Genome-wide analysis of Polycomb targets in Drosophila melanogaster

Nature Genetics

Volumn 38, Issue 6, 2006, Pages 700-705

  Schwartz, Yuri B ^a   Kahn, Tatyana G ^a   Nix, David A ^b,d   Li, Xiao Yong ^b   Bourgon, Richard ^c   Biggin, Mark ^b   Pirrotta, Vincenzo ^a  

^a RUTGERS UNIVERSITY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d CIS Enterprise Data Group   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; ENHANCER OF ZESTE PROTEIN; HISTONE H3; LYSINE; MORPHOGEN; MULTIPROTEIN COMPLEX; POLYCOMB GROUP PROTEIN; POSTERIOR SEX COMBS PROTEIN; RECEPTOR; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING SITE; CHROMATIN; DNA RESPONSIVE ELEMENT; DROSOPHILA MELANOGASTER; GENE FUNCTION; GENE SILENCING; GENOME ANALYSIS; HOMEOBOX; INSECT DEVELOPMENT; METHYLATION; NONHUMAN; POLYCOMB RESPONSE ELEMENT; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; DNA METHYLATION; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENOME; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

DROSOPHILA MELANOGASTER; VERTEBRATA;

EID: 33745225872     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1817     Document Type: Article

References (30)

1. Pirrotta, V. PcG complexes and chromatin silencing. Curr. Opin. Genet. Dev. 7, 249-258 (1997).
2. Lund, A.H. & van Lohuizen, M. Polycomb complexes and silencing mechanisms. Curr. Opin. Cell Biol. 16, 239-246 (2004).
3. Rastelli, L., Chan, C.S. & Pirrotta, V. Related chromosome binding sites for zeste, suppressors of zeste and Polycomb group proteins in Drosophila and their dependence on Enhancer of zeste function. EMBO J. 12, 1513-1522 (1993).
4. Chan, C.-S., Rastelli, L. & Pirratta, V. A Polycomb response element in the Ubx gene that determines an epigenetically inherited state of repression. EMBO J. 13, 2553-2564 (1994).
5. Sengupta, A.K., Kuhrs, A. & Muller, J. General transcriptional silencing by a Polycomb response element in Drosophila. Development 131, 1959-1965 (2004).
6. Saurin, A.J., Shao, Z., Erdjument-Bromage, H., Tempst, P. & Kingston, R.E. A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. Nature 412, 655-660 (2001).
7. Czermin, B. et al. Drosophila Enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185-196 (2002).
8. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039-1043 (2002).
9. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 22, 2893-2905 (2002).
10. Müller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb Group repressor complex. Cell 111, 197-208 (2002).
11. Fischle, W. et al. Molecular basis for the discrimination of repressive methyllysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17, 1870-1881 (2003).
12. Jones, R.S. & Gelbart, W.M. Genetic analysis of the Enhancer of zeste locus and its role in gene regulation in Drosophila melanogaster. Genetics 126, 185-199 (1990).
13. Phillips, M.D. & Shearn, A. Mutations in polycombeotic, a Drosophila Polycomb-group gene, cause a wide range of maternal and zygotic phenotypes. Genetics 125, 91-101 (1990).
14. Strutt, H. & Paro, R. The polycomb group protein complex of Drosophila melanogaster has different composition at different target genes. Mol. Cell. Biol. 17, 6773-6783 (1997).
15. Bloyer, S., Cavalli, G., Brock, H.W. & Dura, J.-M. Identification and characterization of polyhomeotic PREs and TREs. Dev. Biol. 261, 426-442 (2003).
16. Reim, I., Lee, H.-H. & Frasch, M. The T-box-encoding Dorsocross genes function in amnioserosa development and the patterning of the dorsolateral germ band downstream of Dpp. Development 130, 3187-3204 (2003).
17. Jagla, K., Bellard, M. & Frasch, M. A cluster of Drosophila homeobox genes involved in mesoderm differentiation programs. Bioessays 23, 125-133 (2001).
18. Chiang, A., O'Connor, M.B., Paro, R., Simon, J. & Bender, W. Discrete Polycomb-binding sites in each parasegmental domain of the bithorax complex. Development 121, 1681-1689 (1995).
19. Shimell, M.J., Peterson, A.J., Burr, J., Simon, J.A. & O'Connor, M. Functional analysis of repressor binding sites in the iab-2 regulatory region of the abdominal-A homeotic gene. Dev. Biol. 218, 38-52 (2000).
20. Busturia, A., Wightman, C.D. & Sakonju, S. A silencer is required for maintenance of transcriptional repression throughout Drosophila development. Development 124, 4343-4350 (1997).
21. Mihaly, J., Hogga, I., Gausz, J., Gyurkovics, H. & Karch, F. In situ dissection of the Fab-7 region of the bithorax complex into a chromatin domain boundary and a Polycomb-response element. Development 124, 1809-1820 (1997).
22. Barges, S. et al. The Fab-8 boundary defines the distal limit of the bithorax complex iab-7 domain and insulates iab-7 from initiation elements and a PRE in the adjacent iab-8 domain. Development 127, 779-790 (2000).
23. Orlando, V. & Paro, R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell 75, 1187-1198 (1993).
24. Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261 (2004).
25. 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).
26. Brunk, B.P., Martin, E.C. & Adler, P.N. Drosophila genes Posterior Sex Combs and Suppressor two of zeste encode proteins with homology to the murine bmi-1 oncogene. Nature 353, 351-353 (1991).
27. Lee, T.I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301-313 (2006).
28. Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).
29. Négre, N. et al. Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol. 4, e170 (2006).
30. Schneider, I. Cell lines derived from the late embryonic stages of Drosophila melanogaster. J. Embryol. Exp. Morphol. 27, 353-356 (1972).