The role of RNA interference in heterochromatic silencing (original) (raw)

• Heitz, E. Das heterochromatin der Moose. Jehrb. Wiss. Botanik 69, 762–818 (1928).
  Google Scholar
• Hennig, W. Heterochromatin. Chromosoma 108, 1–9 (1999).
  CAS PubMed Google Scholar
• Muller, H. J. Types of visible variations induced by X-rays in Drosophila. J. Genetics 22, 299–334 (1930).
  Google Scholar
• Comfort, N. C. From controlling elements to transposons: Barbara McClintock and the Nobel Prize. Trends Genet. 17, 475–478 (2001).
  CAS PubMed Google Scholar
• Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001).
  CAS PubMed Google Scholar
• Lachner, M. & Jenuwein, T. The many faces of histone lysine methylation. Curr. Opin. Cell Biol. 14, 286–298 (2002).
  Article CAS PubMed Google Scholar
• Brehm, A., Tufteland, K. R., Aasland, R. & Becker, P. B. The many colours of chromodomains. Bioessays 26, 133–140 (2004).
  CAS PubMed Google Scholar
• Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genet. 33 (Suppl.), 245–254 (2003).
  CAS PubMed Google Scholar
• Tamaru, H. & Selker, E. U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414, 277–283 (2001).
  Article ADS CAS PubMed Google Scholar
• Lindroth, A. M. et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077–2080 (2001).
  CAS PubMed Google Scholar
• Bartee, L., Malagnac, F. & Bender, J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 15, 1753–1758 (2001).
  CAS PubMed PubMed Central Google Scholar
• Jackson, J. P., Lindroth, A. M., Cao, X. & Jacobsen, S. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556–560 (2002).
  ADS CAS PubMed Google Scholar
• Malagnac, F., Bartee, L. & Bender, J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J. 21, 6842–6852 (2002).
  CAS PubMed PubMed Central Google Scholar
• Tariq, M. et al. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc. Natl Acad. Sci. USA 100, 8823–8827 (2003).
  ADS CAS PubMed PubMed Central Google Scholar
• Lippman, Z., May, B., Yordan, C., Singer, T. & Martienssen, R. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1, E67 (2003).
  PubMed PubMed Central Google Scholar
• Johnson, L., Cao, X. & Jacobsen, S. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr. Biol. 12, 1360–1367 (2002).
  CAS PubMed Google Scholar
• Fuks, F., Hurd, P. J., Deplus, R. & Kouzarides, T. The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 31, 2305–2312 (2003).
  CAS PubMed PubMed Central Google Scholar
• Fuks, F. et al. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol. Chem. 278, 4035–4040 (2003).
  CAS PubMed Google Scholar
• Lehnertz, B. et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 1192–1200 (2003).
  CAS PubMed Google Scholar
• Nguyen, C. T. et al. Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2′-deoxycytidine. Cancer Res. 62, 6456–6461 (2002).
  CAS PubMed Google Scholar
• Jeddeloh, J. A., Stokes, T. L. & Richards, E. J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nature Genet. 22, 94–97 (1999).
  CAS PubMed Google Scholar
• Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V. & Martienssen, R. A. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297, 1871–1873 (2002).
  ADS CAS PubMed Google Scholar
• Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926–1928 (1993).
  ADS CAS PubMed Google Scholar
• Kankel, M. W. et al. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163, 1109–1122 (2003).
  CAS PubMed PubMed Central Google Scholar
• Martienssen, R. A. & Colot, V. DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293, 1070–1074 (2001).
  CAS PubMed Google Scholar
• Lippman, Z. L. et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471–476 (2004).
  ADS CAS PubMed Google Scholar
• Kato, M., Miura, A., Bender, J., Jacobsen, S. E. & Kakutani, T. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr. Biol. 13, 421–426 (2003).
  CAS PubMed Google Scholar
• Matzke, M. et al. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim. Biophys. Acta 1677, 129–141 (2004).
  CAS PubMed Google Scholar
• Grewal, S. I. Transcriptional silencing in fission yeast. J. Cell Physiol. 184, 311–318 (2000).
  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
• Reinhart, B. J. & Bartel, D. P. Small RNAs correspond to centromere heterochromatic repeats. Science 297, 1831 (2002).
  CAS PubMed Google Scholar
• Bernard, P. et al. Requirement of heterochromatin for cohesion at centromeres. Science 294, 2539–2542 (2001).
  ADS CAS PubMed Google Scholar
• Volpe, T. et al. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11, 137–146 (2003).
  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. Sci. USA 100, 193–198 (2003).
  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
• Martienssen, R. A. Maintenance of heterochromatin by RNA interference of tandem repeats. Nature Genet. 35, 213–214 (2003).
  CAS PubMed Google Scholar
• Jacobs, S. A. & Khorasanizadeh, S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295, 2080–2083 (2002).
