Finnegan EJ, Matzke MA: The small RNA world. Journal of cell science. 2003, 116: 4689-4693. 10.1242/jcs.00838.
Article
PubMed
CAS
Google Scholar
Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, Moulton V, Dalmay T: High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC genomics. 2008, 9: 593-10.1186/1471-2164-9-593.
Article
PubMed
PubMed Central
Google Scholar
Jagadeeswaran G, Zheng Y, Li YF, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W, Sunkar R: Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. The New phytologist. 2009, 184: 85-98. 10.1111/j.1469-8137.2009.02915.x.
Article
PubMed
CAS
Google Scholar
Trindade I, Capitão C, Dalmay T, Fevereiro MP, Santos DMD: miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta. 2010, 231: 705-716. 10.1007/s00425-009-1078-0.
Article
PubMed
CAS
Google Scholar
Eamens A, Wang MB, Smith NA, Waterhouse PM: RNA silencing in plants: yesterday, today, and tomorrow. Plant physiology. 2008, 147: 456-468. 10.1104/pp.108.117275.
Article
PubMed
CAS
PubMed Central
Google Scholar
Farazi TA, Juranek SA, Tuschl T: The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development. 2008, 135: 1201-1214. 10.1242/dev.005629.
Article
PubMed
CAS
Google Scholar
Voinnet O: Origin, biogenesis, and activity of plant microRNAs. Cell. 2009, 136: 669-687. 10.1016/j.cell.2009.01.046.
Article
PubMed
CAS
Google Scholar
Ramachandran V, Chen X: Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science. 2008, 321: 1490-1492. 10.1126/science.1163728.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kurihara Y, Watanabe Y: Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proceedings of the National Academy of Sciences. 2004, 101: 12753-12758. 10.1073/pnas.0403115101.
Article
CAS
Google Scholar
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC: Genetic and functional diversification of small RNA pathways in plants. PLoS biology. 2004, 2: E104-10.1371/journal.pbio.0020104.
Article
PubMed
PubMed Central
Google Scholar
Yoshikawa M, Peragine A, Park MY, Poethig RS: A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes & development. 2005, 19: 2164-2175. 10.1101/gad.1352605.
Article
CAS
Google Scholar
Margis R, Fusaro AF, Smith NA, Curtin SJ, Watson JM, Finnegan EJ, Waterhouse PM: The evolution and diversification of Dicers in plants. FEBS letters. 2006, 580: 2442-2450. 10.1016/j.febslet.2006.03.072.
Article
PubMed
CAS
Google Scholar
Olmedo G, Guzman P: Processing precursors with RNase III in plants. Plant Science. 2008, 175: 741-746. 10.1016/j.plantsci.2008.07.001.
Article
CAS
Google Scholar
Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA: Structural basis for double-stranded RNA processing by Dicer. Science. 2006, 311: 195-198. 10.1126/science.1121638.
Article
PubMed
CAS
Google Scholar
Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA: Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction. RNA. 2010, 16: 474-481. 10.1261/rna.1965310.
Article
PubMed
CAS
PubMed Central
Google Scholar
Morel JB, Godon C, Mourrain P, Béclin C, Boutet S, Feuerbach F, Proux F, Vaucheret H: Fertile Hypomorphic ARGONAUTE (ago1) Mutants Impaired in Post-Transcriptional Gene Silencing and Virus Resistance. The Plant Cell. 2002, 14: 629-639. 10.1105/tpc.010358.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nonomura K, Morohoshi A, Nakano M, Eiguchi M, Miyao A, Hirochika H, Kurata N: A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. The Plant cell. 2007, 19: 2583-2594. 10.1105/tpc.107.053199.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kapoor M, Arora R, Lama T, Nijhawan A, Khurana JP, Tyagi AK, Kapoor S: Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC genomics. 2008, 9: 451-10.1186/1471-2164-9-451.
Article
PubMed
PubMed Central
Google Scholar
Baumberger N, Baulcombe DC: Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proceedings of the National Academy of Sciences. 2005, 102: 11928-11933. 10.1073/pnas.0505461102.
Article
CAS
Google Scholar
Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O: Widespread translational inhibition by plant miRNAs and siRNAs. Science. 2008, 320: 1185-1190. 10.1126/science.1159151.
Article
PubMed
CAS
Google Scholar
Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, Dunn RM, Schwach F, Doonan JH, Baulcombe DC: The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. The Plant cell. 2010, 22: 321-334. 10.1105/tpc.109.072199.
Article
PubMed
CAS
PubMed Central
Google Scholar
Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC: Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell. 2008, 133: 128-141. 10.1016/j.cell.2008.02.033.
