Molecular pathways: Transcription factories and chromosomal translocations

Clinical Cancer Research

Volumn 20, Issue 2, 2014, Pages 296-300

  Osborne, Cameron S ^a  

^a BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CARCINOGENICITY; CHROMOSOME TRANSLOCATION; DNA REPAIR; DNA REPLICATION; DOUBLE STRANDED DNA BREAK; GENE CLUSTER; GENE REARRANGEMENT; GENE TRANSLOCATION; GENETIC SUSCEPTIBILITY; GENOME ANALYSIS; GENOMIC INSTABILITY; HUMAN; MOLECULAR MODEL; NEOPLASM; NONHUMAN; NUCLEAR IMPORT; PRIORITY JOURNAL; RNA PROCESSING; RNA TRANSCRIPTION; TRANSCRIPTION FACTORY; TRANSCRIPTION INITIATION;

ANIMALS; HUMANS; NEOPLASMS; TRANSCRIPTION FACTORS; TRANSLOCATION, GENETIC;

EID: 84892778153     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-12-3667     Document Type: Article

References (47)

1. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al. Landscape of transcription in human cells. Nature 2012;489: 101-8
2. Grande MA, van der Kraan I, de Jong L, van Driel R. Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J Cell Sci 1997;110:1781-91
3. Iborra FJ, Pombo A, Jackson DA, Cook PR. Active RNA polymerases are localizedwithin discrete transcription "factories" in human nuclei. J Cell Sci 1996;109:1427-36
4. Jackson DA, Hassan AB, Errington RJ, Cook PR. Visualization of focal sites of transcription within human nuclei. EMBO J 1993;12: 1059-65
5. Pombo A, Jackson DA, Hollinshead M, Wang Z, Roeder RG, Cook PR. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J 1999;18:2241-53
6. Razin SV, Gavrilov AA, Pichugin A, Lipinski M, Iarovaia OV, Vassetzky YS. Transcription factories in the context of the nuclear and genome organization. Nucleic Acids Res 2011;39:9085-92
7. Sutherland H, Bickmore WA. Transcription factories: gene expression in unions? Nat Rev Genet 2009;10:457-66
8. Kimura H, Sugaya K, Cook PR. The transcription cycle of RNA polymerase II in living cells. J Cell Biol 2002;159:777-82
9. Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, et al. Real-time dynamics ofRNApolymerase II clustering in live human cells. Science 2013;341:664-7
10. Ghamari A, van de Corput MP, Thongjuea S, van Cappellen WA, van Ijcken W, van Haren J, et al. In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev 2013;27:767-77
11. Eskiw CH, Fraser P. Ultrastructural study of transcription factories in mouse erythroblasts. J Cell Sci 2011;124:3676-83
12. Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 2004;36:1065-71
13. Melnik S, Deng B, Papantonis A, Baboo S, Carr IM, Cook PR. The proteomes of transcription factories containing RNA polymerases I, II, or III. Nat Methods 2011;8:963-8
14. Mitchell JA, Fraser P. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev 2008; 22:20-5
15. Moir RD, Yoon M, Khuon S, Goldman RD. Nuclear lamins A and B1: different pathways of assembly during nuclear envelope formation in living cells. J Cell Biol 2000;151:1155-68
16. Martin C, Chen S, Maya-Mendoza A, Lovric J, Sims PF, Jackson DA. Lamin B1 maintains the functional plasticity of nucleoli. J Cell Sci 2009;122:1551-62
17. Tang CW, Maya-Mendoza A, Martin C, Zeng K, Chen S, Feret D, et al. The integrity of a lamin-B1-dependent nucleoskeleton is a fundamental determinant of RNA synthesis in human cells. J Cell Sci 2008; 121:1014-24
18. Ragoczy T, Bender MA, Telling A, Byron R, Groudine M. The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 2006;20:1447-57
19. Schoenfelder S, Sexton T,Chakalova L,Cope NF, Horton A, AndrewsS, et al. Preferential associations between coregulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 2010;42:53-61
20. Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, et al.Mycdynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol 2007;5:e192
21. Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, et al. TNFalpha signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J 2012;31:4404-14
