The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density (original) (raw)

• Andreozzi L, Federico C, Motta S, Saccone S, Sazanova AL, Sazanov AA, Smirnov AF, Galkina SA, Lukina NA, Rodionov AV, Carels N, Bernardi G (2001) Compositional mapping of chicken chromosomes and identification of the gene-richest regions. Chromosom Res 9:521–532
  Article CAS Google Scholar
• Andrulis ED, Neiman AM, Zappulla DC, Sternglanz R (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394:592–595
  Article PubMed CAS Google Scholar
• Bernardi G (2004) Structural and evolutionary genomics. Natural selection in genome evolution. Elsevier, Amsterdam, The Netherlands
  Google Scholar
• Bickmore WA, van der Maarel SM (2003) Perturbations of chromatin structure in human genetic disease: recent advances. Hum Mol Genet 12:207–213
  Article CAS Google Scholar
• Boggs BA, Chinault AC (1997) Analysis of DNA replication by fluorescence in situ hybridization. Methods 13:259–270
  Article PubMed CAS Google Scholar
• Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, Muller S, Eils R, Cremer C, Speicher MR, Cremer T (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3(5):e157
  Article PubMed CAS Google Scholar
• Boutanaev AM, Mikhaylova LM, Nurminsky DI (2005) The pattern of chromosome folding in interphase is outlined by the linear gene density profile. Mol Cell Biol 25:8379–8386
  Article PubMed CAS Google Scholar
• Boyle S, Gilchrist S, Bridger JM, Mahy NL, Elis JA, Bickmore WA (2001) The spatial organization of human chromosome within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10:211–219
  Article PubMed CAS Google Scholar
• Bridger JM, Boyle S, Kill IR, Bickmore WA (2000) Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr Biol 10:149–152
  Article PubMed CAS Google Scholar
• Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG (1997) Association of transcriptionally silent genes with ikaros complexes at centromeric heterochromatin. Cell 91:845–854
  Article PubMed CAS Google Scholar
• Clemson CM, Hall LL, Byron M, McNeil J, Lawrence B (2006) The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc Natl Acad Sci USA 103:7688–7693
  Article PubMed CAS Google Scholar
• Cockell M, Gasser SM (1999) Nuclear compartments and gene regulation. Curr Op Genet Dev 9:199–205
  Article PubMed CAS Google Scholar
• Costantini M, Clay O, Federico C, Saccone S, Auletta F, Bernardi G (2007) Human chromosomal bands: nested structure, high definition map and molecular basis. Chromosoma 116:36–49
  Article CAS Google Scholar
• Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Genet 2:292–301
  Article CAS Google Scholar
• Croft JA, Bridger JM, Boyle S, Perry P, 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
• D’Antoni S, Mattina T, Di Mare P, Federico C, Motta S, Saccone S (2004) Altered replication timing of the HIRA/Tuple1 locus in the DiGeorge and velocardiofacial syndromes. Gene 333:111–119
  Article PubMed CAS Google Scholar
• D’Onofrio G, Ghosh TC, Saccone S (2007) Different functional classes of genes are characterized by different compositional properties. FEBS Lett 581:5819–5824
  Article PubMed CAS Google Scholar
• Dutrillaux B, Couturier J, Richer C-L, Viegas-Pequinot E (1976) Sequence of DNA replication in 277 R- and Q-bands of human chromosomes using a BrdU treatment. Chromosoma 58:51–61
  Article PubMed CAS Google Scholar
• Federico C, Saccone S, Bernardi G (1998) The gene-richest bands of human chromosomes replicate at the onset of the S-phase. Cytogenet Cell Genet 80:83–88
  Article PubMed CAS Google Scholar
• Federico C, Andreozzi L, Saccone S, Bernardi G (2000) Gene density in the Giemsa bands of human chromosomes. Chromosom Res 8:737–746
  Article CAS Google Scholar
• Federico C, Saccone S, Andreozzi L, Motta S, Russo V, Carels N, Bernardi G (2004) The pig genome: compositional analysis and indentification of the gene-richest regions in chromosomes and nuclei. Gene 343:245–251
  Article PubMed CAS Google Scholar
• Federico C, Cantarella CD, Scavo C, Saccone S, Bed’Hom B, Bernardi G (2005) Avian genomes: different karyotypes but a similar distribution of the GC-richest chromosome regions at interphase. Chromosom Res 13:785–793
  Article CAS Google Scholar
• Federico C, Scavo C, Cantarella CD, Motta S, Saccone S, Bernardi G (2006) Gene-rich and gene-poor chromosomal regions have different locations in the interphase nuclei of cold-blooded vertebrates. Chromosoma 115:123–128
  Article PubMed CAS Google Scholar
• Ferreira J, Paolella G, Ramos C, Lamond AI (1997) Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. Cell Biol 139:1597–1610
  Article CAS Google Scholar
