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Original Articles

Cajal Bodies and Plant RNA Metabolism

Pages 258-270 | Published online: 01 May 2012

REFERENCES

  • Amé , J.-C. , Spenlehauer , C. and de Murcia , G. 2004 . The PARP superfamily . BioEssays , 26 : 882 – 893 .
  • Amedeo , P. , Habu , Y. , Afsar , K. , Mittelsten-Scheid , O. and Paszkowski , J. 2000 . Disruption of the plant gene MOM releases transcriptional silencing of methylated genes . Nature , 405 : 203 – 206 .
  • Andrade , L. E. C. , Chan , E. K. L. , Raska , I. , Pebbles , C. L. , Roos , G. and Tan , E. M. 1991 . Human auto-antibody to a novel protein of the nuclear coiled body: immunological characterization and cDNA cloning of p80-coilin . J. Exp.Med. , 173 : 1407 – 1419 .
  • Babiychuk , E. , Cottrill , P. B. , Storozhenko , S. , Fuangthong , M. , Chen , Y. , O’Farrell , M. K. , Van Montagu , M. , Inze , D. and Kushnir , S. 1998 . Higher plants possess two structurally different poly(ADP-ribose) polymerases . Plant J. , 15 : 635 – 645 .
  • Bachellerie , J. P. , Cavaille , J. and Huttenhofer , A. 2002 . The expanding snoRNA world . Biochimie , 84 : 775 – 790 .
  • Barcaroli , D. , Dinsdale , D. , Neale , M. H. , Bongiorno-Borbone , L. , Ranatti , M. , Munarriz , E. , Sayan , A E. , McWilliam , J. M. , Smith , T. M. , Fava , E. , Knight , R. A. , Melino , G. and De Laurenzi , V. 2006 . FLASH is an essential component of Cajal bodies . Proc. Natl. Acad. Sci. , 103 : 14802 – 14807 .
  • Barneche , F. , Gaspin , C. , Guyot , R. and Echeverría , M. 2001 . Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2′-O-methylation sites . J. Mol. Biol , 311 : 57 – 73 .
  • Barneche , F. , Steinmetz , F. and Echeverría , M. 2000 . Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana . J. Biol. Chem , 275 : 27212 – 27220 .
  • Bartel , D. P. 2004 . MicroRNAs: Genomics, biogenesis, mechanism and function . Cell , 116 : 281 – 297 .
  • Baulcombe , D. 2006 . Short silencing RNA: the dark matter of genetics? . Cold Spring Harb, Symp. Quant. Biol , 71 : 13 – 20 .
  • Beck , J. S. 1961 . Variations in the morphological patterns of “autoimmune” nuclear fluorescence . Lancet , 1 : 1203 – 1205 .
  • Beven , A. F. , Simpson , G. G. , Brown , J. W. S. and Shaw , P. J. 1995 . The organization of spliceosomal components in the nuclei of higher plants . J. Cell Sci. , 108 : 509 – 518 .
  • Bongiorno-Borbone , L. , De Cola , A. , Vernole , P. , Finos , L. , Barcaroli , D. , Knight , R. A. , Melino , G. and De Laurenzi , V. 2008 . FLASH and NPAT positive but not coilin positive Cajal bodies correlate with cell ploidy . Cell Cycle , 7 : 2357 – 2367 .
  • Bonneau , L. , Ge , Y. , Drury , G. E. and Gallois , P. 2008 . What happened to plant caspases? . J. Exp. Bot. , 59 : 491 – 499 .
  • Boudonck , K. , Dolan , L. and Shaw , P. J. 1999 . The movement of coiled bodies visualized in living plant cells by the green fluorescent protein . Mol. Biol. Cell , 10 : 2297 – 2307 .
  • Branco , M. R. and Pombo , A. 2006 . Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations . PloS. Biol. , 4 : e138 doi:10.1371/journal.pbio.0040138
  • Brodersen , P. , Sakvarelidze-Achard , L. , Bruun-Rasmussen , M. , Dunoyer , P. , Yamamoto , Y. Y. , Sieburth , L. and Voinnet , O. 2008 . Widespread translational inhibition by plant miRNAs and siRNAs . Science , 320 : 1185 – 1190 .
