Architecture of a Polycomb Nucleoprotein Complex

Molecular Cell

Volumn 24, Issue 1, 2006, Pages 91-100

  Mohd Sarip, Adone ^a   van der Knaap, Jan A ^a   Wyman, Claire ^a   Kanaar, Roland ^a   Schedl, Paul ^b   Verrijzer, C Peter ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

DNA

Indexed keywords

DEOXYRIBONUCLEASE I; NUCLEASE; NUCLEOPROTEIN;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; DNA DETERMINATION; DNA FOOTPRINTING; NUCLEOSOME; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCANNING FORCE MICROSCOPY; STRUCTURE ANALYSIS;

ANIMALS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; DNA; DNA FOOTPRINTING; DNA-BINDING PROTEINS; DROSOPHILA; DROSOPHILA PROTEINS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; MICROSCOPY, ATOMIC FORCE; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; RESPONSE ELEMENTS; TRANSCRIPTION FACTORS;

EID: 33749054895     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2006.08.007     Document Type: Article

References (44)

1. Barges S., Mihaly J., Galloni M., Hagstrom K., Muller M., Shanower G., Schedl P., Gyurkovics H., and Karch F. 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 (2000) 779-790
2. Bender W., Akam M., Karch F., Beachy P., Peifer M., Spierer P., Lewis E., and Hogness D. Molecular genetics of the bithorax complex in Drosophila melanogaster. Science 221 (1983) 23-29
3. Blastyak A., Mishra R.K., Karch F., and Gyurkovics H. Efficient and specific targeting of Polycomb group proteins requires cooperative interaction between grainyhead and pleiohomeotic. Mol. Cell. Biol. 26 (2006) 1434-1444
4. Brown J.L., Mucci D., Whiteley M., Dirksen M.L., and Kassis J.A. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA-binding protein with homology to the transcription factor YY1. Mol. Cell 1 (1998) 1057-1064
5. Brown J.L., Fritsch C., Mueller J., and Kassis J.A. The Drosophila pho-like gene encodes a YY1-related DNA-binding protein that is redundant with pleiohomeotic in homeotic gene silencing. Development 130 (2003) 285-294
6. Brown J.L., Grau D.J., DeVido S.K., and Kassis J.A. An Sp1/KLF binding site is important for the activity of a Polycomb group response element from the Drosophila engrailed gene. Nucleic Acids Res. 33 (2005) 5181-5189
7. Busturia A., Lloyd A., Bejarano F., Zavortink M., Xin H., and Sakonju S. The MCP silencer of the Drosophila Abd-B gene requires both Pleiohomeotic and GAGA factor for the maintenance of repression. Development 128 (2001) 2163-2173
8. Carey M. The enhanceosome and transcriptional synergy. Cell 92 (1998) 5-8
9. Chalkley G.E., and Verrijzer C.P. Immuno-depletion and purification strategies to study chromatin-remodeling factors in vitro. Methods Enzymol. 377 (2004) 421-442
10. Dejardin J., Rappaillles A., Cuvier O., Grimaud C., Decoville M., Locker D., and Cavalli G. Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1. Nature 434 (2005) 533-538
11. Francis N.J., and Kingston R.E. Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell Biol. 2 (2001) 409-421
12. Francis N.J., Saurin A.J., Shao Z., and Kingston R.E. Reconstitution of a functional core Polycomb repressive complex. Mol. Cell 8 (2001) 545-556
13. Francis N.J., Kingston R.E., and Woodcock C.L. Chromatin compaction by a polycomb group protein complex. Science 306 (2004) 1574-1577
14. Fritsch C., Brown J.L., Kassis J.A., and Muller J. The DNA-binding polycomb group protein pleiohomeotic mediates silencing of a Drosophila homeotic gene. Development 126 (1999) 3905-3913
15. Kahn T.G., Schwartz Y.B., Dellino G.I., and Pirrotta V. Polycomb complexes and the propagation of the methylation mark at the Drosophila Ubx gene. J. Biol. Chem. (2006) 10.1074/jbc.M605430200 in press. Published online August 2, 2006
16. Karch F., Galloni M., Sipos L., Gausz J., Gyurkovics H., and Schedl P. Mcp and Fab-7: molecular analysis of putative boundaries of cis-regulatory domains in the bithorax complex of Drosophila melanogaster. Nucleic Acids Res. 22 (1994) 3138-3146
17. Katsani K.R., Arredondo J.J., Kal A.J., and Verrijzer C.P. A homeotic mutation in the trithorax SET domain impedes histone binding. Genes Dev. 15 (2001) 2197-2202
18. Klug A., Rhodes D., Smith J., Finch J.T., and Thomas J.O. A low resolution structure for the histone core of the nucleosome. Nature 287 (1980) 509-516
19. Klymenko T., Papp B., Fischle W., Kocher T., Schelder M., Fritsch C., Wild B., Wilm M., and Muller J. A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. Genes Dev. 20 (2006) in press
