Identification of RNA silencing components in soybean and sorghum

[1]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[2]  Yongchao Dou,et al.  Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis , 2012, Proceedings of the National Academy of Sciences.

[3]  Lijia Ma,et al.  Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. , 2012, The Plant journal : for cell and molecular biology.

[4]  S. Machida,et al.  Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE , 2011, Nucleic acids research.

[5]  Hongliang Zhu,et al.  Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development , 2011, Cell.

[6]  Yexiong Qian,et al.  Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize , 2011, Plant Cell Reports.

[7]  Xuemei Chen,et al.  ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two MicroRNAs in Arabidopsis , 2011, PLoS genetics.

[8]  S. Chen,et al.  Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing , 2011 .

[9]  O. Yu,et al.  Misexpression of miR482, miR1512, and miR1515 Increases Soybean Nodulation1[W][OA] , 2010, Plant Physiology.

[10]  N. Chua,et al.  Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. , 2010, Structure.

[11]  J. Zhai,et al.  siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis , 2010, Nucleic acids research.

[12]  Jianxing Song,et al.  Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction. , 2010, RNA.

[13]  Thomas J. Hardcastle,et al.  The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci[W][OA] , 2010, Plant Cell.

[14]  Bin Yu,et al.  Translational inhibition by microRNAs in plants. , 2010, Progress in molecular and subcellular biology.

[15]  Xuemei Chen,et al.  RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana , 2009, Proceedings of the National Academy of Sciences.

[16]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[17]  Hong Ma,et al.  Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups. , 2009, Gene.

[18]  Qixing Huang,et al.  Structural insights into mechanisms of the small RNA methyltransferase HEN1 , 2009, Nature.

[19]  Xuemei Chen,et al.  Small RNAs and their roles in plant development. , 2009, Annual review of cell and developmental biology.

[20]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[21]  C. Pikaard,et al.  RNA Polymerase V transcription guides ARGONAUTE4 to chromatin , 2009, Nature Genetics.

[22]  Christopher J. Hale,et al.  RNA Polymerase IV Functions in Paramutation in Zea mays , 2009, Science.

[23]  L. Paša-Tolić,et al.  Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. , 2009, Molecular cell.

[24]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[25]  Alexandra M. E. Jones,et al.  An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II , 2009, Nature Structural &Molecular Biology.

[26]  C. Pikaard,et al.  Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes , 2008, Cell.

[27]  Jitendra P Khurana,et al.  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 , 2008, BMC Genomics.

[28]  Xuemei Chen,et al.  The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis , 2008, Proceedings of the National Academy of Sciences.

[29]  James C. Carrington,et al.  Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation , 2008, Cell.

[30]  D. Baulcombe,et al.  PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis , 2008, Proceedings of the National Academy of Sciences.

[31]  H. Vaucheret,et al.  Plant ARGONAUTES. , 2008, Trends in plant science.

[32]  S. Jacobsen,et al.  Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. , 2007, Genes & development.

[33]  Y. Ohba,et al.  Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis. , 2007, Plant & cell physiology.

[34]  Yuda Fang,et al.  Identification of Nuclear Dicing Bodies Containing Proteins for MicroRNA Biogenesis in Living Arabidopsis Plants , 2007, Current Biology.

[35]  N. Fedoroff,et al.  Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body , 2007, Proceedings of the National Academy of Sciences.

[36]  Xianwu Zheng,et al.  Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing , 2007, The EMBO journal.

[37]  Leemor Joshua-Tor,et al.  Slicer and the argonautes. , 2007, Nature chemical biology.

[38]  Nicolas Bouché,et al.  An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs , 2006, The EMBO journal.

[39]  I. Henderson,et al.  Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning , 2006, Nature Genetics.

[40]  Rogerio Margis,et al.  The evolution and diversification of Dicers in plants , 2006, FEBS letters.

[41]  M. Wassenegger,et al.  Nomenclature and functions of RNA-directed RNA polymerases. , 2006, Trends in plant science.

[42]  R. Poethig,et al.  A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. , 2005, Genes & development.

[43]  Edwards Allen,et al.  DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[44]  S. Lerbs-Mache,et al.  Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. , 2005, Genes & development.

[45]  Xuemei Chen,et al.  Methylation Protects miRNAs and siRNAs from a 3′-End Uridylation Activity in Arabidopsis , 2005, Current Biology.

[46]  D. Baulcombe,et al.  Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[47]  David P. Kreil,et al.  Atypical RNA polymerase subunits required for RNA-directed DNA methylation , 2005, Nature Genetics.

[48]  D. Baulcombe,et al.  RNA Polymerase IV Directs Silencing of Endogenous DNA , 2005, Science.

[49]  Thomas Tuschl,et al.  Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein , 2005, Nature.

[50]  D. Barford,et al.  Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex , 2005, Nature.

[51]  C. Pikaard,et al.  Plant Nuclear RNA Polymerase IV Mediates siRNA and DNA Methylation-Dependent Heterochromatin Formation , 2005, Cell.

[52]  Gang Wu,et al.  Nuclear processing and export of microRNAs in Arabidopsis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Xuemei Chen,et al.  Methylation as a Crucial Step in Plant microRNA Biogenesis , 2005, Science.

[54]  BMC Bioinformatics , 2005 .

[55]  D. Baulcombe.  RNA silencing in plants , 2004, Nature.

[56]  J. M. Thomson,et al.  Argonaute2 Is the Catalytic Engine of Mammalian RNAi , 2004, Science.

[57]  Adam M. Gustafson,et al.  Genetic and Functional Diversification of Small RNA Pathways in Plants , 2004, PLoS biology.

[58]  H. Vaucheret,et al.  The Nuclear dsRNA Binding Protein HYL1 Is Required for MicroRNA Accumulation and Plant Development, but Not Posttranscriptional Transgene Silencing , 2004, Current Biology.

[59]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[60]  Jennifer Daub,et al.  Expressed sequence tags: medium-throughput protocols. , 2004, Methods in molecular biology.

[61]  Xiaofeng Cao,et al.  ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation , 2003, Science.

[62]  V. Brendel,et al.  GeneSeqer@PlantGDB: Gene structure prediction in plant genomes. , 2003, Nucleic acids research.

[63]  J. Kelly,et al.  ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation , 2003 .

[64]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[65]  R. Shoemaker,et al.  Genome duplication in soybean (Glycine subgenus soja). , 1996, Genetics.

[66]  M. Boguski,et al.  dbEST — database for “expressed sequence tags” , 1993, Nature Genetics.