22. Larkin JD, Papantonis A, Cook PR. Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J Cell Sci 2013;126:2052-9
23. Kang J, Xu B, Yao Y, Lin W, Hennessy C, Fraser P, et al. A dynamical model reveals gene co-localizations in nucleus. PLoS Comput Biol 2011;7:e1002094
24. Kozubek S, Lukasova E, Mareckova A, Skalnikova M, Kozubek M, Bartova E, et al. The topological organization of chromosomes 9 and 22 in cell nuclei has a determinative role in the induction of t9,22 translocations and in the pathogenesis of t9,22 leukemias. Chromosoma 1999;108:426-35
25. Neves H, Ramos C, da Silva MG, Parreira A, Parreira L. 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 1999;93:1197-207
26. Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T. Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet 2003;34:287-91
27. Aten JA, Stap J, Krawczyk PM, van Oven CH, Hoebe RA, Essers J, et al. Dynamics of DNA double-strand breaks revealed by clustering of damaged chromosome domains. Science 2004;303:92-5
28. Krawczyk PM, Borovski T, Stap J, Cijsouw T, ten Cate R, Medema JP, et al. Chromatin mobility is increased at sites of DNA double-strand breaks. J Cell Sci 2012;125:2127-33
29. Soutoglou E, Dorn JF, Sengupta K, Jasin M, Nussenzweig A, Ried T, et al. Positional stability of single double-strand breaks in mammalian cells. Nat Cell Biol 2007;9:675-82
30. Roukos V, Voss TC, Schmidt CK, Lee S, Wangsa D, Misteli T. Spatial dynamics of chromosome translocations in living cells. Science 2013;341:660-4
31. Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 1987;84:7024-7
32. Kouzine F, Gupta A, Baranello L, Wojtowicz D, Ben-Aissa K, Liu J, et al. Transcription-dependent dynamic supercoiling is a short-range genomic force. Nat Struct Mol Biol 2013;20:396-403
33. Ju BG, Lunyak VV, Perissi V, Garcia-Bassets I, Rose DW, Glass CK, et al. A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription. Science 2006;312:1798-802
34. Mo X, Dynan WS. Subnuclear localization of Ku protein: functional association with RNA polymerase II elongation sites. Mol Cell Biol 2002;22:8088-99
35. Cowell IG, Sondka Z, Smith K, Lee KC, Manville CM, Sidorczuk- Lesthuruge M, et al. Model for MLL translocations in therapy-related leukemia involving topoisomerase IIbeta-mediated DNA strand breaks and gene proximity. Proc Natl Acad Sci U S A 2012;109:8989-94
36. Chiarle R, Zhang Y, Frock RL, Lewis SM, Molinie B, Ho YJ, et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 2011;147: 107-19
37. Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, et al. Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 2011;147: 95-106
38. Lin C, Yang L, Tanasa B, Hutt K, Ju BG, Ohgi K, et al. Nuclear receptorinduced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 2009;139:1069-83
39. Osborne CS, Ewels PA, Young AN. Meet the neighbours: tools to dissect nuclear structure and function. Brief Funct Genomics 2011; 10:11-7
40. Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 2012;148:908-21
41. Hakim O, Resch W, Yamane A, Klein I, Kieffer-Kwon KR, Jankovic M, et al. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature 2012;484:69-74
42. Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, et al. Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell 2012;47:873-85
43. Casellas R, Resch W, Hakim O, Nussenzweig MC. The origin of B cell recurrent chromosomal translocations: proximity versus DNA damage. Mol Cell 2013;51:275-6
44. Rocha PP, Micsinai M, Kluger Y, Skok JA. Response to Casellas et al. Mol Cell 2013;51:277-8
45. Allan JM, Travis LB. Mechanisms of therapy-related carcinogenesis. Nat Rev Cancer 2005;5:943-55
46. Zhang Y, Rowley JD. Chromatin structural elements and chromosomal translocations in leukemia. DNA Repair 2006;5:1282-97
47. Cowell IG, Austin CA. Mechanism of generation of therapy related leukemia in response to anti-topoisomerase II agents. Int J Environ Res Public Health 2012;9:2075-91