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Chromosome Structure and Dynamics

The Pattern of Chromosome Folding in Interphase Is Outlined by the Linear Gene Density Profile

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Pages 8379-8386 | Received 29 Oct 2004, Accepted 11 Jul 2005, Published online: 27 Mar 2023

REFERENCES

  • Alvarez, M., S. J. Rhodes, and J. P. Bidwell. 2003. Context-dependent transcription: all politics is local. Gene 313:43–57.
  • Arbeitman, M. N., E. E. Furlong, F. Imam, E. Johnson, B. H. Null, B. S. Baker, M. A. Krasnow, M. P. Scott, R. W. Davis, and K. P. White. 2002. Gene expression during the life cycle of Drosophila melanogaster. Science 297:2270–2275.
  • Belmont, A. S. 2001. Visualizing chromosome dynamics with GFP. Trends Cell Biol. 11:250–257.
  • Boutanaev, A. M., A. I. Kalmykova, Y. Y. Shevelyov, and D. I. Nurminsky. 2002. Large clusters of co-expressed genes in the Drosophila genome. Nature 420:666–669.
  • Brown, K. E., S. S. Guest, S. T. Smale, K. Hahm, M. Merkenschlager, and A. G. Fisher. 1997. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91:845–854.
  • Byrd, K., and V. G. Corces. 2003. Visualization of chromatin domains created by the gypsy insulator of Drosophila. J. Cell Biol. 162:565–574.
  • Bystritskiy, A. A., and S. V. Razin. 2004. Breakpoint clusters: reason or consequence. Crit. Rev. Eukaryot. Gene Expr. 14:65–77.
  • Chambeyron, S., and W. A. Bickmore. 2004. Does looping and clustering in the nucleus regulate gene expression. Curr. Opin. Cell Biol. 16:256–262.
  • Chambeyron, S., and W. A. Bickmore. 2004. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 18:1119–1130.
  • Cremer, T., and C. Cremer. 2001. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2:292–301.
  • Csink, A. K., and S. Henikoff. 1998. Large-scale chromosomal movements during interphase progression in Drosophila. J. Cell Biol. 143:13–22.
  • Dietzel, S., A. Jauch, D. Kienle, G. Qu, H. Holtgreve-Grez, R. Eils, C. Munkel, M. Bittner, P. S. Meltzer, J. M. Trent, and T. Cremer. 1998. Separate and variably shaped chromosome arm domains are disclosed by chromosome arm painting in human cell nuclei. Chromosome Res. 6:25–33.
  • Fransz, P., J. H. De Jong, M. Lysak, M. R. Castiglione, and I. Schubert. 2002. Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc. Natl. Acad. Sci. USA 99:14584–14589.
  • Frisch, M., K. Frech, A. Klingenhoff, K. Cartharius, I. Liebich, and T. Werner. 2002. In silico prediction of scaffold/matrix attachment regions in large genomic sequences. Genome Res. 12:349–354.
  • Grogan, J. L., M. Mohrs, B. Harmon, D. A. Lacy, J. W. Sedat, and R. M. Locksley. 2001. Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity 14:205–215.
  • Jackson, D. A. 2003. The anatomy of transcription sites. Curr. Opin. Cell Biol. 15:311–317.
  • Kurz, A., S. Lampel, J. E. Nickolenko, J. Bradl, A. Benner, R. M. Zirbel, T. Cremer, and P. Lichter. 1996. Active and inactive genes localize preferentially in the periphery of chromosome territories. J. Cell Biol. 135:1195–1205.
  • Lercher, M. J., A. O. Urrutia, and L. D. Hurst. 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31:180–183.
  • Ma, H., A. J. Siegel, and R. Berezney. 1999. Association of chromosome territories with the nuclear matrix. Disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins. J. Cell Biol. 146:531–542.
  • Mahy, N. L., P. E. Perry, S. Gilchrist, R. A. Baldock, and W. A. Bickmore. 2002. Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J. Cell Biol. 157:579–589.
  • Mahy, N. L., P. E. Perry, and W. A. Bickmore. 2003. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J. Cell Biol. 159:753–763.
  • Moen, P. T., Jr., C. V. Johnson, M. Byron, L. S. Shopland, I. de la Serna, A. Imbalzano, and J. B. Lawrence. 2004. Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis. Mol. Biol. Cell 15:197–206.
  • Ragoczy, T., A. Telling, T. Sawado, M. Groudine, and S. T. Kosak. 2003. A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res. 11:513–525.
  • Roy, P. J., J. M. Stuart, J. Lund, and S. K. Kim. 2002. Chromosomal clustering of muscle-specific genes in Caenorhabditis elegans. Nature 418:975–979.
  • Schardin, M., T. Cremer, H. D. Hager, and M. Lang. 1985. Specific staining of human chromosomes in Chinese hamster x man hybrid cell lines demonstrates interphase chromosome territories. Hum. Genet. 71:281–287.
  • Shopland, L. S., C. V. Johnson, M. Byron, J. McNeil, and J. B. Lawrence. 2003. Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J. Cell Biol. 162:981–990.
  • Solovei, I., A. Cavallo, L. Schermelleh, F. Jaunin, C. Scasselati, D. Cmarko, C. Cremer, S. Fakan, and T. Cremer. 2002. Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp. Cell Res. 276:10–23.
  • Stein, G. S., J. B. Lian, A. J. van Wijnen, J. L. Stein, A. Javed, M. Montecino, S. K. Zaidi, D. Young, J. Y. Choi, S. Gutierrez, and S. Pockwinse. 2003. Nuclear microenvironments support physiological control of gene expression. Chromosome Res. 11:527–536.
  • Versteeg, R., B. D. van Schaik, M. F. van Batenburg, M. Roos, R. Monajemi, H. Caron, H. J. Bussemaker, and A. H. van Kampen. 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. 13:1998–2004.
  • Volpi, E. V., E. Chevret, T. Jones, R. Vatcheva, J. Williamson, S. Beck, R. D. Campbell, M. Goldsworthy, S. H. Powis, J. Ragoussis, J. Trowsdale, and D. Sheer. 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.
  • Zink, D., T. Cremer, R. Saffrich, R. Fischer, M. F. Trendelenburg, W. Ansorge, and E. H. Stelzer. 1998. Structure and dynamics of human interphase chromosome territories in vivo. Hum. Genet. 102:241–251.

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