Chromosome territories have a highly nonspherical morphology and nonrandom positioning (original) (raw)

• Arneodo A, Bacry E, Muzy JF (1995) The thermodynamics of fractals revisited with wavelets. Physica 213A: 232–275.
  Google Scholar
• Arneodo A, Decoster N, Roux S (2000) A wavelet-based method for multifractal image analysis. I. Methodology and test applications on isotropic and anisotropic random rough surfaces. Eur Phys J B 15: 567–600.
  Article CAS Google Scholar
• Arneodo A, Decoster N, Kestener P, Roux SG (2003) A wavelet-based method for multifractal image analysis: from theoretical concepts to experimental applications. Adv Imaging Electron Phys 126: 1–92.
  Google Scholar
• Bickmore WA, Teague P (2002) Influences of chromosome size, gene density and nuclear position on the frequency of constitutional translocations in the human population. Chromosome Res 10: 707–715.
  Article PubMed CAS Google Scholar
• Bolzer A, Kreth G, Solovei I et al. (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3: e157
  Article PubMed CAS Google Scholar
• Bornfleth H, Satzler K, Eils R, Cremer C (1998) High-precision distance measurements and volume-conserving segmentation of objects near and below the resolution limit in three-dimensional confocal fluorescence microscopy. J Microsc 189: 118–136.
  Article Google Scholar
• Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA (2001) The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10: 211–219.
  Article PubMed CAS Google Scholar
• Branco MR, Pombo A (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLOS Biol 4: e138.
  Article PubMed CAS Google Scholar
• Canny J (1986) A computational approach to edge detection. IEEE Trans Pat Ana Mach Intell 36: 961–1005.
  Google Scholar
• Chaikin PM, Donev A, Man W, Stillinger FH, Torquato S (2006) Some observations on the random packing of hard ellipsoids. Ind Eng Chem Res 45: 6960–6965.
  Article CAS Google Scholar
• Cornforth MN, Greulich-Bode KM, Loucas BD et al. (2002) Chromosomes are predominantly located randomly with respect to each other in interphase human cells. J Cell Biol 159: 237–244.
  Article PubMed CAS Google Scholar
• Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2: 292–301.
  Article PubMed CAS Google Scholar
• Cremer T, Cremer M, Dietzel S, Müller S, Solovei I, Fakan S (2006) Chromosome territories—a functional nuclear landscape. Curr Opin Cell Biol 3: 307.
  Article CAS Google Scholar
• Cremer T, Kreth G, Koester H et al. (2000) Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture. Crit Rev Eukaryot Gene Expr 10: 179–212.
  PubMed CAS Google Scholar
• Cremer M, Kupper K, Wagler B et al. (2003) Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol 162: 809–820.
  Article PubMed CAS Google Scholar
• Cremer M, von Hase J, Volm T et al. (2001) The non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 9: 541–567.
  Article PubMed CAS Google Scholar
• Croft JA, Bridger P, Boyle S, Perry JM, Teague P, Bickmore WA (1999) Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145: 1119–1131.
  Article PubMed CAS Google Scholar
• Csink AK, Henikoff S (1998) Large-scale chromosomal movements during interphase progression in drosophilia. J Cell Biol 143: 13–22.
  Article PubMed CAS Google Scholar
• Donev A, Cisse I, Sachs D et al. (2004) Improving the density of jammed disorded packings using ellipsoids. Science 303: 990–993.
  Article PubMed CAS Google Scholar
• Dundr M, Misteli T (2001) Functional architecture in the cell nucleus. Biochem J 356: 297–310.
  Article PubMed CAS Google Scholar
• Edelmann P, Bornfleth H, Zink D, Cremer T, Cremer C (2001) Morphology and dynamics of chromosome territories in living cells. Biochim Biophys Acta 1551: 29–40.
  Google Scholar
• Eils R, Dietzel S, Bertin E et al. (1996) Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. J Cell Biol 135: 1427–1440.
  Article PubMed CAS Google Scholar
• Gerlich D, Beaudouin J, Kalbfuss B, Daigle N, Eils R, Ellenberg J (2003) Global chromosome positions are transmitted through mitosis in mammalian cells. Cell 112: 751–764.
  Article PubMed CAS Google Scholar
• Gilbert N, Gilchrist S, Bickmore WA (2005) Chromatin organization in the mammalian nucleus. Int Rev Cytol 242: 283–336.
  PubMed CAS Google Scholar
• Gue M, Messaoudi C, Sheng Sun J, Boudier T (2005) Smart 3D-FISH: automation of distance analysis in nuclei of interphase cells by image processing. Cytometry Part A 67A: 18–26.
