Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing (original) (raw)

References

  1. Cimbora, D.M. & Groudine, M. The control of mammalian DNA replication: a brief history of space and timing. Cell 104, 643–646 (2001).
    CAS PubMed Google Scholar
  2. Raghuraman, M.K. et al. Replication dynamics of the yeast genome. Science 294, 115–121 (2001).
    Article CAS Google Scholar
  3. Ahmad, K. & Henikoff, S. Centromeres are specialized replication domains in heterochromatin. J. Cell. Biol. 153, 101–110 (2001).
    Article CAS Google Scholar
  4. Dolfini, S., Courgeon, A.M. & Tiepolo, L. The cell cycle of an established line of Drosophila melanogaster cells in vitro. Experientia 26, 1020–1021 (1970).
    Article CAS Google Scholar
  5. Hansen, R.S., Canfield, T.K., Lamb, M.M., Gartler, S.M. & Laird, C.D. Association of fragile X syndrome with delayed replication of the FMR1 gene. Cell 73, 1403–1409 (1993).
    Article CAS Google Scholar
  6. Rubin, G.M. et al. A Drosophila complementary DNA resource. Science 287, 2222–2224 (2000).
    Article CAS Google Scholar
  7. Cleveland, W.S. & Devlin, S.J. Locally-weighted regression: an approach to regression analysis by local fitting. J. Amer. Statist. Assoc. 83, 596–610 (1988).
    Article Google Scholar
  8. Gilbert, D.M. Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol. 14, 377–383 (2002).
    Article CAS Google Scholar
  9. Sullivan, B. & Karpen, G. Centromere identity in Drosophila is not determined in vivo by replication timing. J. Cell. Biol. 154, 683–690 (2001).
    Article CAS Google Scholar
  10. Caizzi, R., Caggese, C. & Pimpinelli, S. Bari-1, a new transposon-like family in Drosophila melanogaster with a unique heterochromatic organization. Genetics 133, 335–345 (1993).
    CAS PubMed PubMed Central Google Scholar
  11. Jakubczak, J.L., Zenni, M.K., Woodruff, R.C. & Eickbush, T.H. Turnover of R1 (type I) and R2 (type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster. Genetics 131, 129–142 (1992).
    CAS PubMed PubMed Central Google Scholar
  12. Wakimoto, B.T. & Hearn, M.G. The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster. Genetics 125, 141–154 (1990).
    CAS PubMed PubMed Central Google Scholar
  13. Eberl, D.F., Duyf, B.J. & Hilliker, A.J. The role of heterochromatin in the expression of a heterochromatic gene, the rolled locus of Drosophila melanogaster. Genetics 134, 277–292 (1993).
    CAS PubMed PubMed Central Google Scholar
  14. Hatton, K.S. et al. Replication program of active and inactive multigene families in mammalian cells. Mol. Cell. Biol. 8, 2149–2158 (1988).
    Article CAS Google Scholar
  15. Cimbora, D.M. et al. Long-distance control of origin choice and replication timing in the human β-globin locus are independent of the locus control region. Mol. Cell. Biol. 20, 5581–5591 (2000).
    Article CAS Google Scholar
  16. Hansen, R.S., Canfield, T.K. & Gartler, S.M. Reverse replication timing for the XIST gene in human fibroblasts. Hum. Mol. Genet. 4, 813–820 (1995).
    Article CAS Google Scholar
  17. Smith, Z.E. & Higgs, D.R. The pattern of replication at a human telomeric region (16p13.3): its relationship to chromosome structure and gene expression. Hum. Mol. Genet. 8, 1373–1386 (1999).
    Article CAS Google Scholar
  18. Kennedy, B.K., Barbie, D.A., Classon, M., Dyson, N. & Harlow, E. Nuclear organization of DNA replication in primary mammalian cells. Genes. Dev. 14, 2855–2868 (2000).
    Article CAS Google Scholar
  19. DePamphilis, M.L. Replication origins in metazoan chromosomes: fact or fiction? Bioessays 21, 5–16 (1999).
    Article CAS Google Scholar
  20. van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 27, 304–308 (2001).
    Article CAS Google Scholar
  21. Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association. Nat. Genet. 28, 327–334 (2001).
    Article CAS Google Scholar
  22. Kooperberg, C., Fazzio, T.G., Delrow, J. & Tsukiyama, T. Improved background correction for spotted DNA microarrays. J. Comput. Biol. 9, 55–66 (2002).
    Article CAS Google Scholar
  23. Yang, Y.H., Dudoit, S., Luu, P. & Speed, T.P. Normalization for cDNA microarrays data. in Microarrays: Optical Technologies and Informatics (eds Bittner, M.L., Chen, Y., Dorsel, A.N. and Dougherty, E.R.) (International Society for Optical Engineering, San Jose, California, 2001).
    Google Scholar
  24. Pritchard, C.C., Hsu, L., Delrow, J. & Nelson, P.S. Project normal: defining normal variance in mouse gene expression. Proc. Natl Acad. Sci. USA 98, 13266–13271 (2001).
    Article CAS Google Scholar
  25. Fan, J. & Gijbels, I. Local Polynomial Modelling and its Applications (Chapman-Hall, London, 1996).
    Google Scholar

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