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References

  • Achard P, Herr A, Baulcombe DC, Harberd NP. 2004. Modulation of floral development by a gibberellin-regulated microRNA. Development 131: 33573365.
  • Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V. 2005. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Research 15: 7891.
  • Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC. 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics 36: 12821290.
  • Allen E, Xie Z, Gustafson AM, Carrington JC. 2005. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207221.
  • Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. 2003. A uniform system for microRNA annotation. Rna 9: 277279.
  • Arazi T, Talmor-Neiman M, Stav R, Riese M, Huijser P, Baulcombe DC. 2005. Cloning and characterization of micro-RNAs from moss. Plant Journal 43: 837848.
  • Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S. 2001. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology 11: 941950.
  • Aufsatz W, Mette MF, Van Der Winden J, Matzke M, Matzke AJ. 2002. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO Journal 21: 68326841.
  • Aukerman MJ, Sakai H. 2003. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15: 27302741.
  • Axtell MJ, Bartel DP. 2005. Antiquity of microRNAs and their targets in land plants. Plant Cell 17: 16581673.
  • Baker CC, Sieber P, Wellmer F, Meyerowitz EM. 2005. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Current Biology 15: 303315.
  • Bao N, Lye KW, Barton MK. 2004. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Developmental Cell 7: 653662.
  • Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281297.
  • Bartel DP, Chen CZ. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Review of Genetics 5: 396400.
  • Baulcombe D. 2004. RNA silencing in plants. Nature 431: 356363.
  • Baulcombe D. 2005. RNA silencing. Trends in Biochemistry and Science 30: 290293.
  • Baumberger N, Baulcombe DC. 2005. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proceedings of the National Academy of Sciences of the USA 102: 1192811933.
  • Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA. 2005. Sorghum genome sequencing by methylation filtration. PLoS Biology 3: e13.
  • Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nature Genetics 37: 766770.
  • Bernstein E, Caudy AA, Hammond SM, Hannon GJ. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363366.
  • Billoud B, De Paepe R, Baulcombe D, Boccara M. 2005. Identification of new small non-coding RNAs from tobacco and Arabidopsis. Biochimie 87: 905910.
  • Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Benning C. 1998. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO Journal 1998: 17 (1): 170–180.
  • Bollman KM, Aukerman MJ, Park MY, Hunter C, Berardini TZ, Poethig RS. 2003. HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 130: 14931504.
  • Bonnet E, Wuyts J, Rouzé P, Van de Peer Y. 2004a. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proceedings of the National Academy of Sciences, USA 101: 1151111516.
  • Bonnet E, Wuyts J, Rouzé P, Van de Peer Y. 2004b. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20: 29112917.
  • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. 2005. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123: 12791291.
  • Boutet S, Vazquez F, Liu J, Béclin C, Fagard M, Gratias A, Morel JB, Crété P, Chen X, Vaucheret H. 2003. Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Current Biology 13: 843848.
  • Britten RJ, Davidson EH. 1969. Gene regulation for higher cells: a theory. Science 165: 349357.
  • Carmell MA, Xuan Z, Zhang MQ, Hannon GJ. 2002. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes and Development 16: 27332742.
  • Carrington JC. 2005. Small RNAs and Arabidopsis. A fast forward look. Plant Physiology 138: 565566.
  • Chapman EJ, Prokhnevsky AI, Gopinath K, Dolja VV, Carrington JC. 2004. Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes and Development 18: 11791186.
  • Chen X. 2004. A MicroRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 20222025.
  • Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL. 2005. Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. Plant Cell 18: 412421.
  • Clote P, Ferrè F, Kranakis E, Krizanc D. 2005. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11: 578591.
  • Cogoni C, Irelan JT, Schumacher M, Schmidhauser TJ, Selker EU, Macino G. 1996. Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA–DNA interactions or DNA methylation. EMBO Journal 15: 31533163.
  • Couzin J. 2002. Breakthrough of the year. Small RNAs make big splash. Science 298: 22962297.
  • Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC. 2000. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543553.
  • Dharmasiri N, Dharmasiri S, Estelle M. 2005. The F-box protein TIR1 is an auxin receptor. Nature 435: 441445.
