Three-dimensional folding and functional organization principles of the Drosophila genome

Cell

Volumn 148, Issue 3, 2012, Pages 458-472

  Sexton, Tom ^a   Yaffe, Eitan ^b   Kenigsberg, Ephraim ^b   Bantignies, Frédéric ^a   Leblanc, Benjamin ^a   Hoichman, Michael ^b   Parrinello, Hugues ^c   Tanay, Amos ^b   Cavalli, Giacomo ^a  

^a CNRS   (France)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^c Montpellier GenomiX IBiSA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

POLYCOMB GROUP PROTEIN;

BINDING SITE; CHROMOSOME; CHROMOSOME STRUCTURE; DROSOPHILA; EPIGENETICS; GENETIC ANALYSIS; GENOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; QUANTITATIVE ANALYSIS; REVIEW;

EID: 84856747483     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2012.01.010     Document Type: Article

References (50)

1. E. Apostolou, and D. Thanos Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression Cell 134 2008 85 96 (Pubitemid 351905745)
2. R.D. Artero, I. Castanon, and M.K. Baylies The immunoglobulin-like protein Hibris functions as a dose-dependent regulator of myoblast fusion and is differentially controlled by Ras and Notch signaling Development 128 2001 4251 4264 (Pubitemid 33077036)
3. F. Bantignies, V. Roure, I. Comet, B. Leblanc, B. Schuettengruber, J. Bonnet, V. Tixier, A. Mas, and G. Cavalli Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila Cell 144 2011 214 226
4. S. Chambeyron, and W.A. Bickmore Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription Genes Dev. 18 2004 1119 1130 (Pubitemid 38669033)
5. 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. USA 108 2011 2294 2299
6. T. Cremer, and M. Cremer Chromosome territories Cold Spring Harb. Perspect. Biol. 2 2010 a003889
7. E. de Wit, U. Braunschweig, F. Greil, H.J. Bussemaker, and B. van Steensel Global chromatin domain organization of the Drosophila genome PLoS Genet. 4 2008 e1000045
8. J. Dekker, K. Rippe, M. Dekker, and N. Kleckner Capturing chromosome conformation Science 295 2002 1306 1311 (Pubitemid 34157624)
9. Z. Duan, M. Andronescu, K. Schutz, S. McIlwain, Y.J. Kim, C. Lee, J. Shendure, S. Fields, C.A. Blau, and W.S. Noble A three-dimensional model of the yeast genome Nature 465 2010 363 367
10. J. Ernst, P. Kheradpour, T.S. Mikkelsen, N. Shoresh, L.D. Ward, C.B. Epstein, X. Zhang, L. Wang, R. Issner, and M. Coyne Mapping and analysis of chromatin state dynamics in nine human cell types Nature 473 2011 43 49
11. G.J. Filion, J.G. van Bemmel, U. Braunschweig, W. Talhout, J. Kind, L.D. Ward, W. Brugman, I.J. de Castro, R.M. Kerkhoven, H.J. Bussemaker, and B. van Steensel Systematic protein location mapping reveals five principal chromatin types in Drosophila cells Cell 143 2010 212 224
12. M.J. Fullwood, M.H. Liu, Y.F. Pan, J. Liu, H. Xu, Y.B. Mohamed, Y.L. Orlov, S. Velkov, A. Ho, and P.H. Mei An oestrogen-receptor-alpha-bound human chromatin interactome Nature 462 2009 58 64
13. 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 (Pubitemid 43344236)
14. L. Handoko, H. Xu, G. Li, C.Y. Ngan, E. Chew, M. Schnapp, C.W. Lee, C. Ye, J.L. Ping, and F. Mulawadi CTCF-mediated functional chromatin interactome in pluripotent cells Nat. Genet. 43 2011 630 638
15. D.W. Heermann Physical nuclear organization: loops and entropy Curr. Opin. Cell Biol. 23 2011 332 337
16. Q. Hu, Y.S. Kwon, E. Nunez, M.D. Cardamone, K.R. Hutt, K.A. Ohgi, I. Garcia-Bassets, D.W. Rose, C.K. Glass, M.G. Rosenfeld, and X.D. Fu Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules Proc. Natl. Acad. Sci. USA 105 2008 19199 19204