  • Brown , J. W. S. , Clark , G. P. , Simpson , C. G. , Leader , D. J. and Lowe , T. M. 2001 . Multiple snoRNA gene clusters from Arabidopsis . RNA , 7 : 5718 – 5732 .
  • Bühler , M. , Haas , W. , Gygi , S. P. and Moazed , D. 2007 . RNAi-dependent and –independent RNA turnover mechanisms contribute to heterochromatic gene silencing . Cell , 129 : 651 – 653 .
  • Calikowski , T. T. , Meulia , T. and Meier , I. 2003 . A proteomic study of the Arabidopsis nuclear matrix . J. Cell. Biochem , 90 : 361 – 378 .
  • Carmo-Fonseca , M. , Ferreira , J. and Lamond , A. I. 1993 . Assembly of snRNP-containing coiled bodies is regulated in interphase and mitosis – evidence that the coiled body is a kinetic nuclear structure . J. Cell Biol. , 120 : 841 – 852 .
  • Chen , D. and Huang , S. 2001 . Nucleolar components involved in ribosome biogenesis cycle between the nucleolus and nucleoplasm in interphase cells . J. Cell Biol. , 153 : 169 – 176 .
  • Chen , H.-M. and Wu , S. H. 2009 . Mining of small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis . Nuc. Acids Res , 37 : e69 doi:10.1093/nar/gkp225
  • Chen , Y. M. , Shall , S. and O’Farrell , M. 1994 . Poly(ADP-ribose) polymerase in plant nuclei . Eur, J. Biochem , 224 : 135 – 142 .
  • Cioce , M. and Lamond , A. I. 2005 . Cajal bodies: a long history of discovery . Annu. Rev. Cell. Dev. Biol. , 21 : 105 – 131 .
  • Collier , S. , Pendle , A. , Boudonck , K. , van Rij , T. , Dolan , L. and Shaw , P. 2006 . A distant coilin homologue is required for the formation of Cajal bodies in Arabidopsis . Mol. Biol. Cell , 17 : 2942 – 2951 .
  • Darzacq , X. , Jády , B. E. , Verheggen , C. , Kiss , A. M. , Bertrans , E. and Kiss , T. 2002 . Cajal body-specific small nuclear RNAs: a novel class of 2′-O-methylation and pseudouridylation guide RNAs . E.M.B.O. J. , 21 : 2746 – 2756 .
  • De Block , M. , Verduyn , C. , De Brouwer , D. and Cornelissen , M. 2005 . Poly(ADP-ribose) polymerase in plants affects energy homeostasis, cell death and stress tolerance . Plant J. , 41 : 95106
  • Derysheva , S. and Gall , J. G. 2009 . Small Cajal body-specific RNAs of Drosophila function in the absence of Cajal bodies . Mol. Biol. Cell , 20 : 5250 – 5259 .
  • Dewitte , W. and Murray , J. A. H. 2003 . The plant cell cycle . Annu. Rev. Plant Biol. , 54 : 235 – 264 .
  • Doucet-Chabeaud , G. , Godon , C. , Brutesco , C. , de Murcia , G. and Kazmaier , M. 2001 . Ionizing radiation induces the expression of PARP-1 and PARP-2 genes in Arabidopsis . Mol. Genet. Genomics , 265 : 954 – 963 .
  • Dundr , M. , Hebert , M. D. , Karpova , T. S. , Stanek , D. , Xu , H. , Shpargel , K. B. , Meier , U. T. , Neugebauer , K. M. , Matera , A. G. and Misteli , T. 2004 . In vivo kinetics of Cajal body components . J. Cell Biol. , 164 : 831 – 842 .
  • Erhardt , M. , Adamska , I. and Franco , O. L. 2010 . Plant nuclear proteomics – inside the cell maestro . FEBS J. , 277 : 3295 – 3307 .
