Skip to main content
SpringerLink
Log in
Book cover

Systems Analysis of Chromatin-Related Protein Complexes in Cancer pp 257–276Cite as

Genome Organization in Cancer Cells

  • Chapter
  • First Online:

  • 1470 Accesses

Abstract

Tumor cells display dramatic changes in gene expression compared to the normal cells in the surrounding tissue. These changes are often due to chromosomal rearrangements or somatic mutations which result in the altered expression or function of proteins that regulate transcription. Indeed, recurrent chromosomal translocations are hallmarks of human cancers and vary between different types of cancer. Recent studies have implicated genome organization and the frequency of DNA double strand breaks as important factors contributing to the formation of specific chromosomal translocations. It has also become increasingly clear that nonrandom organization of the genome regulates gene expression in a cell type-specific manner. Single nucleotide changes in intergenic regions of the genome have been shown to affect gene regulation through the formation of chromatin loops. Therefore, understanding the interplay between genome organization and transcription in normal cell types and its perturbations in cancer will provide important insights into the causes of tumorigenesis.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Abbreviations

AID:

Activation-induced cytidine deaminase

DSBs:

DNA double-strand breaks

FISH:

Fluorescence in situ hybridization

GWAS:

Genome-wide association studies

H3K4me3:

Histone H3 lysine4 trimethylation

H3K9ac:

Histone H3 lysine 9 acetylation

H3K9me2:

Histone H3 lysine 9 dimethylation

H3K9me3:

Histone H3 lysine 9 trimethylation

H4K20me3:

Histone H4 lysine 20 trimethylation

Ig:

Immunoglobulin locus

ISH:

In situ hybridisation

RNAPI:

RNA polymerase I

RNAPII:

RNA polymerase II

RNAPIII:

RNA polymerase III

rRNA:

Ribosomal RNA

SNPs:

Single nucleotide polymorphisms

TCR:

T-cell receptor locus

References

  1. Freed-Pastor WA, Prives C. Mutant p53: one name, many proteins. Genes Dev. 2012;26(12):1268–86.

    Article  PubMed  CAS  Google Scholar 

  2. Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, et al. A global map of p53 transcription-factor binding sites in the human genome. Cell. 2006;124(1):207–19.

    Article  PubMed  CAS  Google Scholar 

  3. Jackson DA, Hassan AB, Errington RJ, Cook PR. Visualization of focal sites of transcription within human nuclei. EMBO J. 1993;12(3):1059–65.

    PubMed  CAS  Google Scholar 

  4. Wansink DG, Schul W, van der Kraan I, van Steensel B, van Driel R, de Jong L. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J Cell Biol. 1993;122(2):283–93.

    Article  PubMed  CAS  Google Scholar 

  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(8):2241–53.

    Article  PubMed  CAS  Google Scholar 

  6. Nemeth A, Langst G. Genome organization in and around the nucleolus. Trends Genet. 2011;27(4):149–56.

    Article  PubMed  CAS  Google Scholar 

  7. 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(10):1065–71.

    Article  PubMed  CAS  Google Scholar 

  8. Faro-Trindade I, Cook PR. A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. Mol Biol Cell. 2006;17(7):2910–20.

    Article  PubMed  CAS  Google Scholar 

  9. Eskiw CH, Fraser P. Ultrastructural study of transcription factories in mouse erythroblasts. J Cell Sci. 2011;124(Pt 21):3676–83.

    Article  PubMed  CAS  Google Scholar 

  10. 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(11):1447–57.

    Article  PubMed  CAS  Google Scholar 

  11. Cook PR. A model for all genomes: the role of transcription factories. J Mol Biol. 2010;395(1):1–10.

    Article  PubMed  CAS  Google Scholar 

  12. Iborra FJ, Pombo A, Jackson DA, Cook PR. Active RNA polymerases are localized within discrete transcription “factories” in human nuclei. J Cell Sci. 1996;109(Pt 6):1427–36.

    PubMed  CAS  Google Scholar 

  13. Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, et al. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol. 2007;5(8):e192.

    Article  PubMed  Google Scholar 

  14. Belmont AS, Braunfeld MB, Sedat JW, Agard DA. Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro. Chromosoma. 1989;98(2):129–43.

