Transcription and RNAi in heterochromatic gene silencing (original) (raw)
Heitz, E. Das heterochromatin der moose. I. Jahrb. Wiss. Botanik69, 762–818 (1928). Google Scholar
Muller, H.J. Types of visible variations induced by X-rays in Drosophila. J. Genet.22, 299–334 (1930). Google Scholar
Richards, E.J. & Elgin, S.C. Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell108, 489–500 (2002). CASPubMed Google Scholar
Grewal, S.I. & Moazed, D. Heterochromatin and epigenetic control of gene expression. Science301, 798–802 (2003). CASPubMed Google Scholar
Moazed, D. Common themes in mechanisms of gene silencing. Mol. Cell8, 489–498 (2001). CASPubMed Google Scholar
Paro, R. & Hogness, D.S. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc. Natl. Acad. Sci. USA88, 263–267 (1991). CASPubMedPubMed Central Google Scholar
Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet.38, 413–443 (2004). CASPubMed Google Scholar
Kornberg, R.D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell98, 285–294 (1999). CASPubMed Google Scholar
Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature389, 251–260 (1997). ArticleCASPubMed Google Scholar
Jenuwein, T. & Allis, C.D. Translating the histone code. Science293, 1074–1080 (2001). CASPubMed Google Scholar
Volpe, T.A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science297, 1833–1837 (2002). CASPubMed Google Scholar
Fukagawa, T. et al. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat. Cell Biol.6, 784–791 (2004). CASPubMed Google Scholar
Kanellopoulou, C. et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev.19, 489–501 (2005). CASPubMedPubMed Central Google Scholar
Motamedi, M.R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell119, 789–802 (2004). ArticleCASPubMed Google Scholar
Moazed, D. et al. Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harb. Symp. Quant. Biol.71, 461–471 (2006). CASPubMed Google Scholar
Henderson, I.R. & Jacobsen, S.E. Epigenetic inheritance in plants. Nature447, 418–424 (2007). CASPubMed Google Scholar
Sijen, T. & Plasterk, R.H. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature426, 310–314 (2003). CASPubMed 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). CASPubMedPubMed Central Google Scholar
Pal-Bhadra, M. et al. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science303, 669–672 (2004). CASPubMed Google Scholar
Bernstein, E. & Allis, C.D. RNA meets chromatin. Genes Dev.19, 1635–1655 (2005). CASPubMed Google Scholar
Buhler, M., Haas, W., Gygi, S.P. & Moazed, D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell129, 707–721 (2007). CASPubMed Google Scholar
Kouzarides, T. Chromatin modifications and their function. Cell128, 693–705 (2007). CASPubMed Google Scholar
Kurdistani, S.K. & Grunstein, M. Histone acetylation and deacetylation in yeast. Nat. Rev. Mol. Cell Biol.4, 276–284 (2003). CASPubMed Google Scholar
Bannister, A.J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature410, 120–124 (2001). CASPubMed 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. Nature410, 116–120 (2001). CASPubMed Google Scholar
Shilatifard, A. Chromatin Modifications by Methylation and Ubiquitination: Implications in the Regulation of Gene Expression. Annu. Rev. Biochem.75, 243–269 (2006). CASPubMed Google Scholar
Lachner, M. & Jenuwein, T. The many faces of histone lysine methylation. Curr. Opin. Cell Biol.14, 286–298 (2002). CASPubMed Google Scholar
Jenuwein, T. Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol.11, 266–273 (2001). CASPubMed Google Scholar
Peters, A.H. et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell12, 1577–1589 (2003). CASPubMed Google Scholar
Rice, J.C. et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell12, 1591–1598 (2003). CASPubMed Google Scholar
James, T.C. et al. Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. Eur. J. Cell Biol.50, 170–180 (1989). CASPubMed 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). CASPubMedPubMed Central 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. Science292, 110–113 (2001). CASPubMed Google Scholar
Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature406, 593–599 (2000). CASPubMed Google Scholar
Melcher, M. et al. Structure-function analysis of SUV39H1 reveals a dominant role in heterochromatin organization, chromosome segregation, and mitotic progression. Mol. Cell. Biol.20, 3728–3741 (2000). CASPubMedPubMed Central Google Scholar