  • Fang , Y. and Spector , D. 2007 . Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants . Curr. Biol. , 17 : 818 – 823 .
  • Frey , M. R. and Matera , A. G. 1995 . Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequences in interphase human cells . Proc. Natl. Acad. Sci USA , 92 : 5915 – 5919 .
  • Fujioka , Y. , Utsumi , M. , Ohba , Y. and Watanabe , Y. 2007 . Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis . Plant Cell Physiol. , 48 : 1243 – 1253 .
  • Gall , J. G. 2000 . Cajal bodies: the first 100 years . Annu. Rev. Cell Dev. Biol. , 16 : 273 – 300 .
  • Gall , J. G. 2003 . The Centennial of the Cajal body . Nat. Rev. Mol. Cell Biol. , 4 : 975 – 980 .
  • Gall , J. G. , Bellini , M. , Wu , Z. and Murphy , C. 1999 . Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes . Mol .Biol. Cell , 10 : 4385 – 4402 .
  • Handwerger , K. E. and Gall , J. G. 2006 . Subnuclear organelles: new insights into form and function . Trends Cell Biol , 16 : 19 – 26 .
  • Hardin , J. H. , Spicer , S. S. and Greene , W. B. 1969 . The paranucleolar structure, accessory body of Cajal, sex chromatin, and related structures in nuclei of rat trigeminal neurons: a cytochemical and ultrastructural study . Anat. Rec. , 164 : 403 – 431 .
  • Hata , S. 1991 . cDNA cloning of a novel cdc2+/CDC28-related protein kinase from rice . FEBS Lett , 279 : 149 – 152 .
  • Hebert , M. D. and Matera , A. G. 2000 . Self-association of coilin reveals a common theme in nuclear body localization . Mol. Biol. Cell , 11 : 4159 – 4171 .
  • Herr , A. J. , Jensen , M. B. , Dalmay , T. and Baulcombe , D. C. 2005 . RNA polymerase IV directs silencing of endogenous DNA . Science , 308 : 118 – 120 .
  • Hunt , L. , Lerner , F. and Ziegler , M. 2004 . NAD: new roles in signaling and gene regulation in plants . New Phytol , 163 : 31 – 44 .
  • Jády , B. E. , Bertrand , E. and Kiss , T. 2004 . Human telomerase RNA and box H/ACA scaRNAs share a common Cajal body-specific localization signal . J. Cell Biol. , 164 : 647 – 652 .
  • Jády , B. E. and Kiss , T. 2001 . A small nucleolar guide RNA functions both in 2′-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA . EMBO J , 20 : 541 – 551 .
  • Jordan , P. , Cunha , C. and Carmo-Fonseca , M. 1997 . The cdk7-cyclin H-MAT1 complex associated with TFIIH is localized in coiled bodies . Mol. Biol. Cell , 8 : 1207 – 1217 .
  • Kannan , K. , Nelson , A. D. and Shippen , D. E. 2008 . Dyskerin is a component of the Arabidopsis telomerase RNP required for telomere maintenance . Mol. Cell Biol , 28 : 2332 – 2341 .
  • Kanno , T. , Huettel , B. , Mette , M. F. , Aufsatz , W. , Jaligot , E. , Daxinger , L. , Kreil , D. P. , Matzke , M. and Matzke , A. J. 2005 . Atypical RNA polymerase subunits required for RNA-directed DNA methylation . Nat. Genet. , 37 : 761 – 765 .
  • Kerényi , Z. , Mérai , Z. , Hiripi , L. , Benkovics , A. , Gyula , P. , Lacomme , C. , Barta , E. , Nagy , F. and Silhavy , D. 2008 . Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay . EMBO J. , 27 : 1585 – 1595 .
  • Kim , S. H. , Koroleva , O. A. , Lewandowska , D. , Pendle , A. F. , Clark , G. P. , Simpson , C. G. , Shaw , P. J. and Brown , J. W. S. 2009 . Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus . Plant Cell , 21 : 2045 – 2057 .
