Spatial organization of the mouse genome and its role in recurrent chromosomal translocations

Cell

Volumn 148, Issue 5, 2012, Pages 908-921

  Zhang, Yu ^a   McCord, Rachel Patton ^b   Ho, Yu Jui ^a   Lajoie, Bryan R ^b   Hildebrand, Dominic G ^a   Simon, Aline C ^a   Becker, Michael S ^a   Alt, Frederick W ^a   Dekker, Job ^b  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANIMAL CELL; ARTICLE; CHROMOSOME TRANSLOCATION; DOUBLE STRANDED DNA BREAK; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENOME; IONIZING RADIATION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EID: 84862778059     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2012.02.002     Document Type: Article

References (50)

1. A. Barreca, E. Lasorsa, L. Riera, R. Machiorlatti, R. Piva, M. Ponzoni, I. Kwee, F. Bertoni, P.P. Piccaluga, S.A. Pileri, G. Inghirami European T-Cell Lymphoma Study Group Anaplastic lymphoma kinase in human cancer J. Mol. Endocrinol. 47 2011 R11 R23
2. A. Bolzer, G. Kreth, I. Solovei, D. Koehler, K. Saracoglu, C. Fauth, S. Müller, R. Eils, C. Cremer, M.R. Speicher, and T. Cremer Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes PLoS Biol. 3 2005 e157
3. S. Boyle, S. Gilchrist, J.M. Bridger, N.L. Mahy, J.A. Ellis, and W.A. Bickmore The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells Hum. Mol. Genet. 10 2001 211 219 (Pubitemid 32123979)
4. A.L. Bredemeyer, G.G. Sharma, C.Y. Huang, B.A. Helmink, L.M. Walker, K.C. Khor, B. Nuskey, K.E. Sullivan, T.K. Pandita, C.H. Bassing, and B.P. Sleckman ATM stabilizes DNA double-strand-break complexes during V(D)J recombination Nature 442 2006 466 470 (Pubitemid 44264797)
5. A.L. Bredemeyer, B.A. Helmink, C.L. Innes, B. Calderon, L.M. McGinnis, G.K. Mahowald, E.J. Gapud, L.M. Walker, J.B. Collins, and B.K. Weaver DNA double-strand breaks activate a multi-functional genetic program in developing lymphocytes Nature 456 2008 819 823
6. R. Chiarle, Y. Zhang, R.L. Frock, S.M. Lewis, B. Molinie, Y.J. Ho, D.R. Myers, V.W. Choi, M. Compagno, and D.J. Malkin Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells Cell 147 2011 107 119
7. T. Cremer, and M. Cremer Chromosome territories Cold Spring Harb. Perspect. Biol. 2 2010 a003889
8. J. Dekker, K. Rippe, M. Dekker, and N. Kleckner Capturing chromosome conformation Science 295 2002 1306 1311 (Pubitemid 34157624)
9. D.O. Ferguson, J.M. Sekiguchi, S. Chang, K.M. Frank, Y. Gao, R.A. DePinho, and F.W. Alt The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations Proc. Natl. Acad. Sci. USA 97 2000 6630 6633 (Pubitemid 30412765)
10. N. Gilbert, S. Boyle, H. Fiegler, K. Woodfine, N.P. Carter, and W.A. Bickmore Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers Cell 118 2004 555 566 (Pubitemid 39179709)
11. M. Gostissa, S. Ranganath, J.M. Bianco, and F.W. Alt Chromosomal location targets different MYC family gene members for oncogenic translocations Proc. Natl. Acad. Sci. USA 106 2009 2265 2270
12. M. Gostissa, C.T. Yan, J.M. Bianco, M. Cogné, E. Pinaud, and F.W. Alt Long-range oncogenic activation of Igh-c-myc translocations by the Igh 3′ regulatory region Nature 462 2009 803 807
13. M. Gostissa, F.W. Alt, and R. Chiarle Mechanisms that promote and suppress chromosomal translocations in lymphocytes Annu. Rev. Immunol. 29 2011 319 350
14. I.A. Klein, W. Resch, M. Jankovic, T. Oliveira, A. Yamane, H. Nakahashi, M. Di Virgilio, A. Bothmer, A. Nussenzweig, and D.F. Robbiani Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes Cell 147 2011 95 106
