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Chromatin Structure and Organization: The Relation with Gene Expression During Development and Disease

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Epigenetics: Development and Disease

Part of the book series: Subcellular Biochemistry ((SCBI,volume 61))

Abstract

The elementary level of chromatin fiber, namely the nucleofilament, is known to undergo a hierarchical compaction leading to local chromatin loops, then chromatin domains and ultimately chromosome territories. These successive folding levels rely on the formation of chromatin loops ranging from few kb to some Mb. In addition to a packaging and structural role, the high-order organization of genomes functionally impacts on gene expression program. This review summarises to which extent each level of chromatin compaction does affect gene regulation. In addition, we point out the structural and functional changes observed in diseases. Emphasis will be mainly placed on the large-scale organization of the chromatin.

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References

  • Adachi Y, Käs E, Laemmli UK (1989) Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J 8(13):3997–4006

    CAS  PubMed  Google Scholar 

  • Alami R, Greally JM, Tanimoto K, Hwang S, Feng YQ, Engel JD, Fiering S, Bouhassira EE (2000) Beta-globin YAC transgenes exhibit uniform expression levels but position effect variegation in mice. Hum Mol Genet 9(4):631–636

    Article  CAS  PubMed  Google Scholar 

  • Allis CD, Jenuwein T, Reinberg D, Caparros ML (2007) Epigenetics. Harbor Laboratory Press, Cold Spring

    Google Scholar 

  • Audit B, Zaghloul L, Vaillant C, Chevereau G, d’Aubenton Carafa Y, Thermes C, Arneodo A (2009) Open chromatin encoded in DNA sequence is the signature of ‘master’ replication origins in human cells. Nucleic Acids Res 37(18):6064–6075

    Article  CAS  PubMed  Google Scholar 

  • Augui S, Filion GJ, Huart S, Nora E, Guggiari M, Maresca M, Stewart AF, Heard E (2007) Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic. Science 318(5856):1632–1636

    Article  CAS  PubMed  Google Scholar 

  • Bacher CP, Guggiari M, Brors B, Augui S, Clerc P, Avner P, Eils R, Heard E (2006) Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol 8(3):293–299

    Article  CAS  PubMed  Google Scholar 

  • Berdasco M, Esteller M (2010) Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell 19(5):698–711

    Article  CAS  PubMed  Google Scholar 

  • Berezney R (2002) Regulating the mammalian genome: the role of nuclear architecture. Adv Enzyme Regul 42:39–52

    Article  CAS  PubMed  Google Scholar 

  • Berezney R, Dubey DD, Huberman JA (2000) Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 108(8):471–484

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Brodie Of Brodie EB, Nicolay S, Touchon M, Audit B, d’Aubenton Carafa Y, Thermes C, Arneodo A (2005) From DNA sequence analysis to modeling replication in the human genome. Phys Rev Lett 94(24):248103

    Article  CAS  PubMed  Google Scholar 

  • Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, Wood WG, Higgs DR, Iborra FJ, Buckle VJ (2006) Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172(2):177–187

    Article  CAS  PubMed  Google Scholar 

  • Brown JM, Green J, Das Neves RP, Wallace HAC, Smith AJH, Hughes J, Gray N, Taylor S, Wood WG, Higgs DR, Iborra FJ, Buckle VJ (2008) Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 182(6):1083–1097

    Article  CAS  PubMed  Google Scholar 

  • Cai S, Han HJ, Kohwi-Shigematsu T (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat Genet 34(1):42–51

    Article  CAS  PubMed  Google Scholar 

  • Cai S, Lee CC, Kohwi-Shigematsu T (2006) SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet 38(11):1278–1288

    Article  CAS  PubMed  Google Scholar 

  • Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voûte PA, Heisterkamp S, van Kampen A, Versteeg R (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291(5507):1289–1292

    Article  CAS  PubMed  Google Scholar 

  • Carter D, Chakalova L, Osborne CS, feng Dai Y, Fraser P (2002) Long-range chromatin regulatory interactions in vivo. Nat Genet 32(4):623–626

    Article  CAS  PubMed  Google Scholar 

  • Casillas MA, Lopatina N, Andrews LG, Tollefsbol TO (2003) Transcriptional control of the DNA methyltransferases is altered in aging and neoplastically-transformed human fibroblasts. Mol Cell Biochem 252(1–2):33–43

    Article  CAS  PubMed  Google Scholar 

  • Chakalova L, Debrand E, Mitchell JA, Osborne CS, Fraser P (2005) Replication and transcription: shaping the landscape of the genome. Nat Rev Genet 6(9):669–677

    Article  CAS  PubMed  Google Scholar 

  • Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18(10):1119–1130

    Article  CAS  PubMed  Google Scholar 

  • Chambeyron S, Silva NRD, Lawson KA, Bickmore WA (2005) Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 132(9):2215–2223