  • Kim , S. H. , MacFarlane , S. , Kalinina , N. O. , Rakitina , D. V. , Ryabov , E. V. , Gillespie , T. , Haupt , S. , Brown , J. W. S. and Taliansky , M. 2007 . Interaction of a plant virus-encoded protein with the major nucleolar protein fibrillarin is required for systemic virus infection . Proc. Nat. Acad. Sci. , 104 : 11115 – 11120 .
  • Kim , S. H. , Spensley , M. , Choi , S. K. , Calixto , C. P. G. , Pendle , A. F. , Koroleva , O. , Shaw , P. J. and Brown , J. W. S. 2010 . Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli . Nucl. Acids Res , 38 : 3054 – 3067 .
  • Kiriyama , M. , Kobayashi , Y. , Saito , M. , Ishikawa , F. and Yonehara , S. 2009 . Interaction of FLASH with arsenite resistance protein 2 is involved in cell cycle progression at S phase . Mol. Cell Biol. , 29 : 4729 – 4741 .
  • Klingauf , M. , Stanek , D. and Neugebauer , K. M. 2006 . Enhancement of U4/U6 small nuclear ribonucleoprotein particle association in Cajal bodies predicted by mathematical modeling . Mol , 17 : 4972 – 4981 . Biol. Cell
  • Kotova , E. , Jarnik , M. and Tulin , A. V. 2009 . Poly (ADP-Ribose) Polymerase 1 is required for protein localization to Cajal body . PloS. Genet. , 5 ( 2 ) : e1000387 doi:10.1371/journal.pgen. 1000387.
  • Kroiss , M. , Schultz , J. , Wiesner , J. , Chari , A. , Sickmann , A. and Fischer , U. 2008 . Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster . Proc. Nat. Acad. Sci , 105 : 10045 – 10050 .
  • Kumakura , N. , Takeda , A. , Fujioka , Y. , Motose , H. , Takano , R. and Watanabe , Y. 2009 . SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies . FEBS Lett. , 583 : 1261 – 1266 .
  • Lamond , A. I. and Earnshaw , W. C. 1998 . Structure and function in the nucleus . Science , 280 : 547 – 553 .
  • Leader , D. J. , Clark , G. P. , Watters , J. A. , Beven , A. F. , Shaw , P. J. and Brown , J. W. S. 1997 . Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs . EMBO J , 16 : 5742 – 5751 .
  • Leader , D. J. , Clark , G. P. , Watters , J. A. , Beven , A. F. , Shaw , P. J. and Brown , J. W. S. 1999 . Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs . Plant Mol. Biol. , 39 : 1091 – 1100 .
  • Lepiniec , L. , Babiychuk , E. , Kushnir , S. , Van Montagu , M. and Inzé , D. 1995 . Characterization of an Arabidopsis thaliana cDNA homologue to animal poly(ADP-ribose) polymerase . FEBS Lett. , 364 : 103 – 108 .
  • Liang , D. , Zhou , H. , Chen , Y.-P. , Chen , X. , Chen , C.-L. and Qu , L.-H. 2002 . A novel gene organisation: intronic snoRNA gene clusters from Oryza sativa . Nucl. Acids Res , 30 : 3262 – 3272 .
  • Li , C. F. , Henderson , I. R. , Song , L. , Fedoroff , N. , Lagrange , T. and Jacobsen , S. E. 2008 . Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana . PloS. Genet , 4 : e27 doi:101371/journal.pgen.0040027
  • Li , C. F. , Pontes , O. , El-Shami , M. , Henderson , I. R. , Bernatavichute , Y. V. , Chan , S. W.-L. , Lagrange , T. , Pikaard , C. S. and Jacobsen , S. E. 2006 . An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana . Cell , 126 : 93 – 106 .
  • Lippman , Z. , May , B. , Yordan , C. , Singer , T. and Martienssen , R. 2003 . Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification . PloS Biol , 1 : e67 doi:10.1371/journal.pbio.0000067
  • Liu , J.-L. , Hebert , M. D. , Ye , Y. , Templeton , D. J. , Kung , H.-J. and Matera , A. G. 2000 . Cell cycle-dependent localization of the CDK2-cyclin E complex in Cajal (coiled) bodies . J. Cell Sci. , 113 : 1543 – 1552 .