Mellone, B.G. et al. Centromere silencing and function in fission yeast is governed by the amino terminus of histone H3. Curr. Biol.13, 1748–1757 (2003). CASPubMed Google Scholar
Nielsen, S.J. et al. Rb targets histone H3 methylation and HP1 to promoters. Nature412, 561–565 (2001). CASPubMed Google Scholar
Vakoc, C.R., Mandat, S.A., Olenchock, B.A. & Blobel, G.A. Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol. Cell19, 381–391 (2005). CASPubMed Google Scholar
de Wit, E., Greil, F. & van Steensel, B. High-resolution mapping reveals links of HP1 with active and inactive chromatin components. PLoS Genet.3, e38 (2007). PubMedPubMed Central Google Scholar
Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science308, 1149–1154 (2005). CASPubMed Google Scholar
Willingham, A.T. et al. Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harb. Symp. Quant. Biol.71, 101–110 (2006). CASPubMed Google Scholar
Breiling, A., Turner, B.M., Bianchi, M.E. & Orlando, V. General transcription factors bind promoters repressed by Polycomb group proteins. Nature412, 651–655 (2001). CASPubMed Google Scholar
Dellino, G.I. et al. Polycomb silencing blocks transcription initiation. Mol. Cell13, 887–893 (2004). CASPubMed Google Scholar
Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R. & Young, R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell130, 77–88 (2007). ArticleCASPubMedPubMed Central Google Scholar
Pirrotta, V. & Gross, D.S. Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol. Cell18, 395–398 (2005). CASPubMed Google Scholar
Steinmetz, E.J. et al. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol. Cell24, 735–746 (2006). CASPubMed Google Scholar
Wyers, F. et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell121, 725–737 (2005). CASPubMed Google Scholar
Davis, C.A. & Ares, M., Jr. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA103, 3262–3267 (2006). CASPubMedPubMed Central Google Scholar
Buhler, M., Verdel, A. & Moazed, D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell125, 873–886 (2006). CASPubMed 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). CASPubMedPubMed Central Google Scholar
Kato, H. et al. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science309, 467–469 (2005). CASPubMed Google Scholar
Sugiyama, T. et al. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell128, 491–504 (2007). CASPubMed Google Scholar
Devlin, R.H., Bingham, B. & Wakimoto, B.T. The organization and expression of the light gene, a heterochromatic gene of Drosophila melanogaster. Genetics125, 129–140 (1990). CASPubMedPubMed Central Google Scholar
Eberl, D.F., Duyf, B.J. & Hilliker, A.J. The role of heterochromatin in the expression of a heterochromatic gene, the rolled locus of Drosophila melanogaster. Genetics134, 277–292 (1993). CASPubMedPubMed Central Google Scholar
Smith, C.D., Shu, S., Mungall, C.J. & Karpen, G.H. The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science316, 1586–1591 (2007). CASPubMedPubMed Central Google Scholar
Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature391, 806–811 (1998). CASPubMed Google Scholar
Hamilton, A.J. & Baulcombe, D.C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science286, 950–952 (1999). CASPubMed Google Scholar
Hammond, S.M., Bernstein, E., Beach, D. & Hannon, G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature404, 293–296 (2000). CASPubMed Google Scholar
Zamore, P.D., Tuschl, T., Sharp, P.A. & Bartel, D.P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell101, 25–33 (2000). CASPubMed Google Scholar
Elbashir, S.M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev.15, 188–200 (2001). CASPubMedPubMed Central Google Scholar
Bernstein, E., Caudy, A.A., Hammond, S.M. & Hannon, G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature409, 363–366 (2001). CASPubMed Google Scholar
Matzke, M.A. & Birchler, J.A. RNAi-mediated pathways in the nucleus. Nat. Rev. Genet.6, 24–35 (2005). CASPubMed Google Scholar
Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116, 281–297 (2004). CASPubMed Google Scholar
Sijen, T. et al. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell107, 465–476 (2001). CASPubMed Google Scholar
Mette, M.F., Aufsatz, W., van der Winden, J., Matzke, M.A. & Matzke, A.J. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J.19, 5194–5201 (2000). CASPubMedPubMed Central Google Scholar