    Article  CAS  PubMed  Google Scholar 

  • Chi P, Allis CD, Wang GG (2010) Covalent histone modifications–miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10(7):457–469

    Article  CAS  PubMed  Google Scholar 

  • Cobb RM, Oestreich KJ, Osipovich OA, Oltz EM (2006) Accessibility control of V(D)J recombination. Adv Immunol 91:45–109

    Article  CAS  PubMed  Google Scholar 

  • Cockerill PN, Garrard WT (1986) Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44(2):273–282

    Article  CAS  PubMed  Google Scholar 

  • Columbaro M, Capanni C, Mattioli E, Novelli G, Parnaik VK, Squarzoni S, Maraldi NM, Lattanzi G (2005) Rescue of heterochromatin organization in Hutchinson-Gilford progeria by drug treatment. Cell Mol Life Sci 62(22):2669–2678

    Article  CAS  PubMed  Google Scholar 

  • Cook PR (1999) The organization of replication and transcription. Science 284(5421):1790–1795

    Article  CAS  PubMed  Google Scholar 

  • Cook PR (2002) Predicting three-dimensional genome structure from transcriptional activity. Nat Genet 32(3):347–352

    Article  CAS  PubMed  Google Scholar 

  • Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2(4):292–301

    Article  CAS  PubMed  Google Scholar 

  • Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K (2009) Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19(1):24–32

    Article  CAS  PubMed  Google Scholar 

  • de Belle I, Cai S, Kohwi-Shigematsu T (1998) The genomic sequences bound to special AT-rich sequence-binding protein 1 (SATB1) in vivo in Jurkat T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops. J Cell Biol 141(2):335–348

    Article  PubMed  Google Scholar 

  • de Laat W, Grosveld F (2003) Spatial organization of gene expression: the active chromatin hub. Chromosome Res 11(5):447–459

    Article  PubMed  Google Scholar 

  • De S, Babu MM (2010) Genomic neighbourhood and the regulation of gene expression. Curr Opin Cell Biol 22(3):326–333

    Article  CAS  PubMed  Google Scholar 

  • Dechat T, Pfleghaar K, Sengupta K, Shimi T, Shumaker DK, Solimando L, Goldman RD (2008) Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes Dev 22(7):832–853

    Article  CAS  PubMed  Google Scholar 

  • Dechat T, Adam SA, Goldman RD (2009) Nuclear lamins and chromatin: when structure meets function. Adv Enzyme Regul 49(1):157–166

    Article  CAS  PubMed  Google Scholar 

  • Dobie KW, Lee M, Fantes JA, Graham E, Clark AJ, Springbett A, Lathe R, McClenaghan M (1996) Variegated transgene expression in mouse mammary gland is determined by the transgene integration locus. Proc Natl Acad Sci U S A 93(13):6659–6664

    Article  CAS  PubMed  Google Scholar 

  • Dorier J, Stasiak A (2010) The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture. Nucleic Acids Res 38(21):7410–7421

    Article  CAS  PubMed  Google Scholar 

  • Dorner D, Gotzmann J, Foisner R (2007) Nucleoplasmic lamins and their interaction partners, LAP2alpha, Rb, and BAF, in transcriptional regulation. FEBS J 274(6):1362–1373

    Article  CAS  PubMed  Google Scholar 

  • Drissen R, Palstra RJ, Gillemans N, Splinter E, Grosveld F, Philipsen S, de Laat W (2004) The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev 18(20):2485–2490

    Article  CAS  PubMed  Google Scholar 

  • Ehrlich M (2005) DNA methylation and cancer-associated genetic instability. Adv Exp Med Biol 570:363–392

    Article  CAS  PubMed  Google Scholar 

  • Eivazova ER, Gavrilov A, Pirozhkova I, Petrov A, Iarovaia OV, Razin SV, Lipinski M, Vassetzky YS (2009) Interaction in vivo between the two matrix attachment regions flanking a single chromatin loop. J Mol Biol 386(4):929–937

    Article  CAS  PubMed  Google Scholar 

  • Ellis L, Atadja PW, Johnstone RW (2009) Epigenetics in cancer: targeting chromatin modifications. Mol Cancer Ther 8(6):1409–1420

    Article  CAS  PubMed  Google Scholar 

  • Eriksson M, Brown WT, Gordon LB, Glynn MW, Singer J, Scott L, Erdos MR, Robbins CM, Moses TY, Berglund P, Dutra A, Pak E, Durkin S, Csoka AB, Boehnke M, Glover TW, Collins FS (2003) Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 423(6937):293–298

