- Grewal, S. I. & Elgin, S. C. Heterochromatin: new possibilities for the inheritance of structure. Curr. Opin. Genet. Dev. 12, 178–187 (2002).
CAS PubMed Google Scholar
- Sun, F. L., Cuaycong, M. H. & Elgin, S. C. Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin. Mol. Cell. Biol. 21, 2867–2879 (2001).
CAS PubMed PubMed Central Google Scholar
- Sugiyama, T. et al. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 128, 491–504 (2007).
CAS PubMed Google Scholar
- Wallrath, L. L. & Elgin, S. C. Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev. 9, 1263–1277 (1995).
CAS PubMed Google Scholar
- Cryderman, D. E., Tang, H., Bell, C., Gilmour, D. S. & Wallrath, L. L. Heterochromatic silencing of Drosophila heat shock genes acts at the level of promoter potentiation. Nucleic Acids Res. 27, 3364–3370 (1999).
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
- Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002).
ADS CAS PubMed Google Scholar
- Ahmad, K. & Henikoff, S. Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila. Cell 104, 839–847 (2001).
CAS PubMed Google Scholar
- Yasuhara, J. C. & Wakimoto, B. T. Oxymoron no more: the expanding world of heterochromatic genes. Trends Genet. 22, 330–338 (2006).
CAS PubMed Google Scholar
- Elgin, S. C. R. & Reuter, G. in Epigenetics (eds Allis, C. D., Jenuwein, T. & Reinberg, R.) 81–100 (Cold Spring Harbor Laboratory Press, Woodbury, 2007).
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
- 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
- Eissenberg, J. C. et al. Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 87, 9923–9927 (1990).
ADS CAS PubMed Google Scholar
- Shaffer, C. D. et al. Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin. Proc. Natl Acad. Sci. USA 99, 14332–14337 (2002).
ADS CAS PubMed Google Scholar
- Reuter, G. et al. Dependence of position-effect variegation in Drosophila on dose of a gene encoding an unusual zinc-finger protein. Nature 344, 219–223 (1990).
ADS CAS PubMed Google Scholar
- Tschiersch, B. et al. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. Embo J. 13, 3822–3831 (1994).
CAS PubMed PubMed Central Google Scholar
- Greil, F., de Wit, E., Bussemaker, H. J. & van Steensel, B. HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. Embo J. 26, 741–751 (2007).
CAS PubMed PubMed Central Google Scholar
- Talbert, P. B. & Henikoff, S. Spreading of silent chromatin: inaction at a distance. Nature Rev. Genet. 7, 793–803 (2006).
CAS PubMed 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
- Grewal, S. I. & Jia, S. Heterochromatin revisited. Nature Rev. Genet. 8, 35–46 (2007).
CAS PubMed Google Scholar
- Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).
ADS 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).
ADS 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
- Hong, E. J. E., Villen, J., Gerace, E. L., Gygi, S. & Moazed, D. A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol. 2, 106–111 (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
- 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
- Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).
ADS CAS PubMed Google Scholar
- Partridge, J. F., Scott, K. S., Bannister, A. J., Kouzarides, T. & Allshire, R. C. _cis_-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site. Curr. Biol. 12, 1652–1660 (2002).
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
- Cam, H. P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nature Genet. 37, 809–819 (2005).
CAS PubMed Google Scholar
- Grewal, S. I. & Klar, A. J. A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast. Genetics 146, 1221–1238 (1997).
CAS PubMed PubMed Central Google Scholar
- Kanoh, J., Sadaie, M., Urano, T. & Ishikawa, F. Telomere binding protein Taz1 establishes Swi6 heterochromatin independently of RNAi at telomeres. Curr. Biol. 15, 1808–1819 (2005).
CAS PubMed Google Scholar
- Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002).
ADS CAS PubMed Google Scholar
- Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).
ADS CAS PubMed Google Scholar
- Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).
ADS 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
- Sugiyama, T., Cam, H., Verdel, A., Moazed, D. & Grewal, S. I. RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc. Natl Acad. Sci. USA 102, 152–157 (2005).
ADS CAS PubMed Google Scholar
- Motamedi, M. R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004).
CAS PubMed Google Scholar
- Irvine, D. V. et al. Argonaute slicing is required for heterochromatic silencing and spreading. Science 313, 1134–1137 (2006).
ADS CAS PubMed Google Scholar
- Zofall, M. & Grewal, S. I. RNAi-mediated heterochromatin assembly in fission yeast. Cold Spring Harb. Symp. Quant. Biol. 71, 487–496 (2006).
CAS PubMed Google Scholar
- Grewal, S. I. & Moazed, D. Heterochromatin and epigenetic control of gene expression. Science 301, 798–802 (2003).
ADS 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).
CAS PubMed Google Scholar
- Djupedal, I. et al. RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev. 19, 2301–2306 (2005).
CAS PubMed PubMed Central Google Scholar
- Kato, H. et al. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309, 467–469 (2005).
ADS CAS PubMed Google Scholar
- Ayoub, N. et al. A novel jmjC domain protein modulates heterochromatization in fission yeast. Mol. Cell. Biol. 23, 4356–4370 (2003).
CAS PubMed PubMed Central Google Scholar
- Klose, R. J., Kallin, E. M. & Zhang, Y. JmjC-domain-containing proteins and histone demethylation. Nature Rev. Genet. 7, 715–727 (2006).
CAS PubMed Google Scholar
- Tsukada, Y. et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439, 811–816 (2006).