    Article  PubMed  CAS  Google Scholar 

  15. Kireev I, Lakonishok M, Liu W, Joshi VN, Powell R, Belmont AS. In vivo immunogold labeling confirms large-scale chromatin folding motifs. Nat Methods. 2008;5(4):311–3.

    PubMed  CAS  Google Scholar 

  16. Ahmed K, Dehghani H, Rugg-Gunn P, Fussner E, Rossant J, Bazett-Jones DP. Global chromatin architecture reflects pluripotency and lineage commitment in the early mouse embryo. PLoS One. 2010;5(5):e10531.

    Article  PubMed  Google Scholar 

  17. Solovei I, Kreysing M, Lanctot C, Kosem S, Peichl L, Cremer T, et al. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell. 2009;137(2):356–68.

    Article  PubMed  CAS  Google Scholar 

  18. Cremer T, Kreth G, Koester H, Fink RH, Heintzmann R, Cremer M, et al. Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture. Crit Rev Eukaryot Gene Expr. 2000;10(2):179–212.

    Article  PubMed  CAS  Google Scholar 

  19. Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet. 2001;10(3):211–9.

    Article  PubMed  CAS  Google Scholar 

  20. Cremer M, Kupper K, Wagler B, Wizelman L, von Hase J, Weiland Y, et al. Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol. 2003;162(5):809–20.

    Article  PubMed  CAS  Google Scholar 

  21. Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA. Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol. 1999;145(6):1119–31.

    Article  PubMed  CAS  Google Scholar 

  22. Parada LA, McQueen PG, Misteli T. Tissue-specific spatial organization of genomes. Genome Biol. 2004;5(7):R44.

    Article  PubMed  Google Scholar 

  23. Kuroda M, Tanabe H, Yoshida K, Oikawa K, Saito A, Kiyuna T, et al. Alteration of chromosome positioning during adipocyte differentiation. J Cell Sci. 2004;117(Pt 24):5897–903.

    Article  PubMed  CAS  Google Scholar 

  24. Branco MR, Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol. 2006;4(5):e138.

    Article  PubMed  Google Scholar 

  25. Urbach D, Lupien M, Karagas MR, Moore JH. Cancer heterogeneity: origins and implications for genetic association studies. Trends Genet. 2012;28(11):538–43.

    Article  PubMed  CAS  Google Scholar 

  26. Manolio TA. Genomewide association studies and assessment of the risk of disease. N Engl J Med. 2010;363(2):166–76.

    Article  PubMed  CAS  Google Scholar 

  27. Negrini S, Gorgoulis VG, Halazonetis TD. Genomic instability—an evolving hallmark of cancer. Nat Rev Mol Cell Biol. 2010;11(3):220–8.

    Article  PubMed  CAS  Google Scholar 

  28. Schuster-Bockler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012;488(7412):504–7.

    Article  PubMed  Google Scholar 

  29. Parada LA, McQueen PG, Munson PJ, Misteli T. Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol. 2002;12(19):1692–7.

    Article  PubMed  CAS  Google Scholar 

  30. Harewood L, Schutz F, Boyle S, Perry P, Delorenzi M, Bickmore WA, et al. The effect of translocation-induced nuclear reorganization on gene expression. Genome Res. 2010;20(5):554–64.

    Article  PubMed  CAS  Google Scholar 

  31. Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007;7(4):233–45.

    Article  PubMed  CAS  Google Scholar 

  32. Nowell PC, Hungerford DA. Chromosome studies on normal and leukemic human leukocytes. J Natl Cancer Inst. 1960;25:85–109.

    PubMed  CAS  Google Scholar 

  33. Tsai AG, Lieber MR. Mechanisms of chromosomal rearrangement in the human genome. BMC Genomics. 2010;11 Suppl 1:S1.

    Article  PubMed  Google Scholar 

  34. Jung D, Giallourakis C, Mostoslavsky R, Alt F. Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu Rev Immunol. 2006;24:541–70.

    Article  PubMed  CAS  Google Scholar 

  35. Dudley D, Chaudhuri J, Bassing C, Alt F. Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences. Adv Immunol. 2005;86:43–112.

    Article  PubMed  CAS  Google Scholar 

  36. Misteli T, Soutoglou E. The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat Rev Mol Cell Biol. 2009;10(4):243–54.