  • Lukowiak , A. A. , Narayanan , A. , Li , Z. H. , Terns , R. M. and Terns , M. P. 2001 . The snoRNA domain of vertebrate telomerase RNA functions to localize the RNA within the nucleus . RNA , 7 : 1833 – 1844 .
  • Luo , Z. and Chen , Z. 2007 . Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-mediated RNA silencing in Arabidopsis . Plant Cell , 19 : 943 – 958 .
  • Lyon , C. E. , Bohmann , K. , Sleeman , J. and Lamond , A. I. 1997 . Inhibition of protein dephosphorylation results in the accumulation of splicing snRNPs and coiled bodies within the nucleolus . Exp. Cell Res. , 230 : 84 – 93 .
  • Maceluch , J. , Kmieciak , M. , Szweykowska-Kuliska , Z. and Jarmolowski , A. 2001 . Cloning and characterization of Arabidopsis thaliana AtNAP57— a homologue of yeast pseudouridine synthase Cbf5p . Acta Giochim. Polonica , 48 : 699 – 709 .
  • Makarova , O. V. , Makarov , E. M. , Liu , S. , Vornlocher , H. P. and Luhrmann , R. 2002 . Protein 61K, encoded by a gene (PRPF31) linked to autosomal dominant retinitis pigmentosa, is required for U4/U6·U5 tri-snRNP formation and pre-mRNA splicing . EMBO J , 21 : 1148 – 1157 .
  • Marker , C. , Zemann , A. , Terhorst , T. , Kiefmann , M. , Kastenmayer , J. P. , Green , P. , Bachellerie , J. P. , Brosius , J. and Huttenhofer , A. 2002 . Experimental RNomics: Identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana . Curr. Biol , 12 : 2002 – 2013 .
  • Massenet , S. , Pellizzoni , L. , Paushkin , S. , Mattaj , I. W. and Dreyfuss , G. 2002 . The SMN complex is associated with snRNPs throughout their cytoplasmic assembly pathway . Mol. Cell Biol. , 22 : 6533 – 6541 .
  • Matera , A. G. 1999 . Nuclear bodies: multifaceted subdomains of the interchromatin space . Trends Cell Biol. , 9 : 302 – 309 .
  • Maul , G. G. 1998 . Nuclear domain 10, the site of DNA virus transcription and replication . Bioassays , 20 : 660 – 667 .
  • Maul , G. G. , Negorev , D. , Bell , P. and Ishov , A. M. 2000 . Review: Properties and assembly mechanisms of ND10, PML bodies or PODs . J. Struct. Biol. , 129 : 278 – 287 .
  • McClintock , B. 1934 . The relationship of a particular chromosomal element to the development of the nucleoli in Zea mays . Zeitschr Zellf. Mikr. Anat , 21 : 294 – 328 .
  • Monneron , A. and Bernhard , W. 1969 . Fine structural organization of the interphase nucleus in some mammalian cells . J. Ultrastruct. Res. , 27 : 266 – 288 .
  • Murphy , C. , Wang , Z. , Roeder , R. G. and Gall , J. G. 2002 . RNA polymerase III in Cajal bodies and lampbrush chromosomes of the Xenopus oocyte nucleus . Mol. Biol. Cell , 13 : 3466 – 3476 .
  • Nizami , Z. , Derysheva , S. and Gall , J. G. 2010 . The Cajal body and histone locus body . Cold Spring Harb. Perspect. Biol. , 2 : a0000653
  • Nottrott , S. , Urlaub , H. and Luhrmann , R. 2002 . Hierarchical, clustered protein interactions with U4/U6 snRNA: a biochemical role for U4/U6 proteins . EMBO J , 21 : 5527 – 5538 .