20. Kosikov K.M., Gorin A.A., Zhurkin V.B., and Olson W.K. DNA stretching and compression: large-scale simulations of double helical structures. J. Mol. Biol. 289 (1999) 1301-1326
21. Kwon S.-H., Kim S.H., Chung H.-M., Girton J.R., and Jeon S.-H. The Drosophila pleiohomeotic mutation enhances the Polycomblike and Polycomb mutant phenotypes during embryogenesis and in the adult. Int. J. Dev. Biol. 47 (2003) 389-395
22. Levine S.S., King I.F.G., and Kingston R.E. Division of labour in Polycomb group repression. Trends Biochem. Sci. 29 (2004) 478-485
23. Liu C.L., Kaplan T., Kim M., Buratowski S., Schreiber S.L., Friedman N., and Rando O.J. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3 (2005) e328 10.1371/journal.pbio.0030328
24. Mahmoudi T., and Verrijzer C.P. Chromatin silencing and activation by Polycomb and trithorax group proteins. Oncogene 20 (2001) 3055-3066
25. Mahmoudi T., Zuijderduijn L.M.P., Mohd-Sarip A., and Verrijzer C.P. GAGA facilitates binding of Pleiohomeotic to a chromatinized Polycomb response elements. Nucleic Acids Res. 31 (2003) 4147-4156
26. Mishra R.K., Mihaly J., Barges S., Spierer A., Karch F., Hagstrom K., Schweinsberg S.E., and Schedl P. The iab-7 polycomb response element maps to a nucleosome-free region of chromatin and requires both GAGA and Pleiohomeotic for silencing activity. Mol. Cell. Biol. 21 (2001) 1311-1318
27. Mohd-Sarip A., Venturini F., Chalkley G.E., and Verrijzer C.P. Pleiohomeotic can link polycomb to DNA and mediate transcriptional repression. Mol. Cell. Biol. 22 (2002) 7473-7483
28. Mohd-Sarip A., Cleard F., Mishra R.K., Karch F., and Verrijzer C.P. Synergistic recognition of an epigenetic DNA element by Pleiohomeotic and a Polycomb core complex. Genes Dev. 19 (2005) 1755-1760
29. Muller M., Hagstrom K., Gyurkovics H., Pirrotta V., and Schedl P. The Mcp element from the Drosophila melanogaster bithorax complex mediates long-distance regulatory interactions. Genetics 153 (1999) 1333-1356
30. Mutskov V., and Felsenfeld G. Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9. EMBO J. 23 (2004) 138-149
31. Ogawa T., Yu X., Shinohara A., and Egelman E.H. Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science 259 (1993) 1896-1899
32. Papp B., and Müller J. Histone trimethylation and the maintenance of transcriptional on and off states by trxG and PcG proteins. Genes Dev. 20 (2006) 2041-2054
33. Pokholok D.K., Harbison C.T., Levine S., Cole M., Hannett N.M., Lee T.I., Bell G.W., Walker K., Rolfe P.A., Herbolsheimer E., et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122 (2005) 517-527
34. Ratcliff G.C., and Erie D.A. A novel single-molecule study to determine protein-protein association constants. J. Am. Chem. Soc. 123 (2001) 5632-5635
35. Ringrose L., and Paro R. Epigenetic regulation of cellular memory by the Polycomb group and trithorax group proteins. Annu. Rev. Genet. 38 (2004) 413-443
36. Schwartz Y.B., Kahn T.G., and Pirotta V. Characteristic low density and shear sensitivity of cross-linked chromatin containing polycomb complexes. Mol. Cell. Biol. 25 (2005) 432-439
37. Udvardy A., and Schedl P. Chromatin organization of the 87A7 heat shock locus of Drosophila melanogaster. J. Mol. Biol. 172 (1984) 385-402
38. van der Knaap J.A., Kumar B.R.P., Moshkin Y.M., Langenberg K., Krijgsveld J., Heck A.J.R., Karch F., and Verrijzer C.P. GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7. Mol. Cell 17 (2005) 695-707
39. Wang H., Wang L.J., Erdjument-Bromage H., Vidal M., Tempst P., Jones R.S., and Zhang Y. Role of histone H2A ubiquitination in polycomb silencing. Nature 431 (2004) 873-878
40. Wang L., Brown J.L., Cao R., Zhang Y., Kassis J.A., and Jones R.S. Hierarchical recruitment of Polyomb group silencing complexes. Mol. Cell 14 (2004) 637-646
41. Weinmann A.S., Bartley S.M., Zhang T., Zhang M.Q., and Farnham P.J. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol. Cell. Biol. 21 (2001) 6820-6832
42. White J.H., Cozzarelli N.R., and Bauer W.R. Helical repeat and linking number of surface-wrapped DNA. Science 241 (1988) 323-327
43. Wyman C., Rombel I., North A.K., Bustamante C., and Kustu S. Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science 275 (1997) 1658-1661
44. Yuan G.-C., Liu Y.-J., Dion M.F., Slack M.D., Wu L.F., Altschuler S.J., and Rando O.J. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309 (2005) 626-630