Spreading of silent chromatin: inaction at a distance (original) (raw)

• Muller, H. J. Types of visible variations induced by X-rays in Drosophila. J. Genet. 22, 299–334 (1930).
  Google Scholar
• Schultz, J. Variegation in Drosophila and the inert heterochromatic regions. Proc. Natl Acad. Sci. USA 22, 27–33 (1936).
  CAS PubMed Google Scholar
• Schultz, J. The function of heterochromatin. Proc. Int. Congr. Genet. 7, 257–262 (1939).
  Google Scholar
• Ptashne, M. Gene regulation by proteins acting nearby and at a distance. Nature 322, 697–701 (1986). This review clearly laid out models for how transcription factors bound to enhancers can interact with proteins at a distant promoter.
  CAS PubMed Google Scholar
• Yates, P. A. et al. Silencing of mouse Aprt is a gradual process in differentiated cells. Mol. Cell. Biol. 23, 4461–4470 (2003).
  CAS PubMed PubMed Central Google Scholar
• Arnaud, P., Goubely, C., Pelissier, T. & Deragon, J. M. SINE retroposons can be used in vivo as nucleation centers for de novo methylation. Mol. Cell. Biol. 20, 3434–3441 (2000).
  CAS PubMed PubMed Central Google Scholar
• Heard, E. Delving into the diversity of facultative heterochromatin: the epigenetics of the inactive X chromosome. Curr. Opin. Genet. Dev. 15, 482–489 (2005).
  CAS PubMed Google Scholar
• Straub, T., Dahlsveen, I. K. & Becker, P. B. Dosage compensation in flies: mechanism, models, mystery. FEBS Lett. 579, 3258–3263 (2005).
  CAS PubMed Google Scholar
• Huang, Y. Transcriptional silencing in _Saccharomyces cerevisia_e and _Schizosaccharomyces pomb_e. Nucleic Acids Res. 30, 1465–1482 (2002).
  CAS PubMed PubMed Central Google Scholar
• Gottschling, D. E., Aparicio, O. M., Billington, B. L. & Zakian, V. A. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63, 751–762 (1990).
  CAS PubMed Google Scholar
• Sekinger, E. A. & Gross, D. S. Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105, 403–414 (2001).
  CAS PubMed Google Scholar
• Chen, L. & Widom, J. Mechanism of transcriptional silencing in yeast. Cell 120, 37–48 (2005).
  CAS PubMed Google Scholar
• Renauld, H. et al. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 7, 1133–1145 (1993). A pioneering study that defined the dependence of SIR complex silencing on distance and Sir3 dosage, and presented evidence for continuous spreading.
  CAS PubMed Google Scholar
• Hoppe, G. J. et al. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol. Cell. Biol. 22, 4167–4180 (2002).
  CAS PubMed PubMed Central Google Scholar
• Rusche, L. N., Kirchmaier, A. L. & Rine, J. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell 13, 2207–2222 (2002).
  CAS PubMed PubMed Central Google Scholar
• Liou, G. G., Tanny, J. C., Kruger, R. G., Walz, T. & Moazed, D. Assembly of the SIR complex and its regulation by _O_-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121, 515–527 (2005).
  CAS PubMed Google Scholar
• Boscheron, C. et al. Cooperation at a distance between silencers and proto-silencers at the yeast HML locus. EMBO J. 15, 2184–2195 (1996).
  CAS PubMed PubMed Central Google Scholar
• Lustig, A. J., Liu, C., Zhang, C. & Hanish, J. P. Tethered Sir3p nucleates silencing at telomeres and internal loci in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 2483–2495 (1996).
  CAS PubMed Google Scholar
• Georgel, P. T., Palacios DeBeer, M. A., Pietz, G., Fox, C. A. & Hansen, J. C. Sir3-dependent assembly of supramolecular chromatin structures in vitro. Proc. Natl Acad. Sci. USA 98, 8584–8589 (2001).
  CAS PubMed Google Scholar
• Lebrun, E. et al. Protosilencers in Saccharomyces cerevisiae subtelomeric regions. Genetics 158, 167–176 (2001).
  CAS PubMed PubMed Central Google Scholar
• Fourel, G., Revardel, E., Koering, C. E. & Gilson, E. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J. 18, 2522–2537 (1999).