  • Onodera , Y. , Haag , J. R. , Ream , T. , Nunes , P. C. , Pontes , O. and Pikaard , C. S. 2005 . Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation . Cell , 120 : 613 – 622 .
  • Otto , H. , Reche , P. A. , Bazan , F. , Dittmar , K. , Haag , F. and Koch-Nolte , F. 2005 . In silico characterization of the family of PARP-like poly(ADP-ribosyl) transferases (pARTs) . BMC Genomics , 6 : 139 doi:10.1186/1471–2164-6–139
  • Pendle , A. F. , Clark , G. P. , Boon , R. , Lewandowska , D. , Lam , Y. W. , Andersen , J. , Mann , M. , Lamond , A. I. , Brown , J. W. and Shaw , P. J. 2005 . Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions . Mol. Biol. Cell , 16 : 260 – 269 .
  • Pikaard , C. S. , Haag , J. R. , Ream , T. and Wierzbicki , A. T. 2008 . Roles of RNA polymerase IV in gene silencing . Trends Plant Sci , 13 : 390 – 397 .
  • Platani , M. , Goldberg , I. , Swedlow , J. R. and Lamond , A. I. 2000 . In vivo analysis of Cajal body movement, separation, and joining in live human cells . J. Cell Biol. , 151 : 1561 – 1574 .
  • Platani , M. , Goldberg , I. , Swedlow , J. R. and Lamond , A. I. 2002 . Cajal body dynamics and association with chromatin are ATP-dependent . Nat. Cell Biol. , 4 : 502 – 508 .
  • Pontes , O. , Li , C. F. , Nunes , P. C. , Haag , J. , Ream , T. , Vitins , A. , Jacobsen , S. E. and Pikaard , C. S. 2006 . The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center . Cell , 126 : 79 – 92 .
  • Pontes , O. and Pikaard , C. S. 2008 . SiRNA and miRNA processing: new functions for Cajal bodies . Curr. Opin. Genet. Devel. , 18 : 197 – 203 .
  • Pontier , D. , Yahubyan , G. , Vega , D. , Bulski , A. , Saez-Vasquez , J. , Hakimi , M. A. , Lerbs-Mache , S. , Colot , V. and Lagrange , T. 2005 . Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis . Genes Dev. , 19 : 2030 – 2040 .
  • Prigge , M. J. and Wagner , D. R. 2001 . The Arabidopsis Serrae gene encodes a zinc-finger protein required for normal shoot development . Plant Cell , 13 : 1263 – 1279 .
  • Qu , L. H. , Meng , Q. , Zhou , L. and Chen , Y.-Q. 2001 . Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana . Nucl. Acids Res , 29 : 1623 – 1630 .
  • Ramon y Cajal , S . 1903 . Un sencillo metodo de coloracion seletiva del reticulo protoplasmaticoy sus efectos en los diversos organos nerviosos de vertebrados e invertebrados. [A simple method for selective coloration of the protoplasmic reticulum and its effects on the diverse nervous organs of vertebrates and invertebrates] . Trab. Lab. Invest. Biol. , 2 : 129 – 221 . (Madrid)
  • Raška , I. , Shaw , P. J. and Cmarko , D. 2006 . New insights into nucleolar architecture and activity . Internat. Rev. Cytol. , 255 : 177 – 235 .
  • Rippe , K. 2007 . Dynamic organization of the cell nucleus . Curr. Opin. Genet. Devel. , 17 : 373 – 380 .
  • Samarsky , D. A. , Fournier , M. J. , Singer , R. H. and Bertrand , E. 1998 . The snoRNA box C/D motif directs nucleolar targeting and also couples snoRNA synthesis and localization . EMBO J , 17 : 3747 – 3757 .
  • Schardin , M. , Cremer , T. , Hager , H. D. and Lang , M. 1985 . Specific staining of human chromosome position in Chinese hamster x man hybrid cell lines demonstrates interphase chromosome territories . Hum. Genet. , 71 : 281 – 287 .