ADS CAS PubMed Google Scholar
- Mochizuki, K. & Gorovsky, M. A. Small RNAs in genome rearrangement in Tetrahymena. Curr. Opin. Genet. Dev. 14, 181–187 (2004).
CAS PubMed Google Scholar
- Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006).
ADS CAS PubMed Google Scholar
- Richards, E. J. & Elgin, S. C. Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108, 489–500 (2002).
CAS PubMed Google Scholar
- Pal-Bhadra, M., Bhadra, U. & Birchler, J. A. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell 9, 315–327 (2002).
CAS PubMed 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).
ADS CAS PubMed Google Scholar
- Haynes, K. A., Caudy, A. A., Collins, L. & Elgin, S. C. Element 1360 and RNAi components contribute to HP1-dependent silencing of a pericentric reporter. Curr. Biol. 16, 2222–2227 (2006).
CAS PubMed PubMed Central Google Scholar
- van Rij, R. P. et al. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes Dev. 20, 2985–2995 (2006).
CAS PubMed PubMed Central Google Scholar
- Wang, X. H. et al. RNA interference directs innate immunity against viruses in adult Drosophila. Science 312, 452–454 (2006).
ADS CAS PubMed PubMed Central Google Scholar
- Kalmykova, A. I., Klenov, M. S. & Gvozdev, V. A. Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline. Nucleic Acids Res. 33, 2052–2059 (2005).
CAS PubMed PubMed Central Google Scholar
- Saito, K. et al. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev. 20, 2214–2222 (2006).
CAS PubMed PubMed Central Google Scholar
- Deshpande, G., Calhoun, G. & Schedl, P. Drosophila argonaute-2 is required early in embryogenesis for the assembly of centric/centromeric heterochromatin, nuclear division, nuclear migration, and germ-cell formation. Genes Dev. 19, 1680–1685 (2005).
CAS PubMed PubMed Central Google Scholar
- Allshire, R. C., Nimmo, E. R., Ekwall, K., Javerzat, J. P. & Cranston, G. Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9, 218–233 (1995).
CAS PubMed Google Scholar
- Fukagawa, T. et al. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nature Cell Biol. 6, 784–791 (2004).
CAS PubMed Google Scholar
- Hall, I. M., Noma, K. & Grewal, S. I. RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc. Natl Acad. Sc.i USA 100, 193–198 (2003).
ADS CAS Google Scholar
- Peng, J. C. & Karpen, G. H. H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nature Cell Biol. 9, 25–35 (2007).
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).
ADS 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).
CAS PubMed Google Scholar
- Schultz, D., Ayyanathan, K., Negorev, D., Maul, G. & Rauscher, F. R. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 16, 1855–1869 (2002).
Google Scholar
- Aulner, N. et al. The AT-hook protein D1 is essential for Drosophila melanogaster development and is implicated in position-effect variegation. Mol. Cell. Biol. 22, 1218–1232 (2002).
CAS PubMed PubMed Central Google Scholar
- Blattes, R. et al. Displacement of D1, HP1 and topoisomerase II from satellite heterochromatin by a specific polyamide. Embo J. 25, 2397–2408 (2006).
CAS PubMed PubMed Central Google Scholar
- Huertas, D., Cortes, A., Casanova, J. & Azorin, F. Drosophila DDP1, a multi-KH-domain protein, contributes to centromeric silencing and chromosome segregation. Curr. Biol. 14, 1611–1620 (2004).
CAS PubMed 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. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337–350 (2003).
CAS PubMed Google Scholar
- Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001).
CAS PubMed Google Scholar
- Cheutin, T. et al. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299, 721–725 (2003).
ADS CAS PubMed Google Scholar
- Festenstein, R. et al. Modulation of heterochromatin protein 1 dynamics in primary mammalian cells. Science 299, 719–721 (2003).
ADS CAS PubMed Google Scholar
- Nakayama, J., Klar, A. J. & Grewal, S. I. A chromodomain protein, Swi6, performs imprinting functions in fission yeast during mitosis and meiosis. Cell 101, 307–317 (2000).
CAS PubMed Google Scholar
- Grishok, A., Sinskey, J. L. & Sharp, P. A. Transcriptional silencing of a transgene by RNAi in the soma of C. elegans. Genes Dev. 19, 683–696 (2005).
CAS PubMed PubMed Central Google Scholar
- Robert, V. J., Sijen, T., van Wolfswinkel, J. & Plasterk, R. H. Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences. Genes Dev. 19, 782–787 (2005).
CAS PubMed PubMed Central Google Scholar
- Vastenhouw, N. L. et al. Gene expression: long-term gene silencing by RNAi. Nature 442, 882 (2006).
ADS CAS PubMed Google Scholar
- Sullivan, B. A. & Karpen, G. H. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nature Struct. Mol. Biol. 11, 1076–1083 (2004).
CAS Google Scholar
- George, J. A. & Pardue, M. L. The promoter of the heterochromatic Drosophila telomeric retrotransposon, HeT-A, is active when moved into euchromatic locations. Genetics 163, 625–635 (2003).
CAS PubMed PubMed Central Google Scholar
- Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).
CAS PubMed Google Scholar
- Gunawardane, L.S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315, 1587–1590 (2007).
ADS CAS PubMed Google Scholar
- Rudolph, T. et al. Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3. Mol. Cell 26, 103–115 (2007).
CAS PubMed Google Scholar
- Zofall, M. & Grewal, S. I. HULC, a histone H2B ubiquitinating complex, modulates heterochromatin independent of histone methylation in fission yeast. J. Biol. Chem. 282, 14065–14072 (2007).
CAS PubMed Google Scholar