3D trajectories adopted by coding and regulatory DNA elements: First-passage times for genomic interactions

Cell

Volumn 158, Issue 2, 2014, Pages 339-352

  Lucas, Joseph S ^a   Zhang, Yaojun ^b   Dudko, Olga K ^b   Murre, Cornelis ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; IMMUNOGLOBULIN HEAVY CHAIN; ENHANCED GREEN FLUORESCENT PROTEIN; IMMUNOGLOBULIN HEAVY CHAIN DIVERSITY H; IMMUNOGLOBULIN HEAVY CHAIN JOINING H; IMMUNOGLOBULIN HEAVY CHAIN VARIABLE H; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; EXPRESSION VECTOR; GENE INTERACTION; GENETIC CODE; NONHUMAN; PRE B LYMPHOCYTE; PRIORITY JOURNAL; REPRESSOR GENE; RETROVIRUS; VISCOELASTICITY; ANIMAL CELL; B LYMPHOCYTE; CELL LINEAGE; CELL MOTION; CHROMATIN; CHROMOSOME DELETION; DNA REPAIR; DYNAMICS; ENHANCER REGION; GENE EXPRESSION; GENE LOCUS; GENE REARRANGEMENT; INTERNAL RIBOSOME ENTRY SITE; LACTOSE OPERON; MITOTIC RECOMBINATION; VDJ RECOMBINATION;

ANIMALS; BIOMECHANICAL PHENOMENA; ELASTICITY; EMBRYONIC STEM CELLS; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; GENETIC VECTORS; IMMUNOGLOBULIN HEAVY CHAINS; MICE; PRECURSOR CELLS, B-LYMPHOID; TRANSDUCTION, GENETIC; V(D)J RECOMBINATION; VISCOSITY;

EID: 84904567038     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.05.036     Document Type: Article

References (54)