  CAS PubMed PubMed Central Google Scholar
• Pryde, F. E. & Louis, E. J. Limitations of silencing at native yeast telomeres. EMBO J. 18, 2538–2550 (1999).
  CAS PubMed PubMed Central Google Scholar
• Strahl-Bolsinger, S., Hecht, A., Luo, K. & Grunstein, M. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11, 83–93 (1997). Chromatin immunoprecipitation was used to locate SIR proteins on the chromosome near telomeres and to provide evidence for looping between telomeres and subtelomeres.
  CAS PubMed Google Scholar
• de Bruin, D., Zaman, Z., Liberatore, R. A. & Ptashne, M. Telomere looping permits gene activation by a downstream UAS in yeast. Nature 409, 109–113 (2001).
  CAS PubMed Google Scholar
• de Bruin, D., Kantrow, S. M., Liberatore, R. A. & Zakian, V. A. Telomere folding is required for the stable maintenance of telomere position effects in yeast. Mol. Cell. Biol. 20, 7991–8000 (2000).
  CAS PubMed PubMed Central Google Scholar
• Lebrun, E., Fourel, G., Defossez, P. A. & Gilson, E. A methyltransferase targeting assay reveals silencer-telomere interactions in budding yeast. Mol. Cell. Biol. 23, 1498–1508 (2003).
  CAS PubMed PubMed Central Google Scholar
• Maillet, L. et al. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev. 10, 1796–1811 (1996).
  CAS PubMed Google Scholar
• Marcand, S., Buck, S. W., Moretti, P., Gilson, E. & Shore, D. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev. 10, 1297–1309 (1996).
  CAS PubMed Google Scholar
• Katan-Khaykovich, Y. & Struhl, K. Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO J. 24, 2138–2149 (2005).
  CAS PubMed PubMed Central Google Scholar
• Cheng, T. H. & Gartenberg, M. R. Yeast heterochromatin is a dynamic structure that requires silencers continuously. Genes Dev. 14, 452–463 (2000). The excision of a ring of silent chromatin demonstrated that the continual presence of silencers or protosilencers is necessary to maintain silent chromatin.
  CAS PubMed PubMed Central Google Scholar
• Huisinga, K. L., Brower-Toland, B. & Elgin, S. C. The contradictory definitions of heterochromatin: transcription and silencing. Chromosoma 115, 110–122 (2006).
  CAS PubMed Google Scholar
• Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000). The authors showed that mammalian SUV39H1 is a histone H3K9 methyltransferase and mapped the catalytic activity to the SET domain.
  CAS PubMed Google Scholar
• Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D. & Grewal, S. I. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113 (2001).
  CAS Google Scholar
• Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).
  CAS Google Scholar
• Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001).
  CAS Google Scholar
• Thon, G. & Verhein-Hansen, J. Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations. Genetics 155, 551–568 (2000).
  CAS PubMed PubMed Central Google Scholar
• Vermaak, D., Henikoff, S. & Malik, H. S. Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila. PLoS Genet. 1, 96–108 (2005).
  CAS PubMed Google Scholar
• Smothers, J. F. & Henikoff, S. The hinge of and chromo shadow domain impart distinct targeting of HP1-like proteins. Mol. Cell. Biol. 21, 2555–2569 (2001).
  CAS PubMed PubMed Central Google Scholar
• Minc, E., Allory, Y., Worman, H. J., Courvalin, J. C. & Buendia, B. Localization and phosphorylation of HP1 proteins during the cell cycle in mammalian cells. Chromosoma 108, 220–234 (1999).
  CAS PubMed Google Scholar
• Hayakawa, T., Haraguchi, T., Masumoto, H. & Hiraoka, Y. Cell cycle behavior of human HP1 subtypes: distinct molecular domains of HP1 are required for their centromeric localization during interphase and metaphase. J. Cell Sci. 116, 3327–3338 (2003).
  CAS PubMed Google Scholar
• Smothers, J. F. & Henikoff, S. The HP1 chromo shadow domain binds a consensus peptide pentamer. Curr. Biol. 10, 27–30 (2000).
  CAS PubMed Google Scholar
• Lechner, M. S., Schultz, D. C., Negorev, D., Maul, G. G. & Rauscher, F. J. 3rd. The mammalian heterochromatin protein 1 binds diverse nuclear proteins through a common motif that targets the chromoshadow domain. Biochem. Biophys. Res. Commun. 331, 929–937 (2005).