  • Dunoyer P, Voinnet O. 2005. The complex interplay between plant viruses and host RNA-silencing pathways. Current Opinions in Plant Biology 8: 415423.
  • Dunoyer P, Lecellier CH, Parizotto EA, Himber C, Voinnet O. 2004. Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell 16: 12351250.
  • Dunoyer P, Himber C, Voinnet O. 2005. DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genetics 37: 13561360.
  • Dunoyer P, Himber C, Voinnet O. 2006. Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens infections. Nat Genetics 38: 258263.
  • Eddy SR. 2001. Non-coding RNA genes and the modern RNA world. Nature Review of Genetics 2: 919929.
  • Elbashir SM, Harborth J, Weber K, Tuschl T. 2002. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26: 199213.
  • Emery JF, Floyd SK, Alvarez J, Eshed Y, Hawker NP, Izhaki A, Baum SF, Bowman JL. 2003. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Current Biology 13: 17681774.
  • Fagard M, Boutet S, Morel JB, Bellini C, Vaucheret H. 2000. 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. Proceedings of the National Academy of Sciences, USA 97: 1165011654.
  • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806811.
  • Floyd SK, Bowman JL. 2004. Gene regulation: ancient microRNA target sequences in plants. Nature 428: 485486.
  • Friis EM, Pedersen KR, Crane PR. 2004. Araceae from the early Cretaceous of Portugal: evidence on the emergence of monocotyledons. Proceedings of the National Academy of Sciences, USA 101: 1656516570.
  • Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK. 2005. A miRNA involved in phosphate-starvation response in Arabidopsis. Current Biology 15: 20382043.
  • Gasciolli V, Mallory AC, Bartel DP, Vaucheret H. 2005. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Current Biology 15: 14941500.
  • Gendrel AV, Colot V. 2005. Arabidopsis epigenetics: when RNA meets chromatin. Current Opinions in Plant Biology 8: 142147.
  • Gesteland RF, Cech TR, Atkins JF. 1999. The RNA world. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press.
  • Gilbert W. 1986. The RNA world. Nature 319: 618.
  • Griffiths-Jones S, Grocock RJ, Van Dongen S, Bateman A, Enright AJ. 2006. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Research 34: D140D144.
  • Guo S, Kemphues KJ. 1995. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Series/Thr kinase that is asymmetrically distributed. Cell 81: 611620.
  • Guo HS, Xie Q, Fei JF, Chua NH. 2005. MicroRNA Directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17: 13761386.
  • Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD. 2005. ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Research 33 (Database issue): D637640.
  • Hamilton AJ, Baulcombe DC. 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286: 950952.
  • Hamilton A, Voinnet O, Chappell L, Baulcombe D. 2002. Two classes of short interfering RNA in RNA silencing. EMBO Journal 21: 46714679.
  • Hammond SM, Bernstein E, Beach D, Hannon GJ. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404: 293296.
  • Han MH, Goud S, Song L, Fedoroff N. 2004. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proceedings of the National Academy of Sciences, USA 101: 10931098.
  • Hannon GJ. 2002. RNA interference. Nature 418: 244251.
  • Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. 2005. RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118120.
  • Hiraguri A, Itoh R, Kondo N, Nomura Y, Aizawa D, Murai Y, Koiwa H, Seki M, Shinozaki K, Fukuhara T. 2005. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Molecular Biology 57: 173188.
  • Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. 1994. Fast Folding and Comparison of RNA Secondary Structures. Monatshefte fur Chemie 125: 167188.
  • Huttenhofer A, Kiefmann M, Meier-Ewert S, O’Brien J, Lehrach H, Bachellerie JP, Brosius J. 2001. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO Journal 20: 29432953.
  • Jackson JP, Lindroth AM, Cao X, Jacobsen SE. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556560.
  • Jacob F, Monod J. 1961. Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3: 318356.
  • Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular Cell 14: 787799.
  • Jones-Rhoades MW, Bartel DP, Bartel B. 2006. MicroRNAs and Their Regulatory Roles in Plants. Annual Review of Plant Biology 57: 1953.
  • Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC. 2004. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428: 8488.
  • Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJ. 2005. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genetics 37: 761765.
