Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster

Nature Genetics

Volumn 38, Issue 6, 2006, Pages 694-699

  Tolhuis, Bas ^a   Muijrers, Inhua ^a   De Wit, Elzo ^a   Teunissen, Hans ^a   Talhout, Wendy ^a   Van Steensel, Bas ^a   Van Lohuizen, Maarten ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; NOTCH RECEPTOR; POLYCOMB GROUP PROTEIN; POLYCOMB GROUP PROTEIN 1; POLYCOMB GROUP PROTEIN 2; PROTEIN; REGULATOR PROTEIN; SONIC HEDGEHOG PROTEIN; STEROID HORMONE; UNCLASSIFIED DRUG; WNT1 PROTEIN;

ANIMAL CELL; ARTICLE; CELL PROLIFERATION; CELL RENEWAL; CHROMATIN; DROSOPHILA MELANOGASTER; GENE; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENOME ANALYSIS; NONHUMAN; PRC1 GENE; PRC2 GENE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; STEM CELL; TRANSCRIPTION REGULATION;

ANIMALS; CELL LINE; CHROMATIN; DNA, COMPLEMENTARY; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENE EXPRESSION PROFILING; GENOME; PROMOTER REGIONS (GENETICS); PROTEIN ISOFORMS;

DROSOPHILA MELANOGASTER; ERINACEIDAE;

EID: 33745258986     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1792     Document Type: Article

References (30)

1. Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413-443 (2004).
2. Valk-Lingbeek, M.E., Bruggeman, S.W. & van Lohuizen, M. Stem cells and cancer; the polycomb connection. Cell 118, 409-418 (2004).
3. van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 27, 304-308 (2001).
4. van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 18, 424-428 (2000).
5. Sun, L.V. et al. Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc. Natl. Acad. Sci. USA 100, 9428-9433 (2003).
6. Nègre, N. et al. Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol. 4, e170 (2006).
7. Ringrose, L., Rehmsmeier, M., Dura, J.M. & Paro, R. Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster. Dev. Cell 5, 759-771 (2003).
8. Dejardin, J. et al. Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1. Nature 434, 533-538 (2005).
9. Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev. 17, 2825-2838 (2003).
10. Schubeler, D. et al. Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat. Genet. 32, 438-442 (2002).
11. Schubeler, D. et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263-1271 (2004).
12. Breiling, A., O'Neill, L.P., D'Eliseo, D., Turner, B.M. & Orlando, V. Epigenome changes in active and inactive polycomb-group-controlled regions. EMBO Rep. 5, 976-982 (2004).
13. Stolc, V. et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306, 655-660 (2004).
14. Ficz, G., Heintzmann, R. & Arndt-Jovin, D.J. Polycomb group protein complexes exchange rapidly in living Drosophila. Development 132, 3963-3976 (2005).
15. Hernandez-Munoz, I., Taghavi, P., Kuijl, C., Neefjes, J. & vanLohuizen, M. Assocation of BMI1 with Polycomb bodies is dynamic and requires PRC2/EZH2 and the maintenance DNA methyltransferase DNMT1. Mol. Cell. Biol. 25, 11047-11058 (2005).
16. Harris, M.A. et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261 (2004).
17. Lascaris, R. et al. Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state. Genome Biol. 4, R3 (2003).
18. Kirmizis, A., Bartley, S.M. & Farnham, P.J. Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol. Cancer Ther. 2, 113-121 (2003).
19. Klebes, A. et al. Regulation of cellular plasticity in Drosophila imaginai disc cells by the Polycomb group, trithorax group and lama genes. Development 132, 3753-3765 (2005).
20. Leung, C. et al. Bmi1 is essential for cerebellar development and is overexpressed in human medulloblastomas. Nature 428, 337-341 (2004).
21. Maurange, C. & Paro, R. A cellular memory module conveys epigenetic inheritance of hedgehog expression during Drosophila wing imaginai disc development. Genes Dev. 16, 2672-2683 (2002).
22. Paul, S.M., Ternet, M., Salvaterra, P.M. & Beitel, G.J. The Na+/K+ ATPase is required for septate junction function and epithelial tube-size control in the Drosophila tracheal system. Development 130, 4963-4974 (2003).
23. Warren, J.T. et al. Molecular and biochemical characterization of two P450 enzymes in the ecdysteroidogenic pathway of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99, 11043-11048 (2002).
24. Baehrecke, E.H. Steroid regulation of programmed cell death during Drosophila development. Cell Death Differ. 7, 1057-1062 (2000).
25. Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc. Natl. Acad. Sci. USA 97, 716-721 (2000).
26. Cleveland, W.S. Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc. 74, 829-836 (1979).
27. van Steensel, B., Delrow, J. & Bussemaker, H.J. Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding. Proc. Natl. Acad. Sci. USA 100, 2580-2585 (2003).
28. Baldi, P. & Long, A.D. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17, 509-519 (2001).
29. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodolog. 57, 289-300 (1995).
30. Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. EMBO J. 21, 1389-1397 (2002).