  CAS PubMed Google Scholar
• Schotta, G. et al. Central role of Drosophila SU(VAR)3–9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J. 21, 1121–1131 (2002).
  CAS PubMed PubMed Central Google Scholar
• Yamamoto, K. & Sonoda, M. Self-interaction of heterochromatin protein 1 is required for direct binding to histone methyltransferase, SUV39H1. Biochem. Biophys. Res. Commun. 301, 287–292 (2003).
  CAS PubMed Google Scholar
• Noma, K., Allis, C. D. & Grewal, S. I. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293, 1150–1155 (2001).
  CAS PubMed Google Scholar
• Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002). This paper demonstrated that spreading in the fission yeast mating type region depends on Swi6, and that the RNAi machinery acts with cenH to establish heterochromatin.
  CAS PubMed Google Scholar
• Ayoub, N., Goldshmidt, I., Lyakhovetsky, R. & Cohen, A. A fission yeast repression element cooperates with centromere-like sequences and defines a mat silent domain boundary. Genetics 156, 983–994 (2000).
  CAS PubMed PubMed Central Google Scholar
• Yamada, T., Fischle, W., Sugiyama, T., Allis, C. D. & Grewal, S. I. The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol. Cell 20, 173–185 (2005).
  CAS PubMed Google Scholar
• Jia, S., Noma, K. & Grewal, S. I. RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins. Science 304, 1971–1976 (2004).
  CAS PubMed Google Scholar
• Kim, H. S., Choi, E. S., Shin, J. A., Jang, Y. K. & Park, S. D. Regulation of Swi6/HP1-dependent heterochromatin assembly by cooperation of components of the mitogen-activated protein kinase pathway and a histone deacetylase Clr6. J. Biol. Chem. 279, 42850–42859 (2004). References 49 and 50 demonstrated that there are two redundant pathways for nucleating heterochromatin at the fission yeast mating type locus, one RNAi-dependent and one not.
  CAS PubMed Google Scholar
• Shankaranarayana, G. D., Motamedi, M. R., Moazed, D. & Grewal, S. I. Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast. Curr. Biol. 13, 1240–1246 (2003).
  CAS PubMed Google Scholar
• Hansen, K. R. et al. Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Mol. Cell. Biol. 25, 590–601 (2005).
  CAS PubMed PubMed Central Google Scholar
• Stewart, M. D., Li, J. & Wong, J. Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment. Mol. Cell. Biol. 25, 2525–2538 (2005).
  CAS PubMed PubMed Central Google Scholar
• Cheutin, T., Gorski, S. A., May, K. M., Singh, P. B. & Misteli, T. In vivo dynamics of Swi6 in yeast: evidence for a stochastic model of heterochromatin. Mol. Cell. Biol. 24, 3157–3167 (2004).
  CAS PubMed PubMed Central Google Scholar
• Dialynas, G. K. et al. Methylation-independent binding to Histone H3 and cell cycle-dependent incorporation of HP1β into heterochromatin. J. Biol. Chem. 281, 14350–14360 (2006).
  CAS PubMed Google Scholar
• Meehan, R. R., Kao, C. F. & Pennings, S. HP1 binding to native chromatin in vitro is determined by the hinge region and not by the chromodomain. EMBO J. 22, 3164–3174 (2003).
  CAS PubMed PubMed Central Google Scholar
• Zhao, T., Heyduk, T., Allis, C. D. & Eissenberg, J. C. Heterochromatin protein 1 binds to nucleosomes and DNA in vitro. J. Biol. Chem. 275, 28332–28338 (2000).
  CAS PubMed Google Scholar
• Muchardt, C. et al. Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1α. EMBO Rep. 3, 975–981 (2002).
  CAS PubMed PubMed Central Google Scholar
• Nielsen, A. L. et al. Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. Mol. Cell 7, 729–739 (2001).
  CAS PubMed Google Scholar
• Nakayama, J., Allshire, R. C., Klar, A. J. & Grewal, S. I. A role for DNA polymerase-α in epigenetic control of transcriptional silencing in fission yeast. EMBO J. 20, 2857–2866 (2001).
  CAS PubMed Central Google Scholar
• Cheutin, T. et al. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299, 721–725 (2003).