1. F.W. Alt, G.D. Yancopoulos, T.K. Blackwell, C. Wood, E. Thomas, M. Boss, R. Coffman, N. Rosenberg, S. Tonegawa, and D. Baltimore Ordered rearrangement of immunoglobulin heavy chain variable region segments EMBO J. 3 1984 1209 1219
2. F.W. Alt, Y. Zhang, F.L. Meng, C. Guo, and B. Schwer Mechanisms of programmed DNA lesions and genomic instability in the immune system Cell 152 2013 417 429
3. R. Beroukhim, C.H. Mermel, D. Porter, G. Wei, S. Raychaudhuri, J. Donovan, J. Barretina, J.S. Boehm, J. Dobson, and M. Urashima et al. The landscape of somatic copy-number alteration across human cancers Nature 463 2010 899 905
4. 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
5. T. Boveri Die Blastomerenkerne von Ascaris meglocephala und die Theorie der Chromosomenindividualitaet Archiv. für Zellforschung 3 1909 181 268
6. I. Bronstein, Y. Israel, E. Kepten, S. Mai, Y. Shav-Tal, E. Barkai, and Y. Garini Transient anomalous diffusion of telomeres in the nucleus of mammalian cells Phys. Rev. Lett. 103 2009 018102
7. S.F. Bunting, and A. Nussenzweig End-joining, translocations and cancer Nat. Rev. Cancer 13 2013 443 454
8. G.G. Cabal, A. Genovesio, S. Rodriguez-Navarro, C. Zimmer, O. Gadal, A. Lesne, H. Buc, F. Feuerbach-Fournier, J.C. Olivo-Marin, E.C. Hurt, and U. Nehrbass SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope Nature 441 2006 770 773
9. H. Cedar, and Y. Bergman Epigenetics of haematopoietic cell development Nat. Rev. Immunol. 11 2011 478 488
10. 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 et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells Cell 147 2011 107 119
11. S. Condamin, O. Bénichou, V. Tejedor, R. Voituriez, and J. Klafter First-passage times in complex scale-invariant media Nature 450 2007 77 80
12. S.C. Degner, T.P. Wong, G. Jankevicius, and A.J. Feeney Cutting edge: developmental stage-specific recruitment of cohesin to CTCF sites throughout immunoglobulin loci during B lymphocyte development J. Immunol. 182 2009 44 48
13. S.C. Degner, J. Verma-Gaur, T.P. Wong, C. Bossen, G.M. Iverson, A. Torkamani, C. Vettermann, Y.C. Lin, Z. Ju, and D. Schulz et al. 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. USA 108 2011 9566 9571
14. C.R. Dietrich, and G.N. Newsam Fast and exact simulation of stationary Gaussian processes through circulant embedding of the covariance matrix SIAM J. Sci. Comput. 18 1997 1088 1107
15. 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
16. M. Fuxa, J. Skok, A. Souabni, G. Salvagiotto, E. Roldan, and M. Busslinger Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene Genes Dev. 18 2004 411 422
17. M. Gostissa, B. Schwer, A. Chang, J. Dong, R.M. Meyers, G.T. Marecki, V.W. Choi, R. Chiarle, A.A. Zarrin, and F.W. Alt IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances Proc. Natl. Acad. Sci. USA 111 2014 2644 2649
18. U. Grawunder, T.M. Leu, D.G. Schatz, A. Werner, A.G. Rolink, F. Melchers, and T.H. Winkler Down-regulation of RAG1 and RAG2 gene expression in preB cells after functional immunoglobulin heavy chain rearrangement Immunity 3 1995 601 608
19. C. Guo, T. Gerasimova, H. Hao, I. Ivanova, T. Chakraborty, R. Selimyan, E.M. Oltz, and R. Sen Two forms of loops generate the chromatin conformation of the immunoglobulin heavy-chain gene locus Cell 147 2011 332 343
20. C. Guo, H.S. Yoon, A. Franklin, S. Jain, A. Ebert, H.L. Cheng, E. Hansen, O. Despo, C. Bossen, and C. Vettermann et al. CTCF-binding elements mediate control of V(D)J recombination Nature 477 2011 424 430
21. R.G. Hawley, F.H. Lieu, A.Z. Fong, S.J. Goldman, J.P. Leonard, and T.S. Hawley Retroviral vectors for production of interleukin-12 in the bone marrow to induce a graft-versus-leukemia effect Ann. N Y Acad. Sci. 795 1996 341 345
22. S.L. Hewitt, J. Chaumeil, and J.A. Skok Chromosome dynamics and the regulation of V(D)J recombination Immunol. Rev. 237 2010 43 54
23. J.H. Jeon, and R. Metzler Fractional Brownian motion and motion governed by the fractional Langevin equation in confined geometries Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 81 2010 021103
24. S. Jhunjhunwala, M.C. van Zelm, M.M. Peak, S. Cutchin, R. Riblet, J.J. van Dongen, F.G. Grosveld, T.A. Knoch, and C. Murre The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions Cell 133 2008 265 279
25. D. Jung, C. Giallourakis, R. Mostoslavsky, and F.W. Alt Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus Annu. Rev. Immunol. 24 2006 541 570
26. I.A. Klein, W. Resch, M. Jankovich, T. Oliveira, A. Yamane, H. Nakhashi, M. Di Virgillio, A. Bothmer, A. Nussenzweig, and D.F. Robbiani et al. Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes Cell 147 2011 95 106