    Article  CAS  PubMed  Google Scholar 

  • Esteller M (2005) Aberrant DNA methylation as a cancer-inducing mechanism. Annu Rev Pharmacol Toxicol 45:629–656

    Article  CAS  PubMed  Google Scholar 

  • Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447(7143):433–440

    Article  CAS  PubMed  Google Scholar 

  • Ferrai C, de Castro IJ, Lavitas L, Chotalia M, Pombo A (2010) Gene positioning. Cold Spring Harb Perspect Biol 2(6):a000588

    Article  PubMed  CAS  Google Scholar 

  • Fiorini A, Gouveia F de S, Fernandez MA (2006) Scaffold/Matrix attachment regions and intrinsic DNA curvature. Biochemistry (Mosc) 71(5):481–488

    Article  CAS  Google Scholar 

  • Fraga MF, Esteller M (2007) Epigenetics and aging: the targets and the marks. Trends Genet 23(8):413–418

    Article  CAS  PubMed  Google Scholar 

  • Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M (2005) Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet 37(4):391–400

    Article  CAS  PubMed  Google Scholar 

  • Fraser P (2006) Transcriptional control thrown for a loop. Curr Opin Genet Dev 16(5):490–495

    Article  CAS  PubMed  Google Scholar 

  • Fraser P, Bickmore W (2007) Nuclear organization of the genome and the potential for gene regulation. Nature 447(7143):413–417

    Article  CAS  PubMed  Google Scholar 

  • Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark SJ (2006) Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 38(5):540–549

    Article  CAS  PubMed  Google Scholar 

  • Frouin I, Montecucco A, Spadari S, Maga G (2003) DNA replication: a complex matter. EMBO Rep 4(7):666–670

    Article  CAS  PubMed  Google Scholar 

  • Gasser SM, Laemmli UK (1986) Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46(4):521–530

    Article  CAS  PubMed  Google Scholar 

  • Gaudet F, Hodgson JG, Eden A, Jackson-Grusby L, Dausman J, Gray JW, Leonhardt H, Jaenisch R (2003) Induction of tumors in mice by genomic hypomethylation. Science 300(5618):489–492

    Article  CAS  PubMed  Google Scholar 

  • Gieni RS, Hendzel MJ (2009) Actin dynamics and functions in the interphase nucleus: moving toward an understanding of nuclear polymeric actin. Biochem Cell Biol 87(1):283–306

    Article  CAS  PubMed  Google Scholar 

  • Gierman HJ, Indemans MHG, Koster J, Goetze S, Seppen J, Geerts D, van Driel R, Versteeg R (2007) Domain-wide regulation of gene expression in the human genome. Genome Res 17(9):1286–1295

    Article  CAS  PubMed  Google Scholar 

  • Goetze S, Mateos-Langerak J, Gierman HJ, de Leeuw W, Giromus O, Indemans MHG, Koster J, Ondrej V, Versteeg R, van Driel R (2007) The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol Cell Biol 27(12):4475–4487

    Article  CAS  PubMed  Google Scholar 

  • Goldman RD, Shumaker DK, Erdos MR, Eriksson M, Goldman AE, Gordon LB, Gruenbaum Y, Khuon S, Mendez M, Varga R, Collins FS (2004) Accumulation of mutant lamin A causes progressive changes in nuclear architecture in Hutchinson-Gilford progeria syndrome. Proc Natl Acad Sci U S A 101(24):8963–8968

    Article  CAS  PubMed  Google Scholar 

  • Gonzalo S (2010) Epigenetic alterations in aging. J Appl Physiol 109(2):586–597

    Article  CAS  PubMed  Google Scholar 

  • Green P, Ewing B, Miller W, Thomas PJ, Program NISCCS, Green ED (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33(4):514–517

    Article  CAS  PubMed  Google Scholar 

  • Håkelien AM, Delbarre E, Gaustad KG, Buendia B, Collas P (2008) Expression of the myodystrophic R453W mutation of lamin A in C2C12 myoblasts causes promoter-specific and global epigenetic defects. Exp Cell Res 314(8):1869–1880

    Article  PubMed  CAS  Google Scholar 

  • Heard E, Bickmore W (2007) The ins and outs of gene regulation and chromosome territory organisation. Curr Opin Cell Biol 19(3):311–316

    Article  CAS  PubMed  Google Scholar 

  • Herbig U, Ferreira M, Condel L, Carey D, Sedivy JM (2006) Cellular senescence in aging primates. Science 311(5765):1257

    Article  CAS  PubMed  Google Scholar 

  • Herman JG, Merlo A, Mao L, Lapidus RG, Issa JP, Davidson NE, Sidransky D, Baylin SB (1995) Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res 55(20):4525–4530

    CAS  PubMed  Google Scholar 

  • Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schübeler D, Gilbert DM (2008) Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6(10):e245