  ADS CAS PubMed Google Scholar
• Schramke, V. & Allshire, R. Hairpin RNAs and retrotransposon LTRs affect RNAi and chromatin-based gene silencing. Science 301, 1069–1074 (2003).
  ADS 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
• 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
• Dernburg, A. F., Zalevsky, J., Colaiacovo, M. P. & Villeneuve, A. M. Transgene-mediated cosuppression in the C. elegans germ line. Genes Dev. 14, 1578–1583 (2000).
  CAS PubMed PubMed Central Google Scholar
• Wu-Scharf, D., Jeong, B., Zhang, C. & Cerutti, H. Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-box RNA helicase. Science 290, 1159–1162 (2000).
  ADS 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
• Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337–350 (2003).
  CAS PubMed Google Scholar
• Djikeng, A., Shi, H., Tschudi, C. & Ullu, E. RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retrotransposon-derived 24-26-nucleotide RNAs. RNA 7, 1522–1530 (2001).
  CAS PubMed PubMed Central Google Scholar
• Mochizuki, K., Fine, N., Fujisawa, T. & Gorovsky, M. Analysis of a _piwi_-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110, 689 (2002).
  CAS PubMed Google Scholar
• Taverna, S. D., Coyne, R. S. & Allis, C. D. Methylation of histone H3 at lysine 9 targets programmed DNA elimination in Tetrahymena. Cell 110, 701–711 (2002).
  CAS PubMed Google Scholar
• Xie, Z. et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104 (2004).
  PubMed PubMed Central Google Scholar
• Sijen, T. & Plasterk, R. H. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 426, 310–314 (2003).
  ADS CAS PubMed Google Scholar
• Zilberman, D., Cao, X. & Jacobsen, S. E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299, 716–719 (2003).
  ADS CAS PubMed Google Scholar
• Lynn, K. et al. The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development 126, 469–481 (1999).
  CAS PubMed Google Scholar
• Soppe, W. J. et al. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell 6, 791–802 (2000).
  CAS PubMed Google Scholar
• Kinoshita, T. et al. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303, 521–523 (2004).
  ADS CAS PubMed Google Scholar
• Chan, S. W. et al. RNA silencing genes control de novo DNA methylation. Science 303, 1336 (2004).
  CAS PubMed Google Scholar
• Cao, X. & Jacobsen, S. E. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138–1144 (2002).
  CAS PubMed Google Scholar
• Cao, X. et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr. Biol. 13, 2212–2217 (2003).
  CAS PubMed Google Scholar
• Bender, J. & Fink, G. R. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83, 725–734 (1995).
  CAS PubMed 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).
  CAS PubMed PubMed Central Google Scholar
• Melquist, S. & Bender, J. Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. Genes Dev. 17, 2036–2047 (2003).
  CAS PubMed PubMed Central Google Scholar
• Zilberman, D. et al. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr. Biol. 14, 1214–1220 (2004).
  CAS PubMed Google Scholar
• Fagard, M., Boutet, S., Morel, J. B., Bellini, C. & Vaucheret, H. AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc. Natl Acad. Sci. USA 97, 11650–11654 (2000).
  ADS 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).
  ADS 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
• Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81 (2004).
  CAS PubMed Google Scholar
• Kelly, W. G. et al. X-chromosome silencing in the germline of C. elegans. Development 129, 479–492 (2002).
  CAS PubMed Google Scholar
• Maison, C. et al. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nature Genet. 30, 329–334 (2002).
  PubMed Google Scholar
• Bernstein, E. et al. Dicer is essential for mouse development. Nature Genet. 35, 215–217 (2003).
  CAS PubMed Google Scholar
• Rudert, F., Bronner, S., Garnier, J. M. & Dolle, P. Transcripts from opposite strands of gamma satellite DNA are differentially expressed during mouse development. Mamm. Genome 6, 76–83 (1995).
  CAS PubMed Google Scholar
• Deng, W. & Lin, H. miwi a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev. Cell 2, 819–830 (2002).
  CAS PubMed Google Scholar
• Kuramochi-Miyagawa, S. et al. Mili a mammalian member of piwi family gene, is essential for spermatogenesis. Development 131, 839–849 (2004).
  CAS PubMed Google Scholar
• Kelley, R. L. & Kuroda, M. I. Noncoding RNA genes in dosage compensation and imprinting. Cell 103, 9–12 (2000).
  CAS PubMed Google Scholar
• Reik, W. & Walter, J. Genomic imprinting: parental influence on the genome. Nature Rev. Genet. 2, 21–32 (2001).
  CAS PubMed Google Scholar
• Kiyosue, T. et al. Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc. Natl Acad. Sci. USA 96, 4186–4191 (1999).
  ADS CAS PubMed PubMed Central Google Scholar
• Baroux, C., Spillane, C. & Grossniklaus, U. Genomic imprinting during seed development. Adv. Genet. 46, 165–214 (2002).