  • Shaw , P. J. , Beven , A. F. , Leader , D. J. and Brown , J. W. 1998 . Localization and processing from polycistronic precursor of novel snoRNAs in maize . J. Cell Sci. , 111 : 2121 – 2128 .
  • Schaffert , N. , Hossbach , M. , Heintzmann , R. , Achsel , T. and Luhrmann , R. 2004 . RNAi knockdown of hPrp31 leads to an accumulation of U4/U6 di-snRNPs in Cajal bodies . EMBO J , 23 : 3000 – 3009 .
  • Schiebel , W. , Haas , B. , Marinkovic , S. , Klanner , A. and Sanger , H. I. 1993 . RNA-directed RNA polymerase from tomato leaves. II. Catalytic in vitro properties . J. Biol. Chem. , 268 : 11858 – 11867 .
  • Schmitz , M. L. and Herrmann , H. 2008 . Functional architecture of the cell nucleus . Biochim. Biophys. Acta , 1783 : 2041 – 2043 .
  • Schul , W. , Groenhout , B. , Koberna , K. , Takagaki , Y. , Jenny , A. , Manders , E. M. , Raška , I. , van Driel , R. and de Jong , L. 1996 . The RNA 3′ cleavage factors CstF 64 kDa and CPSF 100 kDa are concentrated in nuclear domains closely associated with coiled bodies and newly synthesized RNA . EMBO J , 15 : 2883 – 2892 .
  • Schul , W. , van Driel , R. and de Jong , L. 1998 . Coiled bodies and U2 snRNA genes adjacent to coiled bodies are enriched in factors required for snRNA transcription . Mol. Biol. Cell , 9 : 1025 – 1036 .
  • Schwartz , Y. B. and Pirrotta , V. 2007 . Polycomb silencing mechanisms and the management of genomic programmes . Nat. Rev. Genet. , 8 : 9 – 22 .
  • Shimotohno , A. , Matsubayashi , S. , Yamaguchi , M. , Uchimiya , H. and Umeda , M. 2003 . Differential phosphorylation activities of CDK-activating kinases in Arabdiopsis thaliana . FEBS Lett. , 534 : 69 – 74 .
  • Sleeman , J. , Lyon , C. E. , Platani , M. , Kreivi , J.-P. and Lamond , A. I. 1998 . Dynamic interactions between splicing snRNPs, coiled bodies and nucleoli revealed using snRNP protein fusions to the green fluorescent protein . Exp. Cell Res. , 243 : 290 – 304 .
  • Song , L. , Han , M.-H. , Lesicka , J. and Fedoroff , N. 2007 . Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body . Proc. Natl. Acad Sci USA , 104 : 5437 – 5442 .
  • Stanek , D. and Neugebauer , K. M. 2004 . Detection of snRNP assembly intermediates in Cajal bodies by fluorescence resonance energy transfer . J. Cell Biol. , 166 : 1015 – 1025 .
  • Steimer , A. , Amedeo , P. , Afsar , K. , Fransz , P. , Mittelsten-Scheid , O. and Paszkowski , J. 2000 . Endogenous targets of transcriptional gene silencing in Arabidopsis . Plant Cell , 12 : 1165 – 1178 .
  • Swift , H. 1959 . Studies on nuclear fine structure . Brookhaven Symp. Biol. , 12 : 134 – 152 .
  • Taft , R. J. , Glazov , E. A. , Lassmann , T. , Hayashizaki , Y. , Carninci , P. and Mattick , J. S. 2009 . Small RNAs derived from snoRNAs . RNA , 15 : 1233 – 1240 .
  • Tucker , K. E. , Berciano , M. T. , Jacobs , E. Y. , LePage , D. F. , Shpargel , K. B. , Rossire , J. J. , Chan , E. K. L. , Lafarga , M. , Conlon , R. A. and Matera , A. G. 2001 . Residual Cajal bodies in coilin knockout mice fail to recruit Sm snRNPs and SMN, the spinal muscular atrophy gene product . J. Cell Biol. , 154 : 293 – 308 .