    Article  PubMed  CAS  Google Scholar 

  37. Bazett-Jones DP, Ottensmeyer FP. Phosphorus distribution in the nucleosome. Science. 1981;211(4478):169–70.

    Article  PubMed  CAS  Google Scholar 

  38. van de Corput MP, Grosveld FG. Fluorescence in situ hybridization analysis of transcript dynamics in cells. Methods. 2001;25(1):111–8.

    Article  PubMed  Google Scholar 

  39. Bentley DL. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol. 2005;17(3):251–6.

    Article  PubMed  CAS  Google Scholar 

  40. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet. 2010;42(1):53–61.

    Article  PubMed  CAS  Google Scholar 

  41. Ferry JA. Burkitt’s lymphoma: clinicopathologic features and differential diagnosis. Oncologist. 2006;11(4):375–83.

    Article  PubMed  Google Scholar 

  42. Telenius H, Pelmear AH, Tunnacliffe A, Carter NP, Behmel A, Ferguson-Smith MA, et al. Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow-sorted chromosomes. Genes Chromosomes Cancer. 1992;4(3):257–63.

    Article  PubMed  CAS  Google Scholar 

  43. Chubb JR, Boyle S, Perry P, Bickmore WA. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol. 2002;12(6):439–45.

    Article  PubMed  CAS  Google Scholar 

  44. Levi V, Ruan Q, Plutz M, Belmont AS, Gratton E. Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope. Biophys J. 2005;89(6):4275–85.

    Article  PubMed  CAS  Google Scholar 

  45. Bornfleth H, Edelmann P, Zink D, Cremer T, Cremer C. Quantitative motion analysis of subchromosomal foci in living cells using four-dimensional microscopy. Biophys J. 1999;77(5):2871–86.

    Article  PubMed  CAS  Google Scholar 

  46. Muller I, Boyle S, Singer RH, Bickmore WA, Chubb JR. Stable morphology, but dynamic internal reorganisation, of interphase human chromosomes in living cells. PLoS One. 2010;5(7):e11560.

    Article  PubMed  Google Scholar 

  47. Chubb JR, Trcek T, Shenoy SM, Singer RH. Transcriptional pulsing of a developmental gene. Curr Biol. 2006;16(10):1018–25.

    Article  PubMed  CAS  Google Scholar 

  48. Muramoto T, Cannon D, Gierlinski M, Corrigan A, Barton GJ, Chubb JR. Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci USA. 2012;109(19):7350–5.

    Article  PubMed  CAS  Google Scholar 

  49. 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(6):675–82.

    Article  PubMed  CAS  Google Scholar 

  50. Lukásová E, Kozubek S, Kozubek M, Kjeronská J, Rýznar L, Horáková J, et al. Localisation and distance between ABL and BCR genes in interphase nuclei of bone marrow cells of control donors and patients with chronic myeloid leukaemia. Hum Genet. 1997;100(5–6):525–35.

    PubMed  Google Scholar 

  51. Neves H, Ramos C, da Silva M, 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(4):1197–207.

    PubMed  CAS  Google Scholar 

  52. Melo J. The diversity of BCR-ABL fusion proteins and their relationship to leukemia phenotype. Blood. 1996;88(7):2375–84.

    PubMed  CAS  Google Scholar 

  53. Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T. Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet. 2003;34(3):287–91.

    Article  PubMed  CAS  Google Scholar 

  54. Pratt-Hyatt MJ, Kapadia KM, Wilson TE, Engelke DR. Increased recombination between active tRNA genes. DNA Cell Biol. 2006;25(6):359–64.

    Article  PubMed  CAS  Google Scholar 

  55. Nikiforova M, Stringer J, Blough R, Medvedovic M, Fagin J, Nikiforov Y. Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells. Science. 2000;290(5489):138–41.

    Article  PubMed  CAS  Google Scholar 

  56. Roccato E, Bressan P, Sabatella G, Rumio C, Vizzotto L, Pierotti M, et al. Proximity of TPR and NTRK1 rearranging loci in human thyrocytes. Cancer Res. 2005;65(7):2572–6.

    Article  PubMed  CAS  Google Scholar 

  57. Gandhi M, Medvedovic M, Stringer J, Nikiforov Y. Interphase chromosome folding determines spatial proximity of genes participating in carcinogenic RET/PTC rearrangements. Oncogene. 2006;25(16):2360–6.