  • Kasschau KD, Xie Z, Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC. 2003. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Developmental Cell 4: 205217.
  • Kepinski S, Leyser O. 2005. The Arabidopsis F-box protein TIR1 is an Auxin receptor. Nature 435: 446451.
  • Kidner CA, Martienssen RA. 2004. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428: 8184.
  • Kidner CA, Martienssen RA. 2005. The developmental role of microRNA in plants. Current Opinions in Plant Biology 8: 3844.
  • Kim J, Jung JH, Reyes JL, Kim YS, Kim SY, Chung KS, Kim JA, Lee M, Lee Y, Narry Kim V, Chua NH, Park CM. 2005. microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant Journal 42: 8494.
  • Van Der Krol AR, Mur LA, Beld M, Mol JN, Stuitje AR. 1990. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2: 291299.
  • Kurihara Y, Takashi Y, Watanabe Y. 2006. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. Rna 12: 206212.
  • Kurihara Y, Watanabe Y. 2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proceedings of the National Academy of Sciences, USA 101: 1275312758.
  • Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294: 853858.
  • Lakatos L, Szittya G, Silhavy D, Burgyan J. 2004. Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses. EMBO Journal 23: 876884.
  • Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858862.
  • Laufs P, Peaucelle A, Morin H, Traas J. 2004. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131: 43114322.
  • Lauter N, Kampani A, Carlson S, Goebel M, Moose SP. 2005. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proceedings of the National Academy of Sciences, USA 102: 94129417.
  • Lee RC, Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862864.
  • Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843854.
  • Lee R, Feinbaum R, Ambros V. 2004a. A short history of a short RNA. Cell 116: S8992. following S96.
  • Li H, Xu L, Wang H, Yuan Z, Cao X, Yang Z, Zhang D, Xu Y, Huang H. 2005. The putative RNA-dependent RNA polymerase RDR6 acts synergistically with ASYMMETRIC LEAVES1 and 2 to repress BREVIPEDICELLUS and MicroRNA165/166 in Arabidopsis leaf development. Plant Cell 17: 21572171.
  • Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. 2003. Vertebrate microRNA genes. Science 299: 1540.
  • Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769773.
  • Lippman Z, Martienssen R. 2004. The role of RNA interference in heterochromatic silencing. Nature 431: 364370.
  • Lippman Z, May B, Yordan C, Singer T, Martienssen R. 2003. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PloS Biology 1: E67.
  • Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 14371441.
  • Llave C, Kasschau KD, Rector MA, Carrington JC. 2002a. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14: 16051619.
  • Llave C, Xie Z, Kasschau KD, Carrington JC. 2002b. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 20532056.
  • Lu C, Fedoroff N. 2000. A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, Auxin, and cytokinin. Plant Cell 12: 23512366.
  • Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. 2005a. Elucidation of the small RNA component of the transcriptome. Science 309: 15671569.
  • Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL. 2005b. Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17: 21862203.
  • Mallory AC, Reinhart BJ, Bartel D, Vance VB, Bowman LH. 2002. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco. Proceedings of the National Academy of Sciences, USA 99: 1522815233.
  • Mallory AC, Dugas DV, Bartel DP, Bartel B. 2004a. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Current Biology 14: 10351046.
  • Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP. 2004b. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO Journal 23: 33563364.
  • Mallory AC, Bartel DP, Bartel B. 2005. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17: 13601375.
  • Mayer AM, Staples RC. 2002. Laccase: new functions for an old enzyme. Phytochemistry 60: 551565.
  • McHale NA, Koning RE. 2004. MicroRNA-directed cleavage of Nicotiana sylvestris PHAVOLUTA mRNA regulates the vascular cambium and structure of apical meristems. Plant Cell 16: 17301740.
  • Mette MF, Van Der Winden J, Matzke M, Matzke AJ. 2002. Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiology 130: 69.
  • Millar AA, Gubler F. 2005. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are MicroRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17: 705721.
  • Montgomery MK, Xu S, Fire A. 1998. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proceedings of the National Academy of Sciences, USA 95: 1550215507.
  • Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, Feuerbach F, Proux F, Vaucheret H. 2002. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 14: 629639.