    Article  PubMed  CAS  Google Scholar 

  • Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S, Rathjen PD, Gilbert DM (2010) Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res 20(2):155–169

    Article  CAS  PubMed  Google Scholar 

  • Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T (2005) Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet 37(1):31–40

    CAS  PubMed  Google Scholar 

  • Huvet M, Nicolay S, Touchon M, Audit B, d’Aubenton Carafa Y, Arneodo A, Thermes C (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res 17(9):1278–1285

    Article  CAS  PubMed  Google Scholar 

  • Iarovaia OV, Bystritskiy A, Ravcheev D, Hancock R, Razin SV (2004a) Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene. Nucleic Acids Res 32(7):2079–2086

    Article  CAS  PubMed  Google Scholar 

  • Iarovaia OV, Shkumatov P, Razin SV (2004b) Breakpoint cluster regions of the AML-1 and ETO genes contain MAR elements and are preferentially associated with the nuclear matrix in proliferating HEL cells. J Cell Sci 117(Pt 19):4583–4590

    Article  CAS  PubMed  Google Scholar 

  • Iborra FJ, Pombo A, Jackson DA, Cook PR (1996) Active RNA polymerases are localized within discrete transcription ‘factories’ in human nuclei. J Cell Sci 109(Pt 6):1427–1436

    CAS  PubMed  Google Scholar 

  • Kadauke S, Blobel GA (2009) Chromatin loops in gene regulation. Biochim Biophys Acta 1789(1):17–25

    Article  CAS  PubMed  Google Scholar 

  • Kanwal R, Gupta S (2010) Epigenetics and cancer. J Appl Physiol 109(2):598–605

    Article  CAS  PubMed  Google Scholar 

  • Käs E, Chasin LA (1987) Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs in an intragenic region. J Mol Biol 198(4):677–692

    Article  PubMed  Google Scholar 

  • Keaton MA, Taylor CM, Layer RM, Dutta A (2011) Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes. PLoS One 6(3):e17912

    Article  CAS  PubMed  Google Scholar 

  • Keys JR, Tallack MR, Zhan Y, Papathanasiou P, Goodnow CC, Gaensler KM, Crossley M, Dekker J, Perkins AC (2008) A mechanism for Ikaros regulation of human globin gene switching. Br J Haematol 141(3):398–406

    CAS  PubMed  Google Scholar 

  • Koehler D, Zakhartchenko V, Froenicke L, Stone G, Stanyon R, Wolf E, Cremer T, Brero A (2009) Changes of higher order chromatin arrangements during major genome activation in bovine preimplantation embryos. Exp Cell Res 315(12):2053–2063

    Article  CAS  PubMed  Google Scholar 

  • Kohwi-Shigematsu T, Kohwi Y (1990) Torsional stress stabilizes extended base unpairing in suppressor sites flanking immunoglobulin heavy chain enhancer. Biochemistry 29(41):9551–9560

    Article  CAS  PubMed  Google Scholar 

  • Kumar PP, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S (2007) Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat Cell Biol 9(1):45–56

    Article  PubMed  CAS  Google Scholar 

  • Kurukuti S, Tiwari VK, Tavoosidana G, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W, Ohlsson R (2006) CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc Natl Acad Sci U S A 103(28):10684–10689

    Article  CAS  PubMed  Google Scholar 

  • Lande-Diner L, Zhang J, Cedar H (2009) Shifts in replication timing actively affect histone acetylation during nucleosome reassembly. Mol Cell 34(6):767–774

    Article  CAS  PubMed  Google Scholar 

  • Li H, Ma X, Wang J, Koontz J, Nucci M, Sklar J (2007) Effects of rearrangement and allelic exclusion of JJAZ1/SUZ12 on cell proliferation and survival. Proc Natl Acad Sci U S A 104(50):20001–20006

    Article  CAS  PubMed  Google Scholar 

  • Li H, Wang J, Mor G, Sklar J (2008) A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science 321(5894):1357–1361

    Article  CAS  PubMed  Google Scholar 

  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293

    Article  CAS  PubMed  Google Scholar 

  • Liebich I, Bode J, Reuter I, Wingender E (2002) Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs). Nucleic Acids Res 30(15):3433–3442

    Article  CAS  PubMed  Google Scholar 

  • Lin C, Yang L, Tanasa B, Hutt K, Ju BG, Ohgi K, Zhang J, Rose DW, Fu XD, Glass CK, Rosenfeld MG (2009) Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 139(6):1069–1083

    Article  CAS  PubMed  Google Scholar 

  • Ling JQ, Li T, Hu JF, Vu TH, Chen HL, Qiu XW, Cherry AM, Hoffman AR (2006) CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312(5771):269–272