17. P.V. Kharchenko, A.A. Alekseyenko, Y.B. Schwartz, A. Minoda, N.C. Riddle, J. Ernst, P.J. Sabo, E. Larschan, A.A. Gorchakov, and T. Gu Comprehensive analysis of the chromatin landscape in Drosophila melanogaster Nature 471 2011 480 485
18. C. Lanctôt, T. Cheutin, M. Cremer, G. Cavalli, and T. Cremer Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions Nat. Rev. Genet. 8 2007 104 115 (Pubitemid 46122840)
19. 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 (Pubitemid 47500493)
20. E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B.R. Lajoie, P.J. Sabo, and M.O. Dorschner Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
21. M.G. Lowenstein, T.D. Goddard, and J.W. Sedat Long-range interphase chromosome organization in Drosophila: a study using color barcoded fluorescence in situ hybridization and structural clustering analysis Mol. Biol. Cell 15 2004 5678 5692 (Pubitemid 39564758)
22. J. Mateos-Langerak, M. Bohn, W. de Leeuw, O. Giromus, E.M. Manders, P.J. Verschure, M.H. Indemans, H.J. Gierman, D.W. Heermann, R. van Driel, and S. Goetze Spatially confined folding of chromatin in the interphase nucleus Proc. Natl. Acad. Sci. USA 106 2009 3812 3817
23. C. Münkel, R. Eils, S. Dietzel, D. Zink, C. Mehring, G. Wedemann, T. Cremer, and J. Langowski Compartmentalization of interphase chromosomes observed in simulation and experiment J. Mol. Biol. 285 1999 1053 1065 (Pubitemid 29054316)
24. D. Noordermeer, E. de Wit, P. Klous, H. van de Werken, M. Simonis, M. Lopez-Jones, B. Eussen, A. de Klein, R.H. Singer, and W. de Laat Variegated gene expression caused by cell-specific long-range DNA interactions Nat. Cell Biol. 13 2011 944 951
25. R.J. Palstra, B. Tolhuis, E. Splinter, R. Nijmeijer, F. Grosveld, and W. de Laat The beta-globin nuclear compartment in development and erythroid differentiation Nat. Genet. 35 2003 190 194 (Pubitemid 37187640)
26. U. Rath, D. Wang, Y. Ding, Y.Z. Xu, H. Qi, M.J. Blacketer, J. Girton, J. Johansen, and K.M. Johansen Chromator, a novel and essential chromodomain protein interacts directly with the putative spindle matrix protein skeletor J. Cell. Biochem. 93 2004 1033 1047 (Pubitemid 44264156)
27. U. Rath, Y. Ding, H. Deng, H. Qi, X. Bao, W. Zhang, J. Girton, J. Johansen, and K.M. Johansen The chromodomain protein, Chromator, interacts with JIL-1 kinase and regulates the structure of Drosophila polytene chromosomes J. Cell Sci. 119 2006 2332 2341 (Pubitemid 43960322)
28. P.J. Robinson, and D. Rhodes Structure of the '30 nm' chromatin fibre: a key role for the linker histone Curr. Opin. Struct. Biol. 16 2006 336 343 (Pubitemid 43831648)
29. R.K. Sachs, G. van den Engh, B. Trask, H. Yokota, and J.E. Hearst A random-walk/giant-loop model for interphase chromosomes Proc. Natl. Acad. Sci. USA 92 1995 2710 2714
30. S. Schoenfelder, T. Sexton, L. Chakalova, N.F. Cope, A. Horton, S. Andrews, S. Kurukuti, J.A. Mitchell, D. Umlauf, and D.S. Dimitrova Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells Nat. Genet. 42 2010 53 61
31. B. Schuettengruber, M. Ganapathi, B. Leblanc, M. Portoso, R. Jaschek, B. Tolhuis, M. van Lohuizen, A. Tanay, and G. Cavalli Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos PLoS Biol. 7 2009 e13
32. Y.B. Schwartz, T.G. Kahn, P. Stenberg, K. Ohno, R. Bourgon, and V. Pirrotta Alternative epigenetic chromatin states of polycomb target genes PLoS Genet. 6 2010 e1000805