  CAS PubMed Google Scholar
• Festenstein, R. et al. Modulation of heterochromatin protein 1 dynamics in primary mammalian cells. Science 299, 719–721 (2003). References 61 and 62 demonstrated that mammalian HP1 proteins are surprisingly mobile.
  CAS PubMed Google Scholar
• Schmiedeberg, L., Weisshart, K., Diekmann, S., Meyer Zu Hoerste, G. & Hemmerich, P. High- and low-mobility populations of HP1 in heterochromatin of mammalian cells. Mol. Biol. Cell 15, 2819–2833 (2004).
  CAS PubMed PubMed Central Google Scholar
• Krouwels, I. M. et al. A glue for heterochromatin maintenance: stable SUV39H1 binding to heterochromatin is reinforced by the SET domain. J. Cell Biol. 170, 537–549 (2005).
  CAS PubMed PubMed Central Google Scholar
• Vermaak, D., Ahmad, K. & Henikoff, S. Maintenance of chromatin states: an open-and-shut case. Curr. Opin. Cell Biol. 15, 266–274 (2003).
  CAS PubMed Google Scholar
• Martienssen, R. A., Zaratiegui, M. & Goto, D. B. RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. Trends Genet. 21, 450–456 (2005).
  CAS PubMed Google Scholar
• Verdel, A. & Moazed, D. RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett. 579, 5872–5878 (2005).
  CAS PubMed Google Scholar
• Horn, P. J., Bastie, J. N. & Peterson, C. L. A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev. 19, 1705–1714 (2005).
  CAS PubMed PubMed Central Google Scholar
• Li, F. et al. Two novel proteins, Dos1 and Dos2, interact with Rik1 to regulate heterochromatic RNA interference and histone modification. Curr. Biol. 15, 1448–1457 (2005).
  CAS PubMed Google Scholar
• Jia, S., Kobayashi, R. & Grewal, S. I. Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nature Cell Biol. 7, 1007–1013 (2005).
  CAS PubMed Google Scholar
• Sadaie, M., Iida, T., Urano, T. & Nakayama, J. A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J. 23, 3825–3835 (2004).
  CAS PubMed PubMed Central Google Scholar
• Thon, G. et al. The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate heterochromatin formation in the fission yeast Schizosaccharomyces pombe. Genetics 171, 1583–1595 (2005).
  CAS PubMed PubMed Central Google Scholar
• Noma, K. et al. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nature Genet. 36, 1174–1180 (2004).
  CAS PubMed Google Scholar
• Hampsey, M. & Reinberg, D. Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation. Cell 113, 429–432 (2003).
  CAS Google Scholar
• Buhler, M., Verdel, A. & Moazed, D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125, 873–886 (2006). This study demonstrated that tethering the RITS complex to the nascent transcripts of a euchromatic reporter induces heterochromatin and produces siRNAs that act predominantly in cis , but can initiate heterochromatin in trans when the siRNase Eri1 is deleted.
  CAS PubMed Google Scholar
• Frankham, R. Molecular hypotheses for position-effect variegation: anti-sense transcription and promoter occlusion. J. Theor. Biol. 135, 85–107 (1988).
  CAS PubMed Google Scholar
• Ahmad, K. & Golic, K. G. Somatic reversion of chromosomal position effects in Drosophila. Genetics 114, 657–670 (1996).
  Google Scholar
• Demerec, M. & Slizynska, H. Mottled white 258–18 of Drosophila melanogaster. Genetics 22, 641–649 (1937).
  CAS PubMed PubMed Central Google Scholar
• Locke, J., Kotarski, M. A. & Tartof, K. D. Dosage-dependent modifiers of position effect variegation in Drosophila and a mass action model that explains their effect. Genetics 120, 181–198 (1988).
  CAS PubMed PubMed Central Google Scholar
• Wustmann, G., Szidonya, J., Taubert, H. & Reuter, G. The genetics of position-effect variegation modifying loci in Drosophila melanogaster. Mol. Gen. Genet. 217, 520–527 (1989).
  CAS PubMed Google Scholar
• Seum, C., Delattre, M., Spierer, A. & Spierer, P. Ectopic HP1 promotes chromosome loops and variegated silencing in Drosophila. EMBO J. 20, 812–818 (2001). Elegant HP1-tethering experiments demonstrated that ectopic HP1 can nucleate heterochromatin when tethered near dispersed repetitive elements in euchromatin, and form loops to sites of intercalary and pericentric heterochromatin.
