A novel human Polycomb binding site acts as a functional Polycomb response element in Drosophila

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Cuddapah, Suresh ^a   Roh, Tae Young ^b   Cui, Kairong ^b   Jose, Cynthia C ^a   Fuller, Margaret T ^d   Zhao, Keji ^b   Chen, Xin ^c  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYCOMB GROUP PROTEIN; PROTEIN SUZ12; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CD4+ T LYMPHOCYTE; CONTROLLED STUDY; DEVELOPMENT; DROSOPHILA; FEMALE; GENE; GENE REPRESSION; GENETIC ANALYSIS; HOXA13 GENE; HOXA3 GENE; HUMAN; HUMAN CELL; IN VIVO STUDY; MALE; MAMMAL; MOLECULAR BIOLOGY; NONHUMAN; POLYCOMB RESPONSIVE ELEMENT; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REGULATORY SEQUENCE; REPORTER GENE; SLC17A7 GENE; TRANSCRIPTION REGULATION;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; BINDING SITES; CELL CYCLE PROTEINS; CELL LINE; DROSOPHILA; GENE EXPRESSION REGULATION; GENES, REPORTER; HUMANS; POLYCOMB-GROUP PROTEINS; RESPONSE ELEMENTS; TRANSCRIPTION, GENETIC;

MAMMALIA;

EID: 84860528446     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036365     Document Type: Article

References (65)