    Article  PubMed  CAS  Google Scholar 

  58. Grieco M, Santoro M, Berlingieri MT, Melillo RM, Donghi R, Bongarzone I, et al. PTC is a novel rearranged form of the ret proto-oncogene and is frequently detected in vivo in human thyroid papillary carcinomas. Cell. 1990;60(4):557–63.

    Article  PubMed  CAS  Google Scholar 

  59. Bongarzone I, Butti MG, Coronelli S, Borrello MG, Santoro M, Mondellini P, et al. Frequent activation of ret protooncogene by fusion with a new activating gene in papillary thyroid carcinomas. Cancer Res. 1994;54(11):2979–85.

    PubMed  CAS  Google Scholar 

  60. Santoro M, Dathan NA, Berlingieri MT, Bongarzone I, Paulin C, Grieco M, et al. Molecular characterization of RET/PTC3; a novel rearranged version of the RETproto-oncogene in a human thyroid papillary carcinoma. Oncogene. 1994;9(2):509–16.

    PubMed  CAS  Google Scholar 

  61. Bickmore WA, Teague P. Influences of chromosome size, gene density and nuclear position on the frequency of constitutional translocations in the human population. Chromosome Res. 2002;10(8):707–15.

    Article  PubMed  CAS  Google Scholar 

  62. Arsuaga J, Greulich-Bode K, Vazquez M, Bruckner M, Hahnfeldt P, Brenner D, et al. Chromosome spatial clustering inferred from radiogenic aberrations. Int J Radiat Biol. 2004;80(7):507–15.

    Article  PubMed  CAS  Google Scholar 

  63. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295(5558):1306–11.

    Article  PubMed  CAS  Google Scholar 

  64. Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell. 2002;10(6):1453–65.

    Article  PubMed  CAS  Google Scholar 

  65. Palstra RJ, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, de Laat W. The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet. 2003;35(2):190–4.

    Article  PubMed  CAS  Google Scholar 

  66. Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 2006;38(11):1341–7.

    Article  PubMed  CAS  Google Scholar 

  67. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006;38(11):1348–54.

    Article  PubMed  CAS  Google Scholar 

  68. Wurtele H, Chartrand P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended chromosome conformation capture methodology. Chromosome Res. 2006;14(5):477–95.

    Article  PubMed  Google Scholar 

  69. Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289–93.

    Article  PubMed  CAS  Google Scholar 

  70. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80.

    Article  PubMed  CAS  Google Scholar 

  71. Chiarle R, Zhang Y, Frock R, Lewis S, Molinie B, Ho Y-J, et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell. 2011;147(1):107–19.

    Article  PubMed  CAS  Google Scholar 

  72. Klein I, 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(1):95–106.

    Article  PubMed  CAS  Google Scholar 

  73. Hakim O, Resch W, Yamane A, Klein I, Kieffer-Kwon K-R, Jankovic M, et al. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature. 2012;484(7392):69–74.

    PubMed  CAS  Google Scholar 

  74. 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(5):908–21.

    Article  PubMed  CAS  Google Scholar 

  75. Soulas-Sprauel P, Rivera-Munoz P, Malivert L, Le Guyader G, Abramowski V, Revy P, et al. V(D)J and immunoglobulin class switch recombinations: a paradigm to study the regulation of DNA end-joining. Oncogene. 2007;26(56):7780–91.

    Article  PubMed  CAS  Google Scholar 

  76. Ferguson DO, Sekiguchi JM, Chang S, Frank KM, Gao Y, DePinho RA, et al. The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proc Natl Acad Sci USA. 2000;97(12):6630–3.

    Article  PubMed  CAS  Google Scholar 

  77. Yan CT, Boboila C, Souza EK, Franco S, Hickernell TR, Murphy M, et al. IgH class switching and translocations use a robust non-classical end-joining pathway. Nature. 2007;449(7161):478–82.

    Article  PubMed  CAS  Google Scholar 

  78. Mahowald GK, Baron JM, Mahowald MA, Kulkarni S, Bredemeyer AL, Bassing CH, et al. Aberrantly resolved RAG-mediated DNA breaks in Atm-deficient lymphocytes target chromosomal breakpoints in cis. Proc Natl Acad Sci USA. 2009;106(43):18339–44.

