Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

Cell

Volumn 162, Issue 4, 2015, Pages 911-923

  Shachar, Sigal ^a   Voss, Ty C ^a   Pegoraro, Gianluca ^a   Sciascia, Nicholas ^a   Misteli, Tom ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEAR FACTOR; PROTEIN MSH6; SMALL INTERFERING RNA;

ARTICLE; CELL COUNT; CELL CYCLE PROGRESSION; CELL NUCLEUS; CELL NUCLEUS MEMBRANE; CELL VIABILITY; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENE REPLICATION; GENOME ANALYSIS; GENOMICS; HIGH THROUGHPUT IMAGING POSITION MAPPING; HISTONE MODIFICATION; HUMAN; HUMAN CELL; MITOSIS; NUCLEAR LAMINA; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA PROCESSING; SKIN FIBROBLAST; CELL LINE; GENE; GENETIC PROCEDURES; GENETICS; IMAGE PROCESSING; PROCEDURES; SINGLE CELL ANALYSIS;

CELL LINE; CELL NUCLEUS; DNA REPLICATION; GENES; GENETIC TECHNIQUES; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; IN SITU HYBRIDIZATION, FLUORESCENCE; SINGLE-CELL ANALYSIS;

EID: 84939489844     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.07.035     Document Type: Article

References (56)