    Article  CAS  PubMed  Google Scholar 

  • Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R (2006) Interchromosomal interactions and olfactory receptor choice. Cell 126(2):403–413

    Article  CAS  PubMed  Google Scholar 

  • Lukásová E, Kozubek S, Kozubek M, Kjeronská J, Rýznar L, Horáková J, Krahulcová E, Horneck G (1997) 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 100(5–6):525–535

    PubMed  Google Scholar 

  • MacAlpine DM, Rodríguez HK, Bell SP (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18(24):3094–3105

    Article  CAS  PubMed  Google Scholar 

  • Mahy NL, Perry PE, Bickmore WA (2002) Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159(5):753–763

    Article  CAS  PubMed  Google Scholar 

  • Malhas A, Lee CF, Sanders R, Saunders NJ, Vaux DJ (2007) Defects in lamin B1 expression or processing affect interphase chromosome position and gene expression. J Cell Biol 176(5):593–603

    Article  CAS  PubMed  Google Scholar 

  • Malyavantham KS, Bhattacharya S, Alonso WD, Acharya R, Berezney R (2008) Spatio-temporal dynamics of replication and transcription sites in the mammalian cell nucleus. Chromosoma 117(6):553–567

    Article  PubMed  Google Scholar 

  • Martens JHA, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A (2002) Scaffold/matrix attachment region elements interact with a p300-scaffold attachment factor A complex and are bound by acetylated nucleosomes. Mol Cell Biol 22(8):2598–2606

    Article  CAS  PubMed  Google Scholar 

  • McNairn AJ, Gilbert DM (2003) Epigenomic replication: linking epigenetics to DNA replication. Bioessays 25(7):647–656

    Article  CAS  PubMed  Google Scholar 

  • Meaburn KJ, Cabuy E, Bonne G, Levy N, Morris GE, Novelli G, Kill IR, Bridger JM (2007) Primary laminopathy fibroblasts display altered genome organization and apoptosis. Aging Cell 6(2):139–153

    Article  CAS  PubMed  Google Scholar 

  • Mehta IS, Amira M, Harvey AJ, Bridger JM (2010) Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts. Genome Biol 11(1):R5

    Article  PubMed  CAS  Google Scholar 

  • Meister P, Towbin BD, Pike BL, Ponti A, Gasser SM (2010) The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev 24(8):766–782

    Article  CAS  PubMed  Google Scholar 

  • Mewborn SK, Puckelwartz MJ, Abuisneineh F, Fahrenbach JP, Zhang Y, MacLeod H, Dellefave L, Pytel P, Selig S, Labno CM, Reddy K, Singh H, McNally E (2010) Altered chromosomal positioning, compaction, and gene expression with a lamin A/C gene mutation. PLoS One 5(12):e14342

    Article  CAS  PubMed  Google Scholar 

  • Mijalski T, Harder A, Halder T, Kersten M, Horsch M, Strom TM, Liebscher HV, Lottspeich F, de Angelis MH, Beckers J (2005) Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proc Natl Acad Sci U S A 102(24):8621–8626

    Article  CAS  PubMed  Google Scholar 

  • Mlynarova L, Loonen A, Heldens J, Jansen RC, Keizer P, Stiekema WJ, Nap JP (1994) Reduced position effect in mature transgenic plants conferred by the chicken lysozyme matrix-associated region. Plant Cell 6(3):417–426

    CAS  PubMed  Google Scholar 

  • Morey C, Silva NRD, Perry P, Bickmore WA (2007) Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 134(5):909–919

    Article  CAS  PubMed  Google Scholar 

  • Morey C, Silva NRD, Kmita M, Duboule D, Bickmore WA (2008) Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd. J Cell Sci 121(Pt 5):571–577

    Article  CAS  PubMed  Google Scholar 

  • Murrell A, Heeson S, Reik W (2004) Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet 36(8):889–893

    Article  CAS  PubMed  Google Scholar 

  • Nakagomi K, Kohwi Y, Dickinson LA, Kohwi-Shigematsu T (1994) A novel DNA-binding motif in the nuclear matrix attachment DNA-binding protein SATB1. Mol Cell Biol 14(3):1852–1860

    CAS  PubMed  Google Scholar 

  • Narita M (2007) Cellular senescence and chromatin organisation. Br J Cancer 96(5):686–691

    Article  CAS  PubMed  Google Scholar 

  • Narita M, Nunez S, Heard E, Narita M, Lin AW, Hearn SA, Spector DL, Hannon GJ, Lowe SW (2003) Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 113(6):703–716

    Article  CAS  PubMed  Google Scholar 

  • Nativio R, Wendt KS, Ito Y, Huddleston JE, Uribe-Lewis S, Woodfine K, Krueger C, Reik W, Peters JM, Murrell A (2009) Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus. PLoS Genet 5(11):e1000739