    Article  PubMed  CAS  Google Scholar 

  79. Stephens P, McBride D, Lin M-L, Varela I, Pleasance E, Simpson J, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 2009;462(7276):1005–10.

    Article  PubMed  CAS  Google Scholar 

  80. Kuppers R, Dalla-Favera R. Mechanisms of chromosomal translocations in B cell lymphomas. Oncogene. 2001;20(40):5580–94.

    Article  PubMed  CAS  Google Scholar 

  81. Taslerova R, Kozubek S, Lukasova E, Jirsova P, Bartova E, Kozubek M. Arrangement of chromosome 11 and 22 territories, EWSR1 and FLI1 genes, and other genetic elements of these chromosomes in human lymphocytes and Ewing sarcoma cells. Hum Genet. 2003;112(2):143–55.

    PubMed  CAS  Google Scholar 

  82. Grant SF, Hakonarson H. Microarray technology and applications in the arena of genome-wide association. Clin Chem. 2008;54(7):1116–24.

    Article  PubMed  CAS  Google Scholar 

  83. Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R. Interchromosomal interactions and olfactory receptor choice. Cell. 2006;126(2):403–13.

    Article  PubMed  CAS  Google Scholar 

  84. Ferrai C, Pombo A. 3D chromatin regulation of Sonic hedgehog in the limb buds. Dev Cell. 2009;16(1):9–11.

    Article  PubMed  CAS  Google Scholar 

  85. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012;489(7414):109–13.

    Article  PubMed  CAS  Google Scholar 

  86. Wright JB, Brown SJ, Cole MD. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol. 2010;30(6):1411–20.

    Article  PubMed  CAS  Google Scholar 

  87. Zhang X, Cowper-Sal Lari R, Bailey SD, Moore JH, Lupien M. Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus. Genome Res. 2012;22(8):1437–46.

    Article  PubMed  CAS  Google Scholar 

  88. Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, et al. A map of open chromatin in human pancreatic islets. Nat Genet. 2010;42(3):255–9.

    Article  PubMed  CAS  Google Scholar 

  89. Palii CG, Perez-Iratxeta C, Yao Z, Cao Y, Dai F, Davison J, et al. Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages. EMBO J. 2011;30(3):494–509.

    Article  PubMed  CAS  Google Scholar 

  90. Kassouf MT, Hughes JR, Taylor S, McGowan SJ, Soneji S, Green AL, et al. Genome-wide identification of TAL1’s functional targets: insights into its mechanisms of action in primary erythroid cells. Genome Res. 2010;20(8):1064–83.

    Article  PubMed  CAS  Google Scholar 

  91. Aifantis I, Raetz E, Buonamici S. Molecular pathogenesis of T-cell leukaemia and lymphoma. Nat Rev Immunol. 2008;8(5):380–90.

    Article  PubMed  CAS  Google Scholar 

  92. Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, et al. Epigenomic enhancer profiling defines a signature of colon cancer. Science. 2012;336(6082):736–9.

    Article  PubMed  CAS  Google Scholar 

  93. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.[see comment]. Nat Genet. 2007;39(3):311–8.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgment 

This work was supported by Canada Foundation for Innovation, Canadian Institutes of Health Research, and the Ontario Ministry of Economic Development and Innovation. We would like to thank members of the Mitchell lab for helpful discussions and critical review.

Author information

Authors and Affiliations

  1. Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada, M5S 3G5

    Harry Yu Zhou B.Sc. & Jennifer A. Mitchell Ph.D.

Authors
  1. Harry Yu Zhou B.Sc.
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jennifer A. Mitchell Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jennifer A. Mitchell Ph.D. .

Editor information

Editors and Affiliations

  1. Banting & Best Dept. Medical Research, University of Toronto Donnelly Ctr Cell. & Biomolecular Res., Toronto, Ontario, Canada

    Andrew Emili

  2. University of Toronto Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada

    Jack Greenblatt

  3. Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario, Canada

    Shoshana Wodak

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this chapter

Cite this chapter

Zhou, H.Y., Mitchell, J.A. (2014). Genome Organization in Cancer Cells. In: Emili, A., Greenblatt, J., Wodak, S. (eds) Systems Analysis of Chromatin-Related Protein Complexes in Cancer. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7931-4_14

Download citation

Publish with us

Policies and ethics

Search

Navigation