories. J Cell Biol 181:615-623.
247. Yaffe E, Tanay A. 2011. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43:1059-1065.
248. Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J. 2013. Transcription factor binding in human cells occurs in dense clusters formed around Cohesin anchor sites. Cell 154:801-813.
249. Zaidi SK, Young DW, Javed A, Pratap J, Montecino M, van Wijnen A, Lian JB, Stein JL, Stein GS. 2007. Nuclear microenvironments in biological control and cancer. Nat Rev Cancer 7:454-463.
250. Zaidi SK, Young DW, Montecino MA, Lian JB, van Wijnen AJ, Stein JL, Stein GS. 2010. Mitotic bookmarking of genes: A novel dimension to epigenetic control. Nat Rev Genet 11:583-589.
251. Zaret KS, Carroll JS. 2011. Pioneer transcription factors: Establishing competence for gene expression. Genes Dev 25:2227-2241.
252. Zaret KS, Caravaca JM, Tulin A, Sekiya T. 2010. Nuclear mobility and mitotic chromosome binding: Similarities between pioneer transcription factor FoxA and linker histone H1. Cold Spring Harb Symp Quant Biol 75:219-226.
253. Zhang Y, Rowley JD. 2006. Chromatin structural elements and chromosomal translocations in leukemia. DNA Repair (Amst) 5:1282-1297.
254. 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.
255. Zorn C, Cremer C, Cremer T, Zimmer J. 1979. Unscheduled DNA synthesis after partial UV irradiation of the cell nucleus. Distribution in interphase and metaphase Exp Cell Res 124:111-119.
256. Zullo JM, Demarco IA, Pique-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H. 2012. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 149:1474-1487.