Article
PubMed
CAS
Google Scholar
Jinek M, Doudna JA: A three-dimensional view of the molecular machinery of RNA interference. Nature. 2009, 457: 405-412. 10.1038/nature07755.
Article
PubMed
CAS
Google Scholar
Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ, Joshua-Tor L: Purified Argonaute2 and an siRNA form recombinant human RISC. Nature structural & molecular biology. 2005, 12: 340-349. 10.1038/nsmb918.
Article
CAS
Google Scholar
Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ: Structure of the guide-strand-containing argonaute silencing complex. Nature. 2008, 456: 209-213. 10.1038/nature07315.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y: Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 2008, 133: 116-127. 10.1016/j.cell.2008.02.034.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xie Z, Kasschau KD, Carrington JC: Negative Feedback Regulation of Dicer-Like1 in Arabidopsis by microRNA-Guided mRNA Degradation. Current Biology. 2003, 13: 784-789. 10.1016/S0960-9822(03)00281-1.
Article
PubMed
CAS
Google Scholar
Vaucheret H, Vazquez F, Crété P, Bartel DP: The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes & development. 2004, 18: 1187-1197. 10.1101/gad.1201404.
Article
CAS
Google Scholar
Rose RJ: Medicago truncatula as a model for understanding plant interactions with other organisms, plant development and stress biology: past, present and future. The Plant Cell. 2008, 253-264.
Google Scholar
Medicago truncatula Sequencing Resources. [http://www.medicago.org/genome]
Zhou ZS, Huang SQ, Yang ZM: Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula. Biochemical and biophysical research communications. 2008, 374: 538-542. 10.1016/j.bbrc.2008.07.083.
Article
PubMed
CAS
Google Scholar
Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M: Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. The Plant cell. 2009, 21: 2780-2796. 10.1105/tpc.109.068130.
Article
PubMed
PubMed Central
Google Scholar
Araújo SDS, Duque As, Dulce Maria Santos DM, Fevereiro MP: An efficient transformation method to regenerate a high number of transgenic plants using a new embryogenic line of Medicago truncatula cv. Jemalong. Plant cell, tissue and organ culture. 2004, 78: 123-131.
Article
Google Scholar
Nunes C, Araújo SDS, Silva JM, Fevereiro MPS, Silva AB: Physiological responses of the legume model Medicago truncatula cv. Jemalong to water deficit. Environmental and Experimental Botany. 2008, 63: 289-296. 10.1016/j.envexpbot.2007.11.004.
Article
CAS
Google Scholar
National Center for Biotechnology Information. [http://www.ncbi.nlm.nih.gov]
Basic Local Alignment Search Tool. [http://blast.ncbi.nlm.nih.gov/Blast.cgi]
Medicago truncatula Sequencing Resources - blast and search. [http://www.medicago.org/genome/blast.php]
Salamov AA, Solovyev VV: Ab initio gene finding in Drosophila genomic DNA. Genome Research. 2000, 10: 516-522. 10.1101/gr.10.4.516.
Article
PubMed
CAS
PubMed Central
Google Scholar
Medicago GBrowse. [http://gbrowse.jcvi.org/cgi-bin/gbrowse/medicago_imgag/]
ExPASy Proteomics Server. [http://www.expasy.ch]
Stothard P: The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques. 2000, 28: 1102-1104.
PubMed
CAS
Google Scholar
Sequence Manipulation Suite: Version 2. [http://www.bioinformatics.org/sms2]
Marchler-Bauer A, Bryant SH: CD-Search: protein domain annotations on the fly. Nucleic acids research. 2004, 32: W327-W331. 10.1093/nar/gkh454.
Article
PubMed
CAS
PubMed Central
Google Scholar
Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH: CDD: specific functional annotation with the Conserved Domain Database. Nucleic acids research. 2009, 37: D205-D210. 10.1093/nar/gkn845.
Article
PubMed
CAS
PubMed Central
Google Scholar
Search for Conserved Domains within a protein sequence. [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi]
Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of molecular biology. 2000, 302: 205-217. 10.1006/jmbi.2000.4042.
Article
PubMed
CAS
Google Scholar
Poirot O: Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Research. 2003, 31: 3503-3506. 10.1093/nar/gkg522.
Article
PubMed
CAS
PubMed Central
Google Scholar
T-Coffee. [http://www.ebi.ac.uk/Tools/t-coffee]
Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular biology and evolution. 2007, 24: 1596-1599. 10.1093/molbev/msm092.
Article
PubMed
CAS
Google Scholar
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome biology. 2002, 3: RESEARCH0034-
Article
PubMed
PubMed Central
Google Scholar
Andersen CL, Jensen JL, Ørntoft TF: Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer research. 2004, 64: 5245-5250. 10.1158/0008-5472.CAN-04-0496.