1. W. Akhtar, J. de Jong, A.V. Pindyurin, L. Pagie, W. Meuleman, J. de Ridder, A. Berns, L.F. Wessels, M. van Lohuizen, and B. van Steensel Chromatin position effects assayed by thousands of reporters integrated in parallel Cell 154 2013 914 927
2. W.A. Bickmore The spatial organization of the human genome Annu. Rev. Genomics Hum. Genet. 14 2013 67 84
3. M. Botta, S. Haider, I.X. Leung, P. Lio, and J. Mozziconacci Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide Mol. Syst. Biol. 6 2010 426
4. M.R. Branco, and A. Pombo Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations PLoS Biol. 4 2006 e138
5. I. Chiolo, A. Minoda, S.U. Colmenares, A. Polyzos, S.V. Costes, and G.H. Karpen Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair Cell 144 2011 732 744
6. J.R. Chubb, S. Boyle, P. Perry, and W.A. Bickmore Chromatin motion is constrained by association with nuclear compartments in human cells Curr. Biol. 12 2002 439 445
7. Z. Cvacková, M. Masata, D. Staněk, H. Fidlerová, and I. Raska Chromatin position in human HepG2 cells: although being non-random, significantly changed in daughter cells J. Struct. Biol. 165 2009 107 117
8. E. de Wit, and W. de Laat A decade of 3C technologies: insights into nuclear organization Genes Dev. 26 2012 11 24
9. J.R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J.S. Liu, and B. Ren Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 485 2012 376 380
10. P. Fernandez, P. Scaffidi, E. Markert, J.H. Lee, S. Rane, and T. Misteli Transformation resistance in a premature aging disorder identifies a tumor-protective function of BRD4 Cell Rep. 9 2014 248 260
11. C. Ferrai, I.J. de Castro, L. Lavitas, M. Chotalia, and A. Pombo Gene positioning Cold Spring Harb. Perspect. Biol. 2 2010 a000588
12. L.E. Finlan, D. Sproul, I. Thomson, S. Boyle, E. Kerr, P. Perry, B. Ylstra, J.R. Chubb, and W.A. Bickmore Recruitment to the nuclear periphery can alter expression of genes in human cells PLoS Genet. 4 2008 e1000039
13. D. Gerlich, J. Beaudouin, B. Kalbfuss, N. Daigle, R. Eils, and J. Ellenberg Global chromosome positions are transmitted through mitosis in mammalian cells Cell 112 2003 751 764
14. D.M. Gilbert, S.I. Takebayashi, T. Ryba, J. Lu, B.D. Pope, K.A. Wilson, and I. Hiratani Space and time in the nucleus: developmental control of replication timing and chromosome architecture Cold Spring Harb. Symp. Quant. Biol. 75 2010 143 153
15. L. Guelen, L. Pagie, E. Brasset, W. Meuleman, M.B. Faza, W. Talhout, B.H. Eussen, A. de Klein, L. Wessels, W. de Laat, and B. van Steensel Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions Nature 453 2008 948 951
16. O. Hakim, W. Resch, A. Yamane, I. Klein, K.R. Kieffer-Kwon, M. Jankovic, T. Oliveira, A. Bothmer, T.C. Voss, C. Ansarah-Sobrinho, and et al. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes Nature 484 2012 69 74
17. S.L. Hewitt, F.A. High, S.L. Reiner, A.G. Fisher, and M. Merkenschlager Nuclear repositioning marks the selective exclusion of lineage-inappropriate transcription factor loci during T helper cell differentiation Eur. J. Immunol. 34 2004 3604 3613
18. E.F. Joyce, B.R. Williams, T. Xie, and C.T. Wu Identification of genes that promote or antagonize somatic homolog pairing using a high-throughput FISH-based screen PLoS Genet. 8 2012 e1002667
19. S.T. Kosak, J.A. Skok, K.L. Medina, R. Riblet, M.M. Le Beau, A.G. Fisher, and H. Singh Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development Science 296 2002 158 162
20. R.I. Kumaran, and D.L. Spector A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence J. Cell Biol. 180 2008 51 65
21. E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B.R. Lajoie, P.J. Sabo, M.O. Dorschner, and et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
22. J.Q. Ling, T. Li, J.F. Hu, T.H. Vu, H.L. Chen, X.W. Qiu, A.M. Cherry, and A.R. Hoffman CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1 Science 312 2006 269 272
23. S. Mathas, S. Kreher, K.J. Meaburn, K. Jöhrens, B. Lamprecht, C. Assaf, W. Sterry, M.E. Kadin, M. Daibata, S. Joos, and et al. Gene deregulation and spatial genome reorganization near breakpoints prior to formation of translocations in anaplastic large cell lymphoma Proc. Natl. Acad. Sci. USA 106 2009 5831 5836
24. K.J. Meaburn, and T. Misteli Locus-specific and activity-independent gene repositioning during early tumorigenesis J. Cell Biol. 180 2008 39 50
25. K.J. Meaburn, E. Cabuy, G. Bonne, N. Levy, G.E. Morris, G. Novelli, I.R. Kill, and J.M. Bridger Primary laminopathy fibroblasts display altered genome organization and apoptosis Aging Cell 6 2007 139 153
26. K.J. Meaburn, T. Misteli, and E. Soutoglou Spatial genome organization in the formation of chromosomal translocations Semin. Cancer Biol. 17 2007 80 90
27. K.J. Meaburn, P.R. Gudla, S. Khan, S.J. Lockett, and T. Misteli Disease-specific gene repositioning in breast cancer J. Cell Biol. 187 2009 801 812
