| [1] | Papatsenko D, Levine M (2007) A rationale for the enhanceosome and other evolutionarily constrained enhancers. Curr Biol 17: R955–957.
|
| [2] | Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27. doi:10.1371/journal.pbio.0060027.
|
| [3] | 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.
|
| [4] | 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.
|
| [5] | Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38: 413–443.
|
| [6] | Breiling A, Sessa L, Orlando V (2007) Biology of polycomb and trithorax group proteins. Int Rev Cytol 258: 83–136.
|
| [7] | Schwartz YB, Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8: 9–22.
|
| [8] | Ringrose L, Paro R (2007) Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134: 223–232.
|
| [9] | Negre N, Hennetin J, Sun LV, Lavrov S, Bellis M, et al. (2006) Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol 4: e170. doi:10.1371/journal.pbio.0040170.
|
| [10] | Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, et al. (2006) Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 38: 700–705.
|
| [11] | Tolhuis B, de Wit E, Muijrers I, Teunissen H, Talhout W, et al. (2006) Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat Genet 38: 694–699.
|
| [12] | 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.
|
| [13] | 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.
|
| [14] | 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.
|
| [15] | Ringrose L (2007) Polycomb comes of age: genome-wide profiling of target sites. Curr Opin Cell Biol 19: 290–297.
|
| [16] | Lee N, Maurange C, Ringrose L, Paro R (2005) Suppression of Polycomb group proteins by JNK signalling induces transdetermination in Drosophila imaginal discs. Nature 438: 234–237.
|
| [17] | Sparmann A, van Lohuizen M (2006) Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer 6: 846–856.
|
| [18] | Ringrose L, Rehmsmeier M, Dura JM, Paro R (2003) Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster. Dev Cell 5: 759–771.
|
| [19] | Fiedler T, Rehmsmeier M (2006) jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Res 34: W546–550.
|
| [20] | Dellino GI, Tatout C, Pirrotta V (2002) Extensive conservation of sequences and chromatin structures in the bxd polycomb response element among Drosophilid species. Int J Dev Biol 46: 133–141.
|
| [21] | Wray GA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8: 206–216.
|
| [22] | Prud'homme B, Gompel N, Carroll SB (2007) Emerging principles of regulatory evolution. Proc Natl Acad Sci U S A 104(Suppl 1): 8605–8612.
|
| [23] | Dermitzakis ET, Clark AG (2002) Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 19: 1114–1121.
|
| [24] | Costas J, Casares F, Vieira J (2003) Turnover of binding sites for transcription factors involved in early Drosophila development. Gene 310: 215–220.
|
| [25] | Romano LA, Wray GA (2003) Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development 130: 4187–4199.
|
| [26] | Ludwig MZ, Bergman C, Patel NH, Kreitman M (2000) Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564–567.
|
| [27] | Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, et al. (2005) Functional evolution of a cis-regulatory module. PLoS Biol 3: e93. doi:10.1371/journal.pbio.0030093.
|
| [28] | Gompel N, Prud'homme B, Wittkopp PJ, Kassner VA, Carroll SB (2005) Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433: 481–487.
|
| [29] | Prud'homme B, Gompel N, Rokas A, Kassner VA, Williams TM, et al. (2006) Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440: 1001–1002.
|
| [30] | McGregor AP, Orgogozo V, Delon I, Zanet J, Srinivasan DG, et al. (2007) Morphological evolution through multiple cis-regulatory mutations at a single gene. Nature 448: 587–590.
|
| [31] | King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107–116.
|
| [32] | Carroll SB (1995) Homeotic genes and the evolution of arthropods and chordates. Nature 376: 479–485.
|
| [33] | Andolfatto P (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149–1152.
|
| [34] | Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15: 1–18.
|
| [35] | Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203–218.
|
| [36] | Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219–232.
|
| [37] | Emberly E, Rajewsky N, Siggia ED (2003) Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics 4: 57.
|
| [38] | Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, et al. (2004) Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol 5: R61.
|
| [39] | Sinha S, Schroeder MD, Unnerstall U, Gaul U, Siggia ED (2004) Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. BMC Bioinformatics 5: 1–12.
|
| [40] | King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, et al. (2007) Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res 17: 775–786.