Article
PubMed
CAS
Google Scholar
Zhao S, Fernald RD: Comprehensive algorithm for quantitative real-time polymerase chain reaction. Journal of computational biology. 2005, 12: 1047-1064. 10.1089/cmb.2005.12.1047.
Article
PubMed
CAS
PubMed Central
Google Scholar
Real-time PCR Miner. [http://www.ewindup.info/miner/version2]
Pfaffl MW: A new mathematical model for relative quantification in real-time RT-PCR. Nucleic acids research. 2001, 29: 2002-2007.
Article
Google Scholar
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT: The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry. 2009, 55: 611-622. 10.1373/clinchem.2008.112797.
Article
PubMed
CAS
Google Scholar
Vaucheret H: Plant ARGONAUTES. Trends in plant science. 2008, 13: 350-358. 10.1016/j.tplants.2008.04.007.
Article
PubMed
CAS
Google Scholar
Cerutti L, Mian N, Bateman A: Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. Trends in Biochemical Sciences. 2000, 10: 481-482.
Article
Google Scholar
Song J-J, Smith SK, Hannon GJ, Joshua-Tor L: Crystal structure of Argonaute and its implications for RISC slicer activity. Science. 2004, 305: 1434-1437. 10.1126/science.1102514.
Article
PubMed
CAS
Google Scholar
Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ: Argonaute2 is the catalytic engine of mammalian RNAi. Science. 2004, 305: 1437-1441. 10.1126/science.1102513.
Article
PubMed
CAS
Google Scholar
Vazquez F, Blevins T, Ailhas J, Boller T, Meins F: Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic acids research. 2008, 36: 6429-6438. 10.1093/nar/gkn670.
Article
PubMed
CAS
PubMed Central
Google Scholar
Qi Y, Denli AM, Hannon GJ: Biochemical specialization within Arabidopsis RNA silencing pathways. Molecular cell. 2005, 19: 421-428. 10.1016/j.molcel.2005.06.014.
Article
PubMed
CAS
Google Scholar
Qi Y, He X, Wang XJ, Kohany O, Jurka J, Hannon GJ: Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature. 2006, 443: 1008-1012. 10.1038/nature05198.
Article
PubMed
Google Scholar
Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T: Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Molecular cell. 2004, 15: 185-197. 10.1016/j.molcel.2004.07.007.
Article
PubMed
CAS
Google Scholar
Saito K, Nishida KM, Mori T, Kawamura Y, Miyoshi K, Nagami T, Siomi H, Siomi MC: Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes & development. 2006, 20: 2214-2222. 10.1101/gad.1454806.
Article
CAS
Google Scholar
Vaucheret H, Mallory AC, Bartel DP: AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Molecular cell. 2006, 22: 129-136. 10.1016/j.molcel.2006.03.011.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mallory AC, Vaucheret H: ARGONAUTE 1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways. EMBO reports. 2009, 10: 521-526. 10.1038/embor.2009.32.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mallory AC, Hinze A, Tucker MR, Bouché N, Gasciolli V, Elmayan T, Lauressergues D, Jauvion V, Vaucheret H, Laux T: Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing. PLoS genetics. 2009, 5: e1000646-10.1371/journal.pgen.1000646.
Article
PubMed
PubMed Central
Google Scholar
Allen E, Xie Z, Gustafson AM, Carrington JC: microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants. Cell. 2005, 121: 207-221. 10.1016/j.cell.2005.04.004.
Article
PubMed
CAS
Google Scholar
Hunter C, Sun H, Poethig RS: The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Current Biology. 2003, 13: 1734-1739. 10.1016/j.cub.2003.09.004.
Article
PubMed
CAS
Google Scholar
Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC: Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Current biology. 2006, 16: 939-944. 10.1016/j.cub.2006.03.065.
Article
PubMed
CAS
Google Scholar
Herra J, Jensen MB, Dalmay T, Baulcombe DC: RNA polymerase IV directs silencing of endogenous DNA. Science. 2005, 308: 118-120. 10.1126/science.1106910.
Article
Google Scholar
Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T: Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes & development. 2005, 19: 2030-2040. 10.1101/gad.348405.
Article
CAS
Google Scholar
Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE: RNA silencing genes control de novo DNA methylation. Science. 2004, 303: 1336-10.1126/science.1095989.
Article
PubMed
CAS
Google Scholar
Zilberman D: ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation. Science. 2009, 716-719.
Google Scholar
Zheng X, Zhu J, Kapoor A, Zhu J-kang: Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO Journal. 2007, 26: 1691-1701. 10.1038/sj.emboj.7601603.
Article
PubMed
CAS
PubMed Central
Google Scholar