28. W. Meuleman, D. Peric-Hupkes, J. Kind, J.B. Beaudry, L. Pagie, M. Kellis, M. Reinders, L. Wessels, and B. van Steensel Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence Genome Res. 23 2013 270 280
29. T. Misteli Beyond the sequence: cellular organization of genome function Cell 128 2007 787 800
30. T. Misteli, and E. Soutoglou The emerging role of nuclear architecture in DNA repair and genome maintenance Nat. Rev. Mol. Cell Biol. 10 2009 243 254
31. T.J. Mitchison Small-molecule screening and profiling by using automated microscopy ChemBioChem 6 2005 33 39
32. K. Nandy, P.R. Gudla, R. Amundsen, K.J. Meaburn, T. Misteli, and S.J. Lockett Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images Cytometry A 81 2012 743 754
33. N. Naumova, M. Imakaev, G. Fudenberg, Y. Zhan, B.R. Lajoie, L.A. Mirny, and J. Dekker Organization of the mitotic chromosome Science 342 2013 948 953
34. D. Peric-Hupkes, W. Meuleman, L. Pagie, S.W. Bruggeman, I. Solovei, W. Brugman, S. Gräf, P. Flicek, R.M. Kerkhoven, M. van Lohuizen, and et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation Mol. Cell 38 2010 603 613
35. Z.E. Perlman, M.D. Slack, Y. Feng, T.J. Mitchison, L.F. Wu, and S.J. Altschuler Multidimensional drug profiling by automated microscopy Science 306 2004 1194 1198
36. J.E. Phillips, and V.G. Corces CTCF: master weaver of the genome Cell 137 2009 1194 1211
37. 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
38. K.L. Reddy, J.M. Zullo, E. Bertolino, and H. Singh Transcriptional repression mediated by repositioning of genes to the nuclear lamina Nature 452 2008 243 247
39. J.J. Roix, P.G. McQueen, P.J. Munson, L.A. Parada, and T. Misteli Spatial proximity of translocation-prone gene loci in human lymphomas Nat. Genet. 34 2003 287 291
40. P. Scaffidi, and T. Misteli In vitro generation of human cells with cancer stem cell properties Nat. Cell Biol. 13 2011 1051 1061
41. A. Smellie, C.J. Wilson, and S.C. Ng Visualization and interpretation of high content screening data J. Chem. Inf. Model. 46 2006 201 207
42. S. Sofueva, E. Yaffe, W.C. Chan, D. Georgopoulou, M. Vietri Rudan, H. Mira-Bontenbal, S.M. Pollard, G.P. Schroth, A. Tanay, and S. Hadjur Cohesin-mediated interactions organize chromosomal domain architecture EMBO J. 32 2013 3119 3129
43. M.R. Speicher, and N.P. Carter The new cytogenetics: blurring the boundaries with molecular biology Nat. Rev. Genet. 6 2005 782 792
44. T. Takizawa, K.J. Meaburn, and T. Misteli The meaning of gene positioning Cell 135 2008 9 13
45. P. Therizols, R.S. Illingworth, C. Courilleau, S. Boyle, A.J. Wood, and W.A. Bickmore Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells Science 346 2014 1238 1242
46. 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
47. B.D. Towbin, C. González-Aguilera, R. Sack, D. Gaidatzis, V. Kalck, P. Meister, P. Askjaer, and S.M. Gasser Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery Cell 150 2012 934 947
48. J. Vogelmann, A. Valeri, E. Guillou, O. Cuvier, and M. Nollmann Roles of chromatin insulator proteins in higher-order chromatin organization and transcription regulation Nucleus 2 2011 358 369
49. J. Walter, L. Schermelleh, M. Cremer, S. Tashiro, and T. Cremer Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages J. Cell Biol. 160 2003 685 697
50. A.H. Wang, H. Zare, K. Mousavi, C. Wang, C.E. Moravec, H.I. Sirotkin, K. Ge, G. Gutierrez-Cruz, and V. Sartorelli The histone chaperone Spt6 coordinates histone H3K27 demethylation and myogenesis EMBO J. 32 2013 1075 1086
51. Z. Wei, D. Huang, F. Gao, W.H. Chang, W. An, G.A. Coetzee, K. Wang, and W. Lu Biological implications and regulatory mechanisms of long-range chromosomal interactions J. Biol. Chem. 288 2013 22369 22377
52. R.R. Williams, V. Azuara, P. Perry, S. Sauer, M. Dvorkina, H. Jørgensen, J. Roix, P. McQueen, T. Misteli, M. Merkenschlager, and A.G. Fisher Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus J. Cell Sci. 119 2006 132 140
53. I. Williamson, S. Berlivet, R. Eskeland, S. Boyle, R.S. Illingworth, D. Paquette, J. Dostie, and W.A. Bickmore Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization Genes Dev. 28 2014 2778 2791
54. Y. Zhang, R.P. McCord, Y.J. Ho, B.R. Lajoie, D.G. Hildebrand, A.C. Simon, M.S. Becker, F.W. Alt, and J. Dekker Spatial organization of the mouse genome and its role in recurrent chromosomal translocations Cell 148 2012 908 921
55. Z. Zhao, G. Tavoosidana, M. Sjölinder, A. Göndör, P. Mariano, S. Wang, C. Kanduri, M. Lezcano, K.S. Sandhu, U. Singh, and et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions Nat. Genet. 38 2006 1341 1347
56. J. Zuin, J.R. Dixon, M.I. van der Reijden, Z. Ye, P. Kolovos, R.W. Brouwer, M.P. van de Corput, H.J. van de Werken, T.A. Knoch, I.W.F. van, and et al. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells Proc. Natl. Acad. Sci. USA 111 2014 996 1001