  CAS PubMed PubMed Central Google Scholar
• Li, Y., Danzer, J. R., Alvarez, P., Belmont, A. S. & Wallrath, L. L. Effects of tethering HP1 to euchromatic regions of the Drosophila genome. Development 130, 1817–1824 (2003).
  CAS PubMed Google Scholar
• Danzer, J. R. & Wallrath, L. L. Mechanisms of HP1-mediated gene silencing in Drosophila. Development 131, 3571–3580 (2004).
  CAS PubMed Google Scholar
• van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nature Biotechnol. 18, 424–428 (2000).
  CAS Google Scholar
• Sun, F. L. et al. _Cis_-acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four. Mol. Cell. Biol. 24, 8210–8220 (2004).
  CAS PubMed PubMed Central Google Scholar
• Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster genome. Curr. Biol. 11, 1017–1027 (2001).
  CAS PubMed Google Scholar
• Belyaeva, E. S. & Zhimulev, I. F. Cytogenetic and molecular aspects of position effect variegation in Drosophila III. Continuous and discontinuous compaction of chromosomal material as a result of position effect variegation. Chromosoma 100, 453–466 (1991).
  CAS PubMed Google Scholar
• Csink, A. K., Bounoutas, A., Griffith, M. L., Sabl, J. F. & Sage, B. T. Differential gene silencing by _trans_-heterochromatin in Drosophila melanogaster. Genetics 160, 257–69 (2002).
  CAS PubMed PubMed Central Google Scholar
• Talbert, P. B. & Henikoff, S. A reexamination of spreading of position-effect variegation in the white_–_roughest region of Drosophila melanogaster. Genetics 154, 259–272 (2000). This reexamination of silencing at the two genes originally used to infer continuous spreading of heterochromatin found that inactivation frequencies of the genes are not correlated, and provided evidence for discontinuous spreading and rearrangement-specific effects.
  CAS PubMed PubMed Central Google Scholar
• Dorer, D. R. & Henikoff, S. Transgene repeat arrays interact with distant heterochromatin and cause silencing in cis and trans. Genetics 147, 1181–1190 (1997).
  CAS PubMed PubMed Central Google Scholar
• Talbert, P. B., LeCiel, C. D. S. & Henikoff, S. Modification of the Drosophila heterochromatic mutation brown Dominant by linkage alterations. Genetics 136, 559–571 (1994).
  CAS PubMed PubMed Central Google Scholar
• Sage, B. T. & Csink, A. K. Heterochromatic self-association, a determinant of nuclear organization, does not require sequence homology in Drosophila. Genetics 165, 1183–1193 (2003).
  CAS PubMed PubMed Central Google Scholar
• Dorer, D. R. & Henikoff, S. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77, 993–1002 (1994).
  CAS PubMed Google Scholar
• Henikoff, S. Dosage-dependent modification of position-effect variegation in Drosophila. Bioessays 18, 401–409 (1996).
  CAS PubMed Google Scholar
• Wakimoto, B. T. & Hearn, M. G. The effects of chromosome rearrangements on the expression of heterochromatic genes in Chromosome 2L of Drosophila melanogaster. Genetics 125, 141–154 (1990). The authors put forward an influential proposal that the association of heterochromatic regions within the nucleus favours heterochromatin formation.
  CAS PubMed PubMed Central Google Scholar
• Pal-Bhadra, M. et al. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303, 669–672 (2004).
  CAS PubMed Google Scholar
• Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337–350 (2003).
  CAS PubMed Google Scholar
• Aravin, A. A. et al. Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol. Cell. Biol. 24, 6742–6750 (2004).
  CAS PubMed PubMed Central Google Scholar
• Dreesen, T. D., Henikoff, S. & Loughney, K. A pairing-sensitive element that mediates _trans_-inactivation is associated with the Drosophila brown gene. Genes Dev. 5, 331–340 (1991).
  CAS PubMed Google Scholar
• Martienssen, R. A. Maintenance of heterochromatin by RNA interference of tandem repeats. Nature Genet. 35, 213–214 (2003).