  • Tucker , K. E. and Matera , A. G. 2005 . “ The Cajal body: a nuclear gathering place ” . In Vision of the Cell Nucleus , Edited by: Hemmerich , P. and Diekmann , S. 159 – 171 . CA : American Scientific, Stevenson Ranch .
  • Umeda , M. 2002 . “ CDK-activating kinases in higher plants ” . In CDK-activating Kinase (CAK) , Edited by: Kaldis , P. 55 – 64 . Georgetown , TX : Landes Bioscience .
  • Uren , A. G. , O’Rourke , K. , Aravind , L. A. , Pisabarro , M. T. , Seshagiri , S. , Koonin , E. V. and Dixit , V. M. 2000 . Identification of paracaspases and metacaspases: two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma . Mol. Cell , 6 : 961 – 967 .
  • Vaillant , I. , Schubert , I. , Tourmente , S. and Mathieu , O. 2006 . MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis . EMBO Rep , 7 : 1273 – 1278 .
  • Valentin , G. 1836 . Repertorium föur Anatomie und Physiologie , vol. 1 , Berlin : Verlag von Veitund Comp .
  • Vandepoele , K. , Raes , J. , De Veylder , L. , Rouzé , P. , Rombauts , S. and Inzé , D. 2002 . Genome-wide analysis of core cell cycle genes in Arabidopsis . Plant Cell , 14 : 903 – 916 .
  • Vercammen , D. , van de Cotte , B. , De Jaeger , G. , Eeckhout , D. , Casteels , P. , Vandepoele , K. , Vandenberghe , I. , Van Beeumen , J. , Inzé , D. and Van Breusegem , F. 2004 . Type II metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana cleave substrates after arginine and lysine . J. Biol. Chem , 279 : 45329 – 45336 .
  • Voinnet , O. 2008 . Use, tolerance and avoidance of amplified RNA silencing by plants . Trends in Plant. Sci. , 13 : 317 – 328 .
  • Wang , M. , Wu , W. , Wu , W. , Rosidi , B. , Zhang , L. , Wang , H. and Iliakis , G. 2006 . PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways . Nucl. Acids Res. , 34 : 6170 – 6182 .
  • Wassenegger , M. and Krczal , G. 2006 . Nomenclature and functions of RNA-directed RNA polymerases . Trends Plant Sci , 11 : 142 – 151 .
  • Watanabe , N. and Lam , E. 2005 . Two Arabidopsis metacaspases AtMCP1b and AtMCP2b are arginine/lysine-specific cysteine proteases and activate apoptosis-like cell death in yeast . J. Biol , 280 : 14691 – 14699 . Chem
  • Wierzbicki , A. T. , Haag , J. R. and Pikaard , C. S. 2008 . Noncoding transcription by polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes . Cell , 135 : 635 – 648 .
  • Xu , H. , Pillai , R. S. , Azzouz , T. N. , Shpargel , K. B. , Kambach , C. , Hebert , M. D. , Schumperli , D. and Matera , A. G. 2005 . The C-terminal domain of coilin interacts with Sm proteins and U snRNPs . Chromosoma , 114 : 155 – 166 .
  • Xu , M. and Cook , P. R. 2008 . The role of specialized transcription factories in chromosome pairing . Biochim. Biophys. Acta , 1783 : 2155 – 2160 .
  • Yamaguchi , M. , Fabian , T. , Sauter , M. , Bhalerao , R. P. , Schrader , J. , Sandberg , G. , Umeda , M. and Uchimiya , H. 2000 . Activation of CDK-activating kinase is dependent on interaction with H-type cyclins in plants . Plant J. , 24 : 11 – 20 .
  • Yokthongwattana , C. , Bucher , E. , Caikovski , M. , Vaillant , I. , Nicolet , J. , Mittelsten-Scheid , O. and Paszkowski , J. 2010 . MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing . EMBO J , 29 : 340 – 351 .
  • Zheng , B. , Wang , Z. , Li , S. , Yu , B. , Liu , J.-Y. and Chen , X. 2009 . Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis . Genes & Dev. , 23 : 2850 – 2860 .

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