15. R. Kurzrock, H.M. Kantarjian, B.J. Druker, and M. Talpaz Philadelphia chromosome-positive leukemias: from basic mechanisms to molecular therapeutics Ann. Intern. Med. 138 2003 819 830 (Pubitemid 38124644)
16. G. Li, F.W. Alt, H.L. Cheng, J.W. Brush, P.H. Goff, M.M. Murphy, S. Franco, Y. Zhang, and S. Zha Lymphocyte-specific compensation for XLF/cernunnos end-joining functions in V(D)J recombination Mol. Cell 31 2008 631 640
17. 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
18. C. Lin, L. Yang, B. Tanasa, K. Hutt, B.G. Ju, K. Ohgi, J. Zhang, D.W. Rose, X.D. Fu, C.K. Glass, and M.G. Rosenfeld Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer Cell 139 2009 1069 1083
19. H. Liu, E.H. Cheng, and J.J. Hsieh MLL fusions: pathways to leukemia Cancer Biol. Ther. 8 2009 1204 1211
20. M. Liu, and D.G. Schatz Balancing AID and DNA repair during somatic hypermutation Trends Immunol. 30 2009 173 181
21. P. Liu, A. Erez, S.C. Nagamani, S.U. Dhar, K.E. Kołodziejska, A.V. Dharmadhikari, M.L. Cooper, J. Wiszniewska, F. Zhang, and M.A. Withers Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements Cell 146 2011 889 903
22. G.K. Mahowald, J.M. Baron, M.A. Mahowald, S. Kulkarni, A.L. Bredemeyer, C.H. Bassing, and B.P. Sleckman Aberrantly resolved RAG-mediated DNA breaks in Atm-deficient lymphocytes target chromosomal breakpoints in cis Proc. Natl. Acad. Sci. USA 106 2009 18339 18344
23. R.S. Mani, S.A. Tomlins, K. Callahan, A. Ghosh, M.K. Nyati, S. Varambally, N. Palanisamy, and A.M. Chinnaiyan Induced chromosomal proximity and gene fusions in prostate cancer Science 326 2009 1230
24. W.F. Marshall, A. Straight, J.F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A.W. Murray, D.A. Agard, and J.W. Sedat Interphase chromosomes undergo constrained diffusional motion in living cells Curr. Biol. 7 1997 930 939 (Pubitemid 28017070)
25. S. Mathas, S. Kreher, K.J. Meaburn, K. Jöhrens, B. Lamprecht, C. Assaf, W. Sterry, M.E. Kadin, M. Daibata, and S. Joos 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
26. 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
27. K.J. Meaburn, T. Misteli, and E. Soutoglou Spatial genome organization in the formation of chromosomal translocations Semin. Cancer Biol. 17 2007 80 90 (Pubitemid 46054486)
28. L.A. Mirny The fractal globule as a model of chromatin architecture in the cell Chromosome Res. 19 2011 37 51
29. H. Neves, C. Ramos, M.G. da Silva, A. Parreira, and L. Parreira The nuclear topography of ABL, BCR, PML, and RARalpha genes: evidence for gene proximity in specific phases of the cell cycle and stages of hematopoietic differentiation Blood 93 1999 1197 1207 (Pubitemid 29076134)
30. H. Ohno Pathogenetic and clinical implications of non-immunoglobulin; BCL6 translocations in B-cell non-Hodgkin's lymphoma J. Clin. Exp. Hematop. 46 2006 43 53
31. C.S. Osborne, L. Chakalova, J.A. Mitchell, A. Horton, A.L. Wood, D.J. Bolland, A.E. Corcoran, and P. Fraser Myc dynamically and preferentially relocates to a transcription factory occupied by Igh PLoS Biol. 5 2007 e192
32. T. Rausch, D.T. Jones, M. Zapatka, A.M. Stütz, T. Zichner, J. Weischenfeldt, N. Jäger, M. Remke, D. Shih, and P.A. Northcott Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations Cell 148 2012 59 71