1. Simon JA, (2003) Polycomb group proteins. Curr Biol 13: R79-80.
2. Ringrose L, Paro R, (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38: 413-443.
3. Levine SS, King IF, Kingston RE, (2004) Division of labor in polycomb group repression. Trends Biochem Sci 29: 478-485.
4. Cao R, Zhang Y, (2004) The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3. Curr Opin Genet Dev 14: 155-164.
5. Orlando V, (2003) Polycomb, epigenomes, and control of cell identity. Cell 112: 599-606.
6. Schwartz YB, Kahn TG, Dellino GI, Pirrotta V, (2004) Polycomb silencing mechanisms in Drosophila. Cold Spring Harb Symp Quant Biol 69: 301-308.
7. Francis NJ, Kingston RE, (2001) Mechanisms of transcriptional memory. Nat Rev Mol Cell Biol 2: 409-421.
8. Jacobs JJ, van Lohuizen M, (1999) Cellular memory of transcriptional states by Polycomb-group proteins. Semin Cell Dev Biol 10: 227-235.
9. Schwartz YB, Pirrotta V, (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8: 9-22.
10. Surface LE, Thornton SR, Boyer LA, (2010) Polycomb group proteins set the stage for early lineage commitment. Cell Stem Cell 7: 288-298.
11. Saurin AJ, Shao Z, Erdjument-Bromage H, Tempst P, Kingston RE, (2001) A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. Nature 412: 655-660.
12. Lund AH, van Lohuizen M, (2004) Polycomb complexes and silencing mechanisms. Curr Opin Cell Biol 16: 239-246.
13. Klymenko T, Papp B, Fischle W, Kocher T, Schelder M, et al. (2006) A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. Genes Dev 20: 1110-1122.
14. Scheuermann JC, de Ayala Alonso AG, Oktaba K, Ly-Hartig N, McGinty RK, et al. (2010) Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465: 243-247.
15. Simon JA, Kingston RE, (2009) Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 10: 697-708.
16. Margueron R, Reinberg D, (2011) The Polycomb complex PRC2 and its mark in life. Nature 469: 343-349.
17. Francis NJ, Kingston RE, Woodcock CL, (2004) Chromatin compaction by a polycomb group protein complex. Science 306: 1574-1577.
18. Dellino GI, Schwartz YB, Farkas G, McCabe D, Elgin SC, et al. (2004) Polycomb silencing blocks transcription initiation. Mol Cell 13: 887-893.
19. Wang L, Brown JL, Cao R, Zhang Y, Kassis JA, et al. (2004) Hierarchical recruitment of polycomb group silencing complexes. Mol Cell 14: 637-646.
20. Stock JK, Giadrossi S, Casanova M, Brookes E, Vidal M, et al. (2007) Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol 9: 1428-1435.
21. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, et al. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039-1043.
22. Czermin B, Melfi R, McCabe D, Seitz V, Imhof A, et al. (2002) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111: 185-196.
23. Kuzmichev A, Nishioka K, Erdjument-Bromage H, Tempst P, Reinberg D, (2002) Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev 16: 2893-2905.
24. Muller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, et al. (2002) Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111: 197-208.
25. Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, et al. (2003) Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev 17: 1870-1881.
26. Min J, Zhang Y, Xu RM, (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17: 1823-1828.
27. Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, et al. (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4: e1000242.
28. Schoeftner S, Sengupta AK, Kubicek S, Mechtler K, Spahn L, et al. (2006) Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J 25: 3110-3122.
29. Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, et al. (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431: 873-878.
30. Byrd KN, Shearn A, (2003) ASH1, a Drosophila trithorax group protein, is required for methylation of lysine 4 residues on histone H3. Proc Natl Acad Sci U S A 100: 11535-11540.
31. Klymenko T, Muller J, (2004) The histone methyltransferases Trithorax and Ash1 prevent transcriptional silencing by Polycomb group proteins. EMBO Rep 5: 373-377.
32. Strutt H, Cavalli G, Paro R, (1997) Co-localization of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. Embo J 16: 3621-3632.
33. Mihaly J, Mishra RK, Karch F, (1998) A conserved sequence motif in Polycomb-response elements. Mol Cell 1: 1065-1066.
34. Mulholland NM, King IF, Kingston RE, (2003) Regulation of Polycomb group complexes by the sequence-specific DNA binding proteins Zeste and GAGA. Genes Dev 17: 2741-2746.
35. Dejardin J, Rappailles A, Cuvier O, Grimaud C, Decoville M, et al. (2005) Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1. Nature 434: 533-538.
36. Hur MW, Laney JD, Jeon SH, Ali J, Biggin MD, (2002) Zeste maintains repression of Ubx transgenes: support for a new model of Polycomb repression. Development 129: 1339-1343.
37. Chan CS, Rastelli L, Pirrotta V, (1994) A Polycomb response element in the Ubx gene that determines an epigenetically inherited state of repression. Embo J 13: 2553-2564.
38. Simon J, Chiang A, Bender W, Shimell MJ, O'Connor M, (1993) Elements of the Drosophila bithorax complex that mediate repression by Polycomb group products. Dev Biol 158: 131-144.
39. Kirmizis A, Bartley SM, Kuzmichev A, Margueron R, Reinberg D, et al. (2004) Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev 18: 1592-1605.
40. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125: 301-313.
41. Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349-353.
42. Sing A, Pannell D, Karaiskakis A, Sturgeon K, Djabali M, et al. (2009) A vertebrate Polycomb response element governs segmentation of the posterior hindbrain. Cell 138: 885-897.
43. Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE, (2010) A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell 140: 99-110.
44. Xi H, Yu Y, Fu Y, Foley J, Halees A, et al. (2007) Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res 17: 798-806.
45. Muller J, Kassis JA, (2006) Polycomb response elements and targeting of Polycomb group proteins in Drosophila. Curr Opin Genet Dev 16: 476-484.
46. Ringrose L, Paro R, (2007) Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134: 223-232.
47. Schuettengruber B, Cavalli G, (2009) Recruitment of polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development 136: 3531-3542.
48. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
49. Przybyla-Zawislak BD, Thorn BT, Ali SF, Dennis RA, Amato A, et al. (2005) Identification of Rat Hippocampal mRNAs Altered by the Mitochondrial Toxicant, 3-NPA. Ann N Y Acad Sci 1053: 162-173.
50. Cao R, Zhang Y, (2004) SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol Cell 15: 57-67.
51. Pasini D, Bracken AP, Hansen JB, Capillo M, Helin K, (2007) The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol Cell Biol 27: 3769-3779.
52. Moschetti R, Marsano RM, Barsanti P, Caggese C, Caizzi R, (2004) FB elements can promote exon shuffling: a promoter-less white allele can be reactivated by FB mediated transposition in Drosophila melanogaster. Mol Genet Genomics 271: 394-401.
53. Kassis JA, (2002) Pairing-sensitive silencing, polycomb group response elements, and transposon homing in Drosophila. Adv Genet 46: 421-438.
54. Chen X, Hiller M, Sancak Y, Fuller MT, (2005) Tissue-specific TAFs counteract Polycomb to turn on terminal differentiation. Science 310: 869-872.
55. Whitcomb SJ, Basu A, Allis CD, Bernstein E, (2007) Polycomb Group proteins: an evolutionary perspective. Trends Genet 23: 494-502.
56. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129: 1311-1323.
57. Kotake Y, Cao R, Viatour P, Sage J, Zhang Y, et al. (2007) pRB family proteins are required for H3K27 trimethylation and Polycomb repression complexes binding to and silencing p16INK4alpha tumor suppressor gene. Genes Dev 21: 49-54.
58. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
59. Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K, (2006) Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev 20: 1123-1136.
60. Su Y, Deng B, Xi R, (2011) Polycomb group genes in stem cell self-renewal: a double-edged sword. Epigenetics 6: 16-19.
61. Roh TY, Cuddapah S, Zhao K, (2005) Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 19: 542-552.
62. Liu R, Liu H, Chen X, Kirby M, Brown PO, et al. (2001) Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell 106: 309-318.
63. Wang W, Cote J, Xue Y, Zhou S, Khavari PA, et al. (1996) Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J 15: 5370-5382.
64. Mutskov V, Felsenfeld G, (2004) Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9. Embo J 23: 138-149.
65. Cui K, Tailor P, Liu H, Chen X, Ozato K, et al. (2004) The chromatin-remodeling BAF complex mediates cellular antiviral activities by promoter priming. Mol Cell Biol 24: 4476-4486.