    Article  PubMed  CAS  Google Scholar 

  • Nowell PC (2007) Discovery of the Philadelphia chromosome: a personal perspective. J Clin Invest 117(8):2033–2035

    Article  CAS  PubMed  Google Scholar 

  • Oestreich KJ, Cobb RM, Pierce S, Chen J, Ferrier P, Oltz EM (2006) Regulation of TCRbeta gene assembly by a promoter/enhancer holocomplex. Immunity 24(4):381–391

    Article  CAS  PubMed  Google Scholar 

  • Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36(10):1065–1071

    Article  CAS  PubMed  Google Scholar 

  • Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, Corcoran AE, Fraser P (2007) Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol 5(8):e192

    Article  PubMed  CAS  Google Scholar 

  • Ottaviani D, Lever E, Takousis P, Sheer D (2008) Anchoring the genome. Genome Biol 9(1):201

    Article  PubMed  CAS  Google Scholar 

  • Palstra RJ, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, de Laat W (2003) The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet 35(2):190–194

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Patrinos GP, de Krom M, de Boer E, Langeveld A, Imam AMA, Strouboulis J, de Laat W, Grosveld FG (2004) Multiple interactions between regulatory regions are required to stabilize an active chromatin hub. Genes Dev 18(12):1495–1509

    Article  CAS  PubMed  Google Scholar 

  • Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, Tamir I, Sommer A, Aszodi A, Jenuwein T, Barlow DP (2009) H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 19(2):221–233

    Article  CAS  PubMed  Google Scholar 

  • Pegoraro G, Kubben N, Wickert U, Göhler H, Hoffmann K, Misteli T (2009) Ageing-related chromatin defects through loss of the NURD complex. Nat Cell Biol 11(10):1261–1267

    Article  CAS  PubMed  Google Scholar 

  • Portela A, Esteller M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28(10):1057–1068

    Article  CAS  PubMed  Google Scholar 

  • Potts W, Tucker D, Wood H, Martin C (2000) Chicken beta-globin 5′HS4 insulators function to reduce variability in transgenic founder mice. Biochem Biophys Res Commun 273(3):1015–1018

    Article  CAS  PubMed  Google Scholar 

  • Qiu X, Vu TH, Lu Q, Ling JQ, Li T, Hou A, Wang SK, Chen HL, Hu JF, Hoffman AR (2008) A complex DNA looping configuration associated with the silencing of the maternal Igf2 allele. Mol Endocrinol 22:1476–1488

    Article  CAS  PubMed  Google Scholar 

  • Razin SV (2001) The nuclear matrix and chromosomal DNA loops: is their any correlation between partitioning of the genome into loops and functional domains? Cell Mol Biol Lett 6(1):59–69

    CAS  PubMed  Google Scholar 

  • Romig H, Fackelmayer FO, Renz A, Ramsperger U, Richter A (1992) Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. EMBO J 11(9):3431–3440

    CAS  PubMed  Google Scholar 

  • Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM (2010) Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 20(6):761–770

    Article  CAS  PubMed  Google Scholar 

  • Sandre-Giovannoli AD, Bernard R, Cau P, Navarro C, Amiel J, Boccaccio I, Lyonnet S, Stewart CL, Munnich A, Merrer ML, Lévy N (2003) Lamin a truncation in Hutchinson-Gilford progeria. Science 300(5628):2055

    Article  PubMed  Google Scholar 

  • Sarg B, Koutzamani E, Helliger W, Rundquist I, Lindner HH (2002) Postsynthetic trimethylation of histone H4 at lysine 20 in mammalian tissues is associated with aging. J Biol Chem 277(42):39195–39201

    Article  CAS  PubMed  Google Scholar 

  • Sayegh CE, Sayegh C, Jhunjhunwala S, Riblet R, Murre C (2005) Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells. Genes Dev 19(3):322–327

    Article  CAS  PubMed  Google Scholar 

  • Scaffidi P, Misteli T (2006) Lamin A-dependent nuclear defects in human aging. Science 312(5776):1059–1063

    Article  CAS  PubMed  Google Scholar 

  • Schoenfelder S, Clay I, Fraser P (2010a) The transcriptional interactome: gene expression in 3D. Curr Opin Genet Dev 20(2):127–133

    Article  CAS  PubMed  Google Scholar 

  • Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei CL, Ruan Y, Bieker JJ, Fraser P (2010b) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42(1):53–61

    Article  CAS  PubMed  Google Scholar 

  • Schübeler D, Scalzo D, Kooperberg C, van Steensel B, Delrow J, Groudine M (2002) Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet 32(3):438–442