  • Mourrain P, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA, Vaucheret H. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533542.
  • Napier RM. 2005. TIRs of joy: new receptors for auxin. Bioessays 27: 12131217.
  • Napoli C, Lemieux C, Jorgensen R. 1990. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2: 279289.
  • Nykanen A, Haley B, Zamore PD. 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107: 309321.
  • Olivas WM, Muhlrad D, Parker R. 1997. Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. Nucleic Acids Research 25: 46194625.
  • Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS. 2005. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120: 613622.
  • Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. 2003. Control of leaf morphogenesis by microRNAs. Nature 425: 257263.
  • Palauqui JC, Elmayan T, Pollien JM, Vaucheret H. 1997. Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO Journal 16: 47384745.
  • Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, Van Der Winden J, Matzke M, Matzke AJ. 2003. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiology 132: 13821390.
  • Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O. 2004. In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes and Development 18: 22372242.
  • Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS. 2005. Nuclear processing and export of microRNAs in Arabidopsis. Proceedings of the National Academy of Sciences of the USA 102: 36913696.
  • Park W, Li J, Song R, Messing J, Chen X. 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology 12: 14841495.
  • Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 8689.
  • Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes and Development 18: 23682379.
  • Pham JW, Pellino JL, Lee YS, Carthew RW, Sontheimer EJ. 2004. A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117: 8394.
  • Plasterk RH. 2002. RNA silencing: the genome's immune system. Science 296: 12631265.
  • Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, 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 and Development 19: 20302040.
  • Ranocha P, Chabannes M, Chamayou S, Danoun S, Jauneau A, Boudet AM, Goffner D. 2002. Laccase down-regulation causes alterations in phenolic metabolism and cell wall structure in poplar. Plant Physiology 129: 145155.
  • Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901906.
  • Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. 2002. MicroRNAs in plants. Genes and Development 16: 16161626.
  • Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. 2002. Prediction of plant microRNA targets. Cell 110: 513520.
  • Rivas E, Klein RJ, Jones TA, Eddy SR. 2001. Computational identification of noncoding RNAs in E. coli by comparative genomics. Current Biology 11: 13691373.
  • Ruvkun G, Wightman B, Ha I. 2004. The 20 years it took to recognize the importance of tiny RNAs. Cell 116: S936. following S96.
  • Schauer SE, Jacobsen SE, Meinke DW, Ray A. 2002. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends in Plant Science 7: 487491.
  • Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D. 2005. Specific effects of microRNAs on the plant transcriptome. Developmental Cell 8: 517527.
  • Schwarz DS, Du Hutvágner GT, Xu Z, Aronin N, Zamore PD. 2003. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199208.
  • Simon-Mateo C, Garcia JA. 2006. MicroRNA-guided processing impairs Plum pox virus replication, but the virus readily evolves to escape this silencing mechanism. Journal of Virology 80: 24292436.
  • Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G. 2000. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Molecular Cell 5: 659669.
  • Smith CJ, Watson CF, Bird CR, Ray J, Schuch W, Grierson D. 1990. Expression of a truncated tomato polygalacturonase gene inhibits expression of the endogenous gene in transgenic plants. Molecular General Genetics 224: 477481.
  • Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 14341437.
  • Soutschek J, Akinc A, Bramlage B, Charisse K, Constien R, Donoghue M, Elbashir S, Geick A, Hadwiger P, Harborth J, John M, Kesavan V, Lavine G, Pandey RK, Racie T, Rajeev KG, Rohl I, Toudjarska I, Wang G, Wuschko S, Bumcrot D, Koteliansky V, Limmer S, Manoharan M, Vornlocher HP. 2004. Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature 432: 173178.
  • Sunkar R, Zhu JK. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 20012019.
  • Sunkar R, Girke T, Jain PK, Zhu JK. 2005. Cloning and characterization of MicroRNAs from rice. Plant Cell 17: 13971411.
  • Tang G, Reinhart BJ, Bartel DP, Zamore PD. 2003. A biochemical framework for RNA silencing in plants. Genes and Development 17: 4963.
  • Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD. 2004. A protein sensor for siRNA asymmetry. Science 306: 13771380.