|
| [41] | MacArthur S, Brookfield JFY (2004) Expected rates and modes of evolution of enhancer sequences. Mol Biol Evol 21: 1064–1073.
|
| [42] | Stone J, Wray GA (2001) Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol 18: 1764–1770.
|
| [43] | Hagstrom K, Muller M, Schedl P (1997) A Polycomb and GAGA dependent silencer adjoins the Fab-7 boundary in the Drosophila bithorax complex. Genetics 146: 1365–1380.
|
| [44] | 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.
|
| [45] | Blastyak A, Mishra RK, Karch F, Gyurkovics H (2006) Efficient and specific targeting of Polycomb group proteins requires cooperative interaction between Grainyhead and Pleiohomeotic. Mol Cell Biol 26: 1434–1444.
|
| [46] | Brown JL, Grau DJ, DeVido SK, Kassis JA (2005) 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: 5181–5189.
|
| [47] | Schmitt S, Prestel M, Paro R (2005) Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 19: 697–708.
|
| [48] | Horard B, Tatout C, Poux S, Pirrotta V (2000) Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor. Mol Cell Biol 20: 3187–3197.
|
| [49] | Mishra RK, Mihaly J, Barges S, Spierer A, Karch F, et al. (2001) 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: 1311–1318.
|
| [50] | Dejardin J, Cavalli G (2004) Chromatin inheritance upon Zeste-mediated Brahma recruitment at a minimal cellular memory module. EMBO J 23: 857–868.
|
| [51] | Americo J, Whiteley M, Brown JL, Fujioka M, Jaynes JB, et al. (2002) A complex array of DNA-binding proteins required for pairing-sensitive silencing by a polycomb group response element from the Drosophila engrailed gene. Genetics 160: 1561–1571.
|
| [52] | Fauvarque MO, Dura JM (1993) polyhomeotic regulatory sequences induce developmental regulator-dependent variegation and targeted P-element insertions in Drosophila. Genes Dev 7: 1508–1520.
|
| [53] | Kassis JA (1994) Unusual properties of regulatory DNA from the Drosophila engrailed gene: three “pairing-sensitive” sites within a 1.6-kb region. Genetics 136: 1025–1038.
|
| [54] | Macdonald SJ, Long AD (2006) Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. Genome Biol 7: R67.
|
| [55] | Zuckerkandl E (2002) Why so many noncoding nucleotides? The eukaryote genome as an epigenetic machine. Genetica 115: 105–129.
|
| [56] | Gibert JM, Peronnet F, Schlotterer C (2007) Phenotypic plasticity in Drosophila pigmentation caused by temperature sensitivity of a chromatin regulator network. PLoS Genet 3: e30. doi:10.1371/journal.pgen.0030030.
|
| [57] | Fritsch C, Brown JL, Kassis JA, Muller J (1999) The DNA-binding polycomb group protein pleiohomeotic mediates silencing of a Drosophila homeotic gene. Development 126: 3905–3913.
|
| [58] | Busturia A, Lloyd A, Bejarano F, Zavortink M, Xin H, et al. (2001) The MCP silencer of the Drosophila Abd-B gene requires both Pleiohomeotic and GAGA factor for the maintenance of repression. Development 128: 2163–2173.
|
| [59] | Ng CS, Kopp A (2008) Sex combs are important for male mating success in Drosophila melanogaster. Behav Genet 38: 195–201.
|
| [60] | Barmina O, Kopp A (2007) Sex-specific expression of a HOX gene associated with rapid morphological evolution. Dev Biol 311: 277–286.
|
| [61] | Randsholt NB, Santamaria P (2008) How Drosophila change their combs: the Hox gene Sex combs reduced and sex comb variation among Sophophora species. Evol Dev 10: 121–133.
|
| [62] | Ringrose L, Ehret H, Paro R (2004) Distinct contributions of histone H3 lysine 9 and 27 methylation to locus-specific stability of polycomb complexes. Mol Cell 16: 641–653.
|
| [63] | Corona DF, Armstrong JA, Tamkun JW (2004) Genetic and cytological analysis of Drosophila chromatin-remodeling factors. Methods Enzymol 377: 70–85.
|
| [64] | Orlando V, Jane EP, Chinwalla V, Harte PJ, Paro R (1998) Binding of trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. EMBO J 17: 5141–5150.
|