Pal-Bhadra, M., Bhadra, U. & Birchler, J.A. Cosuppression of nonhomologous transgenes in Drosophila involves mutually related endogenous sequences. Cell99, 35–46 (1999). CASPubMed Google Scholar
Pal-Bhadra, M., Bhadra, U. & Birchler, J.A. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell9, 315–327 (2002). CASPubMed 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). CASPubMedPubMed Central Google Scholar
Taverna, S.D., Coyne, R.S. & Allis, C.D. Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena. Cell110, 701–711 (2002). CASPubMed Google Scholar
Mochizuki, K., Fine, N.A., Fujisawa, T. & Gorovsky, M.A. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell110, 689–699 (2002). CASPubMed Google Scholar
Reinhart, B.J. & Bartel, D.P. Small RNAs correspond to centromere heterochromatic repeats. Science297, 1831 (2002). CASPubMed 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). CASPubMedPubMed Central 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). CASPubMed 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. USA102, 152–157 (2005). CASPubMed Google Scholar
Noma, K. et al. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat. Genet.36, 1174–1180 (2004). CASPubMed Google Scholar
Hong, E.J., Villen, J., Gerace, E.L., Gygi, S.P. & 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). CASPubMed Google Scholar
Colmenares, S.U., Buker, S.M., Buhler, M., Dlakic, M. & Moazed, D. Coupling of Double-Stranded RNA Synthesis and siRNA Generation in Fission Yeast RNAi. Mol. Cell27, 449–461 (2007). CASPubMed Google Scholar
Chan, S.W., Zhang, X., Bernatavichute, Y.V. & Jacobsen, S.E. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol.4, e363 (2006). PubMedPubMed Central Google Scholar
Irvine, D.V. et al. Argonaute slicing is required for heterochromatic silencing and spreading. Science313, 1134–1137 (2006). CASPubMed Google Scholar
Buker, S.M. et al. Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nat. Struct. Mol. Biol.14, 200–207 (2007). CASPubMed Google Scholar
Grewal, S.I. & Jia, S. Heterochromatin revisited. Nat. Rev. Genet.8, 35–46 (2007). CASPubMed Google Scholar
Murakami, H. et al. Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore function. PLoS ONE2, e317 (2007). PubMedPubMed Central Google Scholar
Houseley, J., LaCava, J. & Tollervey, D. RNA-quality control by the exosome. Nat. Rev. Mol. Cell Biol.7, 529–539 (2006). CASPubMed 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. Cell20, 173–185 (2005). CASPubMed Google Scholar
LaCava, J. et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell121, 713–724 (2005). CASPubMed Google Scholar
Vanacova, S. et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol.3, e189 (2005). PubMed Google Scholar
Morris, K.V., Chan, S.W., Jacobsen, S.E. & Looney, D.J. Small interfering RNA-induced tanscriptional gene silencing in human cells. Science305, 1289–1292 (2004). CASPubMed Google Scholar
Kim, D.H., Villeneuve, L.M., Morris, K.V. & Rossi, J.J. Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol.13, 793–797 (2006). CASPubMed Google Scholar
Weinberg, M.S. et al. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA12, 256–262 (2006). CASPubMedPubMed Central Google Scholar
Lau, N.C. et al. Characterization of the piRNA complex from rat testes. Science313, 363–367 (2006). CASPubMed Google Scholar
Girard, A., Sachidanandam, R., Hannon, G.J. & Carmell, M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature442, 199–202 (2006). PubMed Google Scholar
Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature442, 203–207 (2006). CASPubMed Google Scholar
Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell128, 1089–1103 (2007). CASPubMed Google Scholar
Klenov, M.S. et al. Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res.35, 5430–5438 (2007). CASPubMedPubMed Central Google Scholar
Aravin, A.A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G.J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science316, 744–747 (2007). CASPubMed Google Scholar
Yang, P.K. & Kuroda, M.I. Noncoding RNAs and intranuclear positioning in monoallelic gene expression. Cell128, 777–786 (2007). CASPubMed Google Scholar
Rinn, J.L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell129, 1311–1323 (2007). CASPubMedPubMed Central Google Scholar