  Article Google Scholar
• Habermann FA, Cremer M, Walter J et al. (2001) Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res 9: 569–584.
  Article PubMed CAS Google Scholar
• Kestener P, Arneodo A (2003) Three-dimensional wavelet-based multifractal method: the need for revisiting the multifractal description of turbulence dissipation data. Phys Rev Lett 91: 194501.
  Article PubMed CAS Google Scholar
• Khalil A, Joncas G, Nekka F (2004) Morphological analysis of HI features. I. Metric space technique. Astrophys J 601: 352–364.
  Article Google Scholar
• Khalil A, Joncas G, Nekka F, Kestener P, Arneodo A (2006) Morphological analysis of HI features. II. Wavelet-based multifractal formalism. Astrophys J Suppl Ser 165: 512–550.
  Article CAS Google Scholar
• Kreth G, Finsterle J, von Hase J, Cremer M, Cremer C (2004) Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code. Biophys J 86: 2803–2812.
  Article PubMed CAS Google Scholar
• Kurz A, Lampel S, Nickolenko JE et al. (1996) Active and inactive genes localize preferentially in the periphery of chromosome territories. J Cell Biol 135: 1195–1205.
  Article PubMed CAS Google Scholar
• Mallat S (1998) A Wavelet Tour in Signal Processing. New York: Academic Press.
  Google Scholar
• Mayer R, Brero A, von Hase J, Schroeder T, Cremer T, Dietzel S (2005) Common themes and cell type specific variations of higher order chromatin arrangements in the mouse. BMC Cell Biol 6: 44.
  Article PubMed CAS Google Scholar
• Meaburn KJ, Misteli T (2007) Cell biology: chromosome territories. Nature 445: 379–781.
  Article PubMed CAS Google Scholar
• Muzy JF, Bacry E, Arneodo A (1991) Wavelets and multifractal formalism for singular signals: application to turbulence data. Phys Rev Lett 67: 3515–3518.
  Article PubMed Google Scholar
• Muzy JF, Bacry E, Arneodo A (1994) The multifractal formalism revisited with wavelets. Int J Bifurcation Chaos 4: 245–302.
  Article Google Scholar
• Otsu N (1979) A threshold selection method from gray level histograms. IEEE Trans Syst Man Cybernet 9: 62–66.
  Article Google Scholar
• Parada LA, McQueen PG, Misteli T (2004) Tissue-specific spatial organization of genomes. Genome Biol 5: R44.
  Article PubMed Google Scholar
• Parada LA, McQueen PG, Munson PJ, Misteli T (2002) Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol 12: 1692–1697.
  Article PubMed CAS Google Scholar
• Parada LA, Misteli T (2002) Chromosome positioning in the interphase nucleus. Trends Cell Biol 12: 425–432.
  Article PubMed CAS Google Scholar
• Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T (2003) Spatial proximity of translocation prone gene loci in human lymphomas. Nat Genet 34: 287–291.
  Article PubMed CAS Google Scholar
• Sharon E, Galun M, Sharon D, Basri R, Brandt A (2006) Hierarchy and adaptivity in segmenting visual scenes. Nat Lett 442: 810–813.
  Article CAS Google Scholar
• Shopland LS, Lynch CR, Peterson KA et al. (2006) Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J Cell Biol 174: 27–38.
  Article PubMed CAS Google Scholar
• Solovei I, Cavallo A, Schermelleh L et al. (2002) Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp Cell Res 276: 10–23.
  Article PubMed CAS Google Scholar
• Stadler S, Schnapp V, Mayer R et al. (2004) The architecture of chicken chromosome territories changes during differentiation. BMC Cell Biol 5: 44.
  Article PubMed CAS Google Scholar
• Thomson I, Gilchrist S, Bickmore WA, Chubb JR (2004) The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol 14: 166–172.
  Article PubMed CAS Google Scholar
• Visser AE, Eils R, Jauch A et al. (1998) Spatial distributions of early and late replicating chromatin in interphase chromosome territories. Exp Cell Res 243: 398–407.
  Article PubMed CAS Google Scholar
• Weierich C, Brero A, Stein S et al. (2003) Three-dimensional arrangements of centromeres and telomeres in nuclei of human and murine lymphocytes. Chromosome Res 11: 485–502.
  Article PubMed CAS Google Scholar
• Zinc D, Bornfleth H, Visser A, Cremer C, Cremer T (1999) Organization of early and late replicating DNA in human chromosome territories. Exp Cell Res 247: 176–188.
  Article Google Scholar