  CAS PubMed Google Scholar
• Sabl, J. F. & Henikoff, S. Copy number and orientation determine the susceptibility of a gene to silencing by nearby heterochromatin in Drosophila. Genetics 142, 447–458 (1996).
  CAS PubMed PubMed Central Google Scholar
• 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).
  CAS PubMed Google Scholar
• Bender, W. et al. Molecular genetics of the bithorax complex in Drosophila melanogaster. Science 221, 23–29 (1983).
  CAS PubMed Google Scholar
• Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413–43 (2004).
  CAS Google Scholar
• Pirrotta, V. & Rastelli, L. white gene expression, repressive chromatin domains and homeotic gene regulation in Drosophila. Bioessays 16, 549–556 (1994). This survey of chromatin effects proposed an influential model of spreading through association of PcG proteins at PREs and secondary binding sites, and emphasized similarities between PcG silencing and heterochromatin.
  CAS PubMed Google Scholar
• Schwartz, Y. B. et al. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nature Genet. 38, 700–705 (2006). Genomic profiling revealed that H3K27 is widely distributed around PREs, whereas PcG proteins and particularly the histone methyltransferase E(z) are more tightly distributed.
  CAS PubMed Google Scholar
• Phair, R. D. et al. Global nature of dynamic protein–chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol. Cell. Biol. 24, 6393–6402 (2004).
  CAS PubMed PubMed Central Google Scholar
• Luo, K., Vega-Palas, M. A. & Grunstein, M. Rap1–Sir4 binding independent of other Sir, yKu, or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev. 16, 1528–1539 (2002).
  CAS PubMed PubMed Central Google Scholar
• Bose, M. E. et al. The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain. Mol. Cell. Biol. 24, 774–86 (2004).
  CAS PubMed PubMed Central Google Scholar
• Hecht, A., Laroche, T., Strahl-Bolsinger, S., Gasser, S. M. & Grunstein, M. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80, 583–592 (1995).
  CAS PubMed Google Scholar
• Carmen, A. A., Milne, L. & Grunstein, M. Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J. Biol. Chem. 277, 4778–4481 (2002).
  CAS PubMed Google Scholar
• Connelly, J. J. et al. Structure and function of the Saccharomyces cerevisiae Sir3 BAH domain. Mol. Cell. Biol. 26, 3256–3265 (2006).
  CAS PubMed PubMed Central Google Scholar
• de Wit, E., Greil, F. & van Steensel, B. Genome-wide HP1 binding in _Drosophil_a: developmental plasticity and genomic targeting signals. Genome Res. 15, 1265–1273 (2005).
  CAS PubMed PubMed Central Google Scholar
• 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).
  CAS PubMed PubMed Central Google Scholar
• Czermin, B. et al. Physical and functional association of SU(VAR)3-9 and HDAC1 in Drosophila. EMBO Rep. 2, 915–919 (2001).
  CAS PubMed PubMed Central Google Scholar
• Schotta, G. et al. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18, 1251–1262 (2004).
  CAS PubMed PubMed Central Google Scholar
• Ebert, A. et al. Su(var) genes regulate the balance between euchromatin and heterochromatin in Drosophila. Genes Dev. 18, 2973–2983 (2004).
  CAS PubMed PubMed Central Google Scholar
• Zhang, W. et al. The JIL-1 histone H3S10 kinase regulates dimethyl H3K9 modifications and heterochromatic spreading in Drosophila. Development 133, 229–235 (2006).
  CAS PubMed Google Scholar
• Jaquet, Y., Delattre, M., Montoya-Burgos, J., Spierer, A. & Spierer, P. Conserved domains control heterochromatin localization and silencing properties of SU(VAR)3-7. Chromosoma 115, 139–150 (2006).
  CAS PubMed Google Scholar
• Cléard, F., Delattre, M. & Spierer, P. SU(VAR)3-7, a Drosophila heterochromatin-associated protein and companion of HP1 in the genomic silencing of position effect variegation. EMBO J. 16, 5280–5288 (1997).
  PubMed PubMed Central Google Scholar
• Delattre, M., Spierer, A., Jaquet, Y. & Spierer, P. Increased expression of Drosophila Su(var)3-7 triggers Su(var)3-9-dependent heterochromatin formation. J. Cell Sci. 117, 6239–6247 (2004).
  CAS PubMed Google Scholar