• Foster HA, Bridger JM (2005) The genome and the nucleus: a marriage made by evolution. Genome organization and nuclear architecture. Chromosoma 114:212–229
  Article PubMed Google Scholar
• Francke U (1994) Digitized and differentially shaded human chromosome ideograms for genomic applications. Cytogenet Cell Genet 6:206–219
  Article Google Scholar
• Furey TS, Haussler D (2003) Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet 12:1037–1044
  Article PubMed CAS Google Scholar
• Gilbert N, Boyle S, Fiegler H, Woodfine K, Carter NP, Bickmore WA (2004) Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118:555–566
  Article PubMed CAS Google Scholar
• IHGSC (International Human Genome Sequencing Consortium) (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945
  Article CAS Google Scholar
• Kupper K, Kolbl A, Biener D, Dittrich S, von Hase J, Thormeyer T, Fiegler H, Carter NP, Speicher MR, Cremer T, Cremer M (2007) Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116:285–306
  Article PubMed Google Scholar
• Lukasova E, Kozubek S, Kozubek M, Falk M, Amrichova J (2002) The 3D structure of human chromosomes in cell nuclei. Chromosom Res 10:535–48
  Article CAS Google Scholar
• Masny PS, Bengtsson U, Chung S-A, Martin JH, van Engelen B, van der Maarel SM, Winokur ST (2004) Localization of 4q35.2 to the nuclear periphery: is FSHD a nuclear envelope disease? Hum Mol Genet 13:1857–1871
  Article PubMed CAS Google Scholar
• Neusser M, Schubel V, Koch A, Cremer T, Müller S (2007) Evolutionary conserved, cell type and species-specific higher order chromatin arrangements in interphase nuclei of primates. Chromosoma 116:307–320
  Article PubMed Google Scholar
• Ono A, Kono K, Ikebe D, Muto A, Sun J, Kobayashi M, Ueda K, Melo JV, Igarashi K, Tashiro S (2007) Nuclear positioning of the BACH2 gene in BCR-ABL positive leukemic cells. Genes Chromosomes Cancer 46:67–74
  Article PubMed CAS Google Scholar
• Petrova NV, Yarovaya OV, Razin SV (2006) Specific spatial organization of chromosomes in nuclei of primary human fibroblasts is maintained by nuclear matrix. Dokl Biochem Biophys 406:4–6
  Article PubMed CAS Google Scholar
• Roix JJ, McQueen PG, Munson P, Parada LA, Misteli T (2003) Spatial proximity of traslocation-prone gene loci in human lymphomas. Nat. Genet 34:287–291
  Article PubMed CAS Google Scholar
• Saccone S, De Sario A, Della Valle G, Bernardi G (1992) The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc Natl Acad Sci USA 89:4913–4917
  Article PubMed CAS Google Scholar
• Saccone S, Cacciò S, Perani P, Andreozzi L, Rapisarda A, Motta S, Bernardi G (1997) Compositional mapping of mouse chromosomes and identification of the gene-rich regions. Chromosom Res 5:293–300
  Article CAS Google Scholar
• Saccone S, Pavlicek A, Federico C, Paces J, Bernardi G (2001) Genes, isochores and bands in human chromosomes 21 and 22. Chromosom Res 9:533–539
  Article CAS Google Scholar
• Saccone S, Federico C, Bernardi G (2002) Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300:169–178
  Article PubMed CAS Google Scholar
• Sadoni N, Langer S, Fauth C, Bernardi G, Cremer T, Turner BM, Zink D (1999) Nuclear organization of mammalian genomes: polar chromosome territories build up functionally distinct higher order compartments. J Cell Biol 146:1211–1226
  Article PubMed CAS Google Scholar
• Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K et al (2003) Human chromosome 7: DNA sequence and biology. Science 300:767–772
  Article PubMed CAS Google Scholar
• Solovei I, Cavallo A, Schermelleh L, Jaunin F, Scasselati C, Cmarko D, Cremer C, Fakan S, Cremer T (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
• Strouboulis J, Wolffe AP (1996) Functional compartmentalization of the nucleus. J Cell Sci 109:1991–2000
  PubMed CAS Google Scholar
• Tanabe H, Habermann FA, Solovei I, Cremer M, Cremer T (2002a) Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications. Mutat Res 504:37–45
  PubMed CAS Google Scholar
• Tanabe H, Muller S, Neusser M, von Hase J, Calcagno E, Cremer M, Solovei I, Cremet C, Cremer T (2002b) Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci USA 99:4424–4429
  Article PubMed CAS 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 113:1565–1576
  PubMed CAS Google Scholar
• Zhou J, Ermakova OV, Riblet R, Birshtein BK, Schildkraut CL (2002) Replication and subnuclear location dynamics of the immunoglobulin heavy-chain locus in B-lineage cells. Mol Cell Biol 22:4876–4889
  Article PubMed CAS Google Scholar
• Zink D (2006) The temporal program of DNA replication: new insight into old question. Chromosoma 115:273–287
  Article PubMed CAS Google Scholar