  • Tuskan GA, DiFazio SP, Teichmann T. 2004. Poplar genomics is getting popular: the impact of the poplar genome project on tree research. Plant Biology (Stuttgart) 6: 24.
  • Vaucheret H. 2005. MicroRNA-dependent trans-acting siRNA production. Sci STKE 2005: pe43.
  • Vaucheret H, Vazquez F, Crété P, Bartel DP. 2004. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes and Development 18: 11871197.
  • Vaughn MW, Martienssen RA. 2005. Finding the right template: RNA Pol IV, a plant-specific RNA polymerase. Molecular Cell 17: 754756.
  • Vazquez F, Gasciolli V, Crété P, Vaucheret H. 2004a. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Current Biology 14: 346351.
  • Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crété P. 2004b. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Molecular Cell 16: 6979.
  • Voinnet O. 2004. Shaping small RNAs in plants by gene duplication. Nature Genetics 36: 12451246.
  • Voinnet O. 2005. Non-cell autonomous RNA silencing. FEBS Letters 579: 58585871.
  • Voinnet O, Baulcombe DC. 1997. Systemic signalling in gene silencing. Nature 389: 553.
  • Voinnet O, Pinto YM, Baulcombe DC. 1999. Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proceedings of the National Academy of Sciences, USA 96: 1414714152.
  • Wang MB, Bian XY, Wu LM, Liu LX, Smith NA, Isenegger D, Wu RM, Masuta C, Vance VB, Watson JM, Rezaian A, Dennis ES, Waterhouse PM. 2004b. On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proceedings of the National Academy of Sciences, USA 101: 32753280.
  • Wang XJ, Reyes JL, Chua NH, Gaasterland T. 2004a. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biology 5: R65.
  • Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY. 2005. Control of root cap formation by MicroRNA-targeted Auxin response factors in Arabidopsis. Plant Cell 2005: 17 (8): 2204–2216.
  • Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes and Development 15: 16371651.
  • Wassenegger M, Heimes S, Riedel L, Sanger HL. 1994. RNA-directed de novo methylation of genomic sequences in plants. Cell 76: 567576.
  • Wightman B, Ha I, Ruvkun G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855862.
  • Williams L, Carles CC, Osmont KS, Fletcher JC. 2005a. A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proceedings of the National Academy of Sciences, USA 102: 97039708.
  • Williams L, Grigg SP, Xie M, Christensen S, Fletcher JC. 2005b. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development 132: 36573668.
  • Woodward AW, Bartel B. 2005. A receptor for auxin. Plant Cell 17: 24252429.
  • Wu-Scharf D, Jeong B, Zhang C, Cerutti H. 2000. Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-box RNA helicase. Science 290: 11591162.
  • Xie Z, Fan B, Chen C, Chen Z. 2001. An important role of an inducible RNA-dependent RNA polymerase in plant antiviral defense. Proceedings of the National Academy of Sciences, USA 98: 65166521.
  • Xie Z, Kasschau KD, Carrington JC. 2003. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Current Biology 13: 784789.
  • Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PloS Biology 2: E104.
  • Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. 2005a. Expression of Arabidopsis MIRNA genes. Plant Physiology 138: 21452154.
  • Xie Z, Allen E, Wilken A, Carrington JC. 2005b. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 102: 1298412989.
  • Ye K, Malinina L, Patel DJ. 2003. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426: 874878.
  • Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X. 2005. Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932935.
  • Yoo BC, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, Lee YM, Lough TJ, Lucas WJ. 2004. A systemic small RNA signaling system in plants. Plant Cell 16: 19792000.
  • Yoshikawa M, Peragine A, Park MY, Poethig RS. 2005. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes and Development 19: 21642175.
  • Zamore PD. 2002. Ancient pathways programmed by small RNAs. Science 296: 12651269.
  • Zhong R, Ye ZH. 2004. Amphivasal vascular bundle 1, a gain-of-function mutation of the IFL1/REV gene, is associated with alterations in the polarity of leaves, stems and carpels. Plant Cell Physiology 45: 369385.
  • Zilberman D, Cao X, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299: 716719.
  • Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology 14: 12141220.
  • Zuker M, Stiegler P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9: 133148.