33. T. Sexton, H. Schober, P. Fraser, and S.M. Gasser Gene regulation through nuclear organization Nat. Struct. Mol. Biol. 14 2007 1049 1055 (Pubitemid 350060340)
34. T. Sexton, F. Bantignies, and G. Cavalli Genomic interactions: chromatin loops and gene meeting points in transcriptional regulation Semin. Cell Dev. Biol. 20 2009 849 855
35. C. Shelton, K.S. Kocherlakota, S. Zhuang, and S.M. Abmayr The immunoglobulin superfamily member Hbs functions redundantly with Sns in interactions between founder and fusion-competent myoblasts Development 136 2009 1159 1168
36. M. Simonis, P. Klous, E. Splinter, Y. Moshkin, R. Willemsen, E. de Wit, B. van Steensel, and W. de Laat Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) Nat. Genet. 38 2006 1348 1354 (Pubitemid 44646300)
37. H. Tanizawa, O. Iwasaki, A. Tanaka, J.R. Capizzi, P. Wickramasinghe, M. Lee, Z. Fu, and K. Noma 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
38. 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 (Pubitemid 36050885)
39. B. Tolhuis, M. Blom, R.M. Kerkhoven, L. Pagie, H. Teunissen, M. Nieuwland, M. Simonis, W. de Laat, M. van Lohuizen, and B. van Steensel Interactions among Polycomb domains are guided by chromosome architecture PLoS Genet. 7 2011 e1001343
40. H. Weintraub Histone-H1-dependent chromatin superstructures and the suppression of gene activity Cell 38 1984 17 27 (Pubitemid 15216531)
41. A.M. Wood, K. Van Bortle, E. Ramos, N. Takenaka, M. Rohrbaugh, B.C. Jones, K.C. Jones, and V.G. Corces Regulation of chromatin organization and inducible gene expression by a Drosophila insulator Mol. Cell 44 2011 29 38
42. H. Würtele, and P. Chartrand Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology Chromosome Res. 14 2006 477 495 (Pubitemid 44015120)
43. E. Yaffe, and A. Tanay Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture Nat. Genet. 43 2011 1059 1065
44. Z. Zhao, G. Tavoosidana, M. Sjölinder, A. Göndör, P. Mariano, S. Wang, C. Kanduri, M. Lezcano, K.S. Sandhu, and U. Singh Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions Nat. Genet. 38 2006 1341 1347 (Pubitemid 44646299)
45. Fujita, P.A.; Rhead, B.; Zweig, A.S.; Hinrichs, A.S.; Karolchik, D.; Cline, M.S.; Goldman, M.; Barber, G.P.; Clawson, H.; Coelho, A.; et al. (2011). The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39 (Database issue), D876-D882.
46. Hagge, H.; Klous, P.; Braem, C.; Splinter, E.; Dekker, J.; Cathala, G.; de Laat, W.; and Forné, T. (2007). Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722-1733.
47. Misulovin, Z.; Schwartz, Y.B.; Li, X.Y.; Kahn, T.G.; Gause, M.; MacArthur, S.; Fay, J.C.; Eisen, M.B.; Pirrotta, V.; Biggin, M.D.; and Dorsett, D. (2008). Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma 117, 89-102.
48. Roy, S.; Ernst, J.; Kharchenko, P.V.; Kheradpour, P.; Negre, N.; Eaton, M.L.; Landolin, J.M.; Bristow, C.A.; Ma, L.; Lin, M.F.; et al; modENCODE Consortium. (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797.
49. Thomas, S.; Li, X.Y.; Sabo, P.J.; Sandstrom, R.; Thurman, R.E.; Canfield, T.K.; Giste, E.; Fisher, W.; Hammonds, A.; Celniker, S.E.; et al. (2011). Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 12, R43.
50. Zeitlinger, J.; Zinzen, R.P.; Stark, A.; Kellis, M.; Zhang, H.; Young, R.A.; and Levine, M. (2007). Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev. 21, 385-390.