    Article  PubMed  CAS  Google Scholar 

  • Seligson DB, Horvath S, Shi T, Yu H, Tze S, Grunstein M, Kurdistani SK (2005) Global histone modification patterns predict risk of prostate cancer recurrence. Nature 435(7046):1262–1266

    Article  CAS  PubMed  Google Scholar 

  • Seligson DB, Horvath S, McBrian MA, Mah V, Yu H, Tze S, Wang Q, Chia D, Goodglick L, Kurdistani SK (2009) Global levels of histone modifications predict prognosis in different cancers. Am J Pathol 174(5):1619–1628

    Article  CAS  PubMed  Google Scholar 

  • Sexton T, Bantignies F, Cavalli G (2009) Genomic interactions: chromatin loops and gene meeting points in transcriptional regulation. Semin Cell Dev Biol 20(7):849–855

    Article  CAS  PubMed  Google Scholar 

  • Shen S, Liu A, Li J, Wolubah C, Casaccia-Bonnefil P (2008) Epigenetic memory loss in aging oligodendrocytes in the corpus callosum. Neurobiol Aging 29(3):452–463

    Article  CAS  PubMed  Google Scholar 

  • Shumaker DK, Dechat T, Kohlmaier A, Adam SA, Bozovsky MR, Erdos MR, Eriksson M, Goldman AE, Khuon S, Collins FS, Jenuwein T, Goldman RD (2006) Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc Natl Acad Sci U S A 103(23):8703–8708

    Article  CAS  PubMed  Google Scholar 

  • Simonis M, Kooren J, de Laat W (2007) An evaluation of 3c-based methods to capture DNA interactions. Nat Methods 4(11):895–901

    Article  CAS  PubMed  Google Scholar 

  • Sinha S, Malonia SK, Mittal SPK, Singh K, Kadreppa S, Kamat R, Mukhopadhyaya R, Pal JK, Chattopadhyay S (2010) Coordinated regulation of p53 apoptotic targets BAX and PUMA by SMAR1 through an identical MAR element. EMBO J 29(4):830–842

    Article  CAS  PubMed  Google Scholar 

  • Skok JA, Gisler R, Novatchkova M, Farmer D, de Laat W, Busslinger M (2007) Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes. Nat Immunol 8(4):378–387

    Article  CAS  PubMed  Google Scholar 

  • Solovei I, Kreysing M, Lanctôt C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B (2009) Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 137(2):356–368

    Article  CAS  PubMed  Google Scholar 

  • Solovyan VT, Bezvenyuk ZA, Salminen A, Austin CA, Courtney MJ (2002) The role of topoisomerase II in the excision of DNA loop domains during apoptosis. J Biol Chem 277(24):21458–21467

    Article  CAS  PubMed  Google Scholar 

  • Spellman PT, Rubin GM (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1(1):5

    Article  PubMed  Google Scholar 

  • Spilianakis CG, Flavell RA (2004) Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 5(10):1017–1027

    Article  CAS  PubMed  Google Scholar 

  • Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA (2005) Interchromosomal associations between alternatively expressed loci. Nature 435(7042):637–645

    Article  CAS  PubMed  Google Scholar 

  • Sutherland H, Bickmore WA (2009) Transcription factories: gene expression in unions? Nat Rev Genet 10(7):457–466

    Article  CAS  PubMed  Google Scholar 

  • Tanabe H, Müller S, Neusser M, von Hase J, Calcagno E, Cremer M, Solovei I, Cremer C, Cremer T (2002) Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci U S A 99(7):4424–4429

    Article  CAS  PubMed  Google Scholar 

  • Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 10(6):1453–1465

    Article  CAS  PubMed  Google Scholar 

  • Touchon M, Nicolay S, Arneodo A, d’Aubenton Carafa Y, Thermes C (2003) Transcription-coupled TA and GC strand asymmetries in the human genome. FEBS Lett 555(3):579–582

    Article  CAS  PubMed  Google Scholar 

  • Touchon M, Nicolay S, Audit B, Of Brodie EBB, d’Aubenton Carafa Y, Arneodo A, Thermes C (2005) Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc Natl Acad Sci U S A 102(28):9836–9841

    Article  CAS  PubMed  Google Scholar 

  • Towbin BD, Meister P, Gasser SM (2009) The nuclear envelope–a scaffold for silencing? Curr Opin Genet Dev 19(2):180–186

    Article  CAS  PubMed  Google Scholar 

  • Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, Weiss MJ, Dekker J, Blobel GA (2005) Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell 17(3):453–462

    Article  CAS  PubMed  Google Scholar 

  • Versteeg R, van Schaik BDC, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AHC (2003) The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res 13(9):1998–2004