27. 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
28. I.F. Lau, S.R. Filipe, B. Søballe, O.A. Økstad, F.X. Barre, and D.J. Sherratt Spatial and temporal organization of replicating Escherichia coli chromosomes Mol. Microbiol. 49 2003 731 743
29. 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 et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
30. Y.C. Lin, C. Benner, R. Mansson, S. Heinz, K. Miyazaki, M. Miyazaki, V. Chandra, C. Bossen, C.K. Glass, and C. Murre Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate Nat. Immunol. 13 2012 1196 1204
31. T.M. Luby, C.E. Schrader, J. Stavnezer, and E. Selsing The mu switch region tandem repeats are important, but not required, for antibody class switch recombination J. Exp. Med. 193 2001 159 168
32. J.S. Lucas, C. Bossen, and C. Murre Transcription and recombination factories: common features? Curr. Opin. Cell Biol. 23 2011 318 324
33. E. Lutz Fractional Langevin equation Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 64 2001 051106
34. J. Manz, K. Denis, O. Witte, R. Brinster, and U. Storb Feedback inhibition of immunoglobulin gene rearrangement by membrane mu, but not by secreted mu heavy chains J. Exp. Med. 168 1988 1363 1381
35. J. Medvedovic, A. Ebert, H. Tagoh, I.M. Tamir, T.A. Schwickert, M. Novatchkova, Q. Sun, P.J. Huis In 't Veld, C. Guo, and H.S. Yoon et al. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire Immunity 39 2013 229 244
36. E.W. Montroll, and G.H. Weiss Random walks on lattices. II J. Math. Phys. 6 1965 167 181
37. C. Münkel, and J. Langowski Chromosome structure described by a polymer model Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics 57 1998 5888 5896
38. M.C. Nussenzweig, A.C. Shaw, E. Sinn, J. Campos-Torres, and P. Leder Allelic exclusion in transgenic mice carrying mutant human IgM genes J. Exp. Med. 167 1988 1969 1974
39. M. Onozawa, and P.D. Aplan Illegitimate V(D)J recombination involving nonantigen receptor loci in lymphoid malignancy Genes Chromosomes Cancer 51 2012 525 535
40. C. Rabl Über Zellteilung Morphologisches Jahrbuch 10 1885 214 330
41. I. Retter, C. Chevillard, M. Scharfe, A. Conrad, M. Hafner, T.H. Im, M. Ludewig, G. Nordsiek, S. Severitt, and S. Thies et al. Sequence and characterization of the Ig heavy chain constant and partial variable region of the mouse strain 129S1 J. Immunol. 179 2007 2419 2427
42. E. Roldán, M. Fuxa, W. Chong, D. Martinez, M. Novatchkova, M. Busslinger, and J.A. Skok Locus 'decontraction' and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene Nat. Immunol. 6 2005 31 41
43. M.J. Saxton Anomalous diffusion due to obstacles: a Monte Carlo study Biophys. J. 66 1994 394 401
44. M.J. Saxton Anomalous diffusion due to binding: a Monte Carlo study Biophys. J. 70 1996 1250 1262
45. C.E. Sayegh, M.W. Quong, Y. Agata, and C. Murre E-proteins directly regulate expression of activation-induced deaminase in mature B cells Nat. Immunol. 4 2003 586 593
46. J. Sedat, and L. Manuelidis A direct approach to the structure of eukaryotic chromosomes Cold Spring Harb. Symp. Quant. Biol. 42 1978 331 350
47. A. Shimizu, N. Takahashi, Y. Yaoita, and T. Honjo Organization of the constant-region gene family of the mouse immunoglobulin heavy chain Cell 28 1982 499 506
48. N.L. Solimini, Q. Xu, C.H. Mermel, A.C. Liang, M.R. Schlabach, J. Luo, A.E. Burrows, A.N. Anselmo, A.L. Bredemeyer, and M.Z. Li et al. Recurrent hemizygous deletions in cancers may optimize proliferative potential Science 337 2012 104 109
49. S. Urlinger, U. Baron, M. Thellmann, M.T. Hasan, H. Bujard, and W. Hillen Exploring the sequence space for tetracycline-dependent transcriptional activators: novel mutations yield expanded range and sensitivity Proc. Natl. Acad. Sci. USA 97 2000 7963 7968
50. J. Vazquez, A.S. Belmont, and J.W. Sedat Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus Curr. Biol. 11 2001 1227 1239
51. S.C. Weber, A.J. Spakowitz, and J.A. Theriot Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm Phys. Rev. Lett. 104 2010 238102
52. S.C. Weber, M.A. Thompson, W.E. Moerner, A.J. Spakowitz, and J.A. Theriot Analytical tools to distinguish the effects of localization error, confinement, and medium elasticity on the velocity autocorrelation function Biophys. J. 102 2012 2443 2450
53. A.A. Zarrin, C. Del Vecchio, E. Tseng, M. Gleason, P. Zarin, M. Tian, and F.W. Alt Antibody class switching mediated by yeast endonuclease-generated DNA breaks Science 315 2007 377 381
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