33. D.F. Robbiani, A. Bothmer, E. Callen, B. Reina-San-Martin, Y. Dorsett, S. Difilippantonio, D.J. Bolland, H.T. Chen, A.E. Corcoran, A. Nussenzweig, and M.C. Nussenzweig AID is required for the chromosomal breaks in c-myc that lead to c-myc/IgH translocations Cell 135 2008 1028 1038
34. 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 (Pubitemid 36792860)
35. K. Rothkamm, and M. Löbrich Evidence for a lack of DNA double-strand break repair in human cells exposed to very low x-ray doses Proc. Natl. Acad. Sci. USA 100 2003 5057 5062 (Pubitemid 36542657)
36. D.G. Schatz, and P.C. Swanson V(D)J recombination: mechanisms of initiation Annu. Rev. Genet. 45 2011 167 202
37. J. Sekiguchi, D.O. Ferguson, H.T. Chen, E.M. Yang, J. Earle, K. Frank, S. Whitlow, Y. Gu, Y. Xu, A. Nussenzweig, and F.W. Alt Genetic interactions between ATM and the nonhomologous end-joining factors in genomic stability and development Proc. Natl. Acad. Sci. USA 98 2001 3243 3248 (Pubitemid 32220830)
38. K. Sengupta, J. Camps, P. Mathews, L. Barenboim-Stapleton, Q.T. Nguyen, M.J. Difilippantonio, and T. Ried Position of human chromosomes is conserved in mouse nuclei indicating a species-independent mechanism for maintaining genome organization Chromosoma 117 2008 499 509
39. T. Sexton, E. Yaffe, E. Kenigsberg, F. Bantignies, B. Leblanc, M. Hoichman, H. Parrinello, A. Tanay, and G. Cavalli Three-dimensional folding and functional organization principles of the Drosophila genome Cell 148 2012 458 472
40. 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)
41. E. Soutoglou, J.F. Dorn, K. Sengupta, M. Jasin, A. Nussenzweig, T. Ried, G. Danuser, and T. Misteli Positional stability of single double-strand breaks in mammalian cells Nat. Cell Biol. 9 2007 675 682 (Pubitemid 47214730)
42. P.J. Stephens, D.J. McBride, M.L. Lin, I. Varela, E.D. Pleasance, J.T. Simpson, L.A. Stebbings, C. Leroy, S. Edkins, and L.J. Mudie Complex landscapes of somatic rearrangement in human breast cancer genomes Nature 462 2009 1005 1010
43. P.J. Stephens, C.D. Greenman, B. Fu, F. Yang, G.R. Bignell, L.J. Mudie, E.D. Pleasance, K.W. Lau, D. Beare, and L.A. Stebbings Massive genomic rearrangement acquired in a single catastrophic event during cancer development Cell 144 2011 27 40
44. M.R. Stratton Exploring the genomes of cancer cells: progress and promise Science 331 2011 1553 1558
45. A.G. Tsai, and M.R. Lieber Mechanisms of chromosomal rearrangement in the human genome BMC Genomics 11 Suppl 1 2010 S1
46. A.G. Tsai, H. Lu, S.C. Raghavan, M. Muschen, C.L. Hsieh, and M.R. Lieber Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity Cell 135 2008 1130 1142
47. J.H. Wang, M. Gostissa, C.T. Yan, P. Goff, T. Hickernell, E. Hansen, S. Difilippantonio, D.R. Wesemann, A.A. Zarrin, and K. Rajewsky Mechanisms promoting translocations in editing and switching peripheral B cells Nature 460 2009 231 236
48. B. Yalcin, K. Wong, A. Agam, M. Goodson, T.M. Keane, X. Gan, C. Nellker, L. Goodstadt, J. Nicod, and A. Bhomra Sequence-based characterization of structural variation in the mouse genome Nature 477 2011 326 329
49. Y. Zhang, M. Gostissa, D.G. Hildebrand, M.S. Becker, C. Boboila, R. Chiarle, S. Lewis, and F.W. Alt The role of mechanistic factors in promoting chromosomal translocations found in lymphoid and other cancers Adv. Immunol. 106 2010 93 133
50. Yaffe, E., and Tanay, A. (2011). Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet. 43, 1059-1065.