  CAS PubMed Google Scholar
• Sleutels, F. & Barlow, D. P. The origins of genomic imprinting in mammals. Adv. Genet. 46, 119–163 (2002).
  CAS PubMed Google Scholar
• Seitz, H. et al. Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nature Genet. 34, 261–262 (2003).
  ADS CAS PubMed Google Scholar
• Stam, M., Belele, C., Dorweiler, J. E. & Chandler, V. L. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 16, 1906–1918 (2002).
  CAS PubMed PubMed Central Google Scholar
• Avner, P. & Heard, E. X-chromosome inactivation: counting, choice and initiation. Nature Rev. Genet. 2, 59–67 (2001).
  CAS PubMed Google Scholar
• Heard, E. et al. Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell 107, 727–738 (2001).
  CAS PubMed Google Scholar
• Akhtar, A., Zink, D. & Becker, P. B. Chromodomains are protein-RNA interaction modules. Nature 407, 405–409 (2000).
  ADS CAS PubMed Google Scholar
• Merok, J. R., Lansita, J. A., Tunstead, J. R. & Sherley, J. L. Cosegregation of chromosomes containing immortal DNA strands in cells that cycle with asymmetric stem cell kinetics. Cancer Res. 62, 6791–6795 (2002).
  CAS PubMed Google Scholar
• McClintock, B. Chromosome organization and genic expression. Cold Spring Harbor Symp. Quant. Biol. 16, 13–47 (1951).
  CAS PubMed Google Scholar
• McClintock, B., Kato Y., T. A. & Blumenschein, A. Chromosome Constitutions of Races of Maize. Their Significance for Interpreting Relationships Among Races and Strains in the Americas (A monograph.) (Colegio de Postgraduados, Escuela National de Agricultura, Chapingo, Edo. Mexico, 1981).
  Google Scholar
• Fransz, P., Soppe, W. & Schubert, I. Heterochromatin in interphase nuclei of Arabidopsis thaliana. Chromosome Res. 11, 227–240 (2003).
  CAS PubMed Google Scholar
• Osborn, T. C. et al. Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19, 141–147 (2003).
  CAS PubMed Google Scholar
• Heath, E. M. & Simmons, M. J. Genetic and molecular analysis of repression in the P-M system of hybrid dysgenesis in Drosophila melanogaster. Genet. Res. 57, 213–226 (1991).
  CAS PubMed Google Scholar
• Sarot, E., Payen-Groschene, G., Bucheton, A. & Pelisson, A. Evidence for a _piwi_-dependent RNA silencing of the gypsy endogenous retrovirus by the Drosophila melanogaster flamenco gene. Genetics 166, 1313–1321 (2004).
  CAS PubMed PubMed Central Google Scholar
• Sun, X., Le, H. D., Wahlstrom, J. M. & Karpen, G. H. Sequence analysis of a functional Drosophila centromere. Genome Res. 13, 182–194 (2003).
  CAS PubMed PubMed Central Google Scholar
• Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).
• Choo, K. H. Domain organization at the centromere and neocentromere. Dev. Cell 1, 165–177 (2001).
  CAS PubMed Google Scholar
• Ananiev, E. V., Phillips, R. L. & Rines, H. W. Complex structure of knobs and centromeric regions in maize chromosomes. Tsitol. Genet. 34, 11–15 (2000).
  CAS PubMed Google Scholar
• Nagaki, K. et al. Sequencing of a rice centromere uncovers active genes. Nature Genet. 36, 138–145 (2004).
  CAS PubMed Google Scholar
• Selker, E. U. et al. The methylated component of the Neurospora crassa genome. Nature 422, 893–897 (2003).
  ADS CAS PubMed Google Scholar
• Jorgensen, R. A. in RNAi: A Guide to Gene Silencing (ed. Hannon, G. J.) Ch. 1, 5–21 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2003).
  Google Scholar
• Kouzminova, E. & Selker, E. U. dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J. 20, 4309–4323 (2001).
  CAS PubMed PubMed Central Google Scholar
• Xiao, W. et al. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev. Cell 5, 891–901 (2003).
  CAS PubMed Google Scholar
• Colot, V., Maloisel, L. & Rossignol, J. L. Interchromosomal transfer of epigenetic states in Ascobolus: transfer of DNA methylation is mechanistically related to homologous recombination. Cell 86, 855–864 (1996).
  CAS PubMed Google Scholar
• Shiu, P. K. & Metzenberg, R. L. Meiotic silencing by unpaired DNA: properties, regulation and suppression. Genetics 161, 1483–1495 (2002).
  CAS PubMed PubMed Central Google Scholar
• Freitag, M. et al. DNA methylation is independent of RNA interference in Neurospora. Science 304, 1939 (2004).
  CAS PubMed Google Scholar
• Wassenegger, M., Heimes, S., Riedel, L. & Sanger, H. L. RNA-directed de novo methylation of genomic sequences in plants. Cell 76, 567–576 (1994).
  CAS PubMed Google Scholar