    Article  CAS  PubMed  Google Scholar 

  • Volpi EV, Chevret E, Jones T, Vatcheva R, Williamson J, Beck S, Campbell RD, Goldsworthy M, Powis SH, Ragoussis J, Trowsdale J, Sheer D (2000) Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 113(Pt 9):1565–1576

    CAS  PubMed  Google Scholar 

  • Wang L, Di LJ, Lv X, Zheng W, Xue Z, Guo ZC, Liu DP, Liang CC (2009) Inter-MAR association contributes to transcriptionally active looping events in human beta-globin gene cluster. PLoS One 4(2):e4629

    Article  PubMed  CAS  Google Scholar 

  • Wang CM, Tsai SN, Yew TW, Kwan YW, Ngai SM (2010) Identification of histone methylation multiplicities patterns in the brain of senescence-accelerated prone mouse 8. Biogerontology 11(1):87–102

    Article  CAS  PubMed  Google Scholar 

  • Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP (2009) Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 41(2):246–250

    Article  CAS  PubMed  Google Scholar 

  • White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D (2004) DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A 101(51):17771–17776

    Article  CAS  PubMed  Google Scholar 

  • Williams RRE, Broad S, Sheer D, Ragoussis J (2002) Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp Cell Res 272(2):163–175

    Article  CAS  PubMed  Google Scholar 

  • Williams A, Spilianakis CG, Flavell RA (2010) Interchromosomal association and gene regulation in trans. Trends Genet 26(4):188–197

    Article  CAS  PubMed  Google Scholar 

  • Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP (2004) Replication timing of the human genome. Hum Mol Genet 13(2):191–202

    Article  CAS  PubMed  Google Scholar 

  • Woodfine K, Beare DM, Ichimura K, Debernardi S, Mungall AJ, Fiegler H, Collins VP, Carter NP, Dunham I (2005) Replication timing of human chromosome 6. Cell Cycle 4(1):172–176

    Article  CAS  PubMed  Google Scholar 

  • Worman HJ, Ostlund C, Wang Y (2010) Diseases of the nuclear envelope. Cold Spring Harb Perspect Biol 2(2):a000760

    Article  PubMed  CAS  Google Scholar 

  • Xu N, Tsai CL, Lee JT (2006) Transient homologous chromosome pairing marks the onset of X inactivation. Science 311(5764):1149–1152

    Article  CAS  PubMed  Google Scholar 

  • Xu N, Donohoe ME, Silva SS, Lee JT (2007) Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat Genet 39(11):1390–1396

    Article  CAS  PubMed  Google Scholar 

  • Yasui D, Miyano M, Cai S, Varga-Weisz P, Kohwi-Shigematsu T (2002) SATB1 targets chromatin remodelling to regulate genes over long distances. Nature 419(6907):641–645

    Article  CAS  PubMed  Google Scholar 

  • Yokoyama T, Silversides DW, Waymire KG, Kwon BS, Takeuchi T, Overbeek PA (1990) Conserved cysteine to serine mutation in tyrosinase is responsible for the classical albino mutation in laboratory mice. Nucleic Acids Res 18(24):7293–7298

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Xu F, Hashimshony T, Keshet I, Cedar H (2002) Establishment of transcriptional competence in early and late S phase. Nature 420(6912):198–202

    Article  CAS  PubMed  Google Scholar 

  • Zhang R, Poustovoitov MV, Ye X, Santos HA, Chen W, Daganzo SM, Erzberger JP, Serebriiskii IG, Canutescu AA, Dunbrack RL, Pehrson JR, Berger JM, Kaufman PD, Adams PD (2005) Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev Cell 8(1):19–30

    Article  CAS  PubMed  Google Scholar 

  • Zlatanova J, Caiafa P (2009) CCCTC-binding factor: to loop or to bridge. Cell Mol Life Sci 66(10):1647–1660

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We apologize to those whose work could not be discussed here due to space limitations.

The author’s work is supported by grants from Agence Nationale de la Recherche (ANR-07-BLAN-0062-01), Région Rhône-Alpes MIRA 2007 and 2010, Association pour la Recherche sur le Cancer n° ECL2010R01122, CEFIPRA n° 3803-1, and CNRS.

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  1. Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique (CNRS)/Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d’Italie, 69007, Lyon, France

    Benoît Moindrot, Philippe Bouvet & Fabien Mongelard

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  1. Benoît Moindrot
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  2. Philippe Bouvet
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Correspondence to Fabien Mongelard .

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  1. Advanced Scientific Research, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for, Jakkur P.O., Bangalore, 560064, India

    Tapas K. Kundu

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Moindrot, B., Bouvet, P., Mongelard, F. (2013). Chromatin Structure and Organization: The Relation with Gene Expression During Development and Disease. In: Kundu, T. (eds) Epigenetics: Development and Disease. Subcellular Biochemistry, vol 61. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4525-4_16

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