Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis

[1]  J. Deragon,et al.  Parallel action of AtDRB2 and RdDM in the control of transposable element expression , 2015, BMC Plant Biology.

[2]  R. Slotkin,et al.  ARGONAUTE 6 bridges transposable element mRNA‐derived siRNAs to the establishment of DNA methylation , 2015, The EMBO journal.

[3]  O. Voinnet,et al.  Exploring new models of easiRNA biogenesis , 2014, Nature Genetics.

[4]  R. Martienssen,et al.  miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis , 2014, Nature.

[5]  D. Bisaro,et al.  Arabidopsis Double-Stranded RNA Binding Protein DRB3 Participates in Methylation-Mediated Defense against Geminiviruses , 2013, Journal of Virology.

[6]  D. Klessig,et al.  Double-stranded RNA-binding protein 4 is required for resistance signaling against viral and bacterial pathogens. , 2013, Cell reports.

[7]  R. Slotkin,et al.  Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs , 2013, RNA biology.

[8]  R. Slotkin,et al.  The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs1[W][OA] , 2013, Plant Physiology.

[9]  L. Maquat,et al.  Staufen1 dimerizes via a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay , 2013, Nature Structural &Molecular Biology.

[10]  B. Maček,et al.  Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1 , 2012, Cell.

[11]  F. Allain,et al.  RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence , 2012, Cellular and Molecular Life Sciences.

[12]  P. Waterhouse,et al.  DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana , 2012, Plant signaling & behavior.

[13]  P. Waterhouse,et al.  DRB2 Is Required for MicroRNA Biogenesis in Arabidopsis thaliana , 2012, PloS one.

[14]  C. Dean,et al.  Cotranscriptional Role for Arabidopsis DICER-LIKE 4 in Transcription Termination , 2012, Science.

[15]  R. Slotkin,et al.  Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA , 2012, PLoS genetics.

[16]  Nam-Hai Chua,et al.  Arabidopsis DRB4 protein in antiviral defense against Turnip yellow mosaic virus infection. , 2012, The Plant journal : for cell and molecular biology.

[17]  Cristian Chaparro,et al.  Double-stranded RNA binding proteins DRB2 and DRB4 have an antagonistic impact on polymerase IV-dependent siRNA levels in Arabidopsis. , 2011, RNA.

[18]  H. Cerutti,et al.  RNA-Mediated Silencing in Algae: Biological Roles and Tools for Analysis of Gene Function , 2011, Eukaryotic Cell.

[19]  A. Fukudome,et al.  Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4. , 2011, RNA.

[20]  Ryo Okada,et al.  An Arabidopsis RNase III-like protein, AtRTL2, cleaves double-stranded RNA in vitro , 2011, Journal of Plant Research.

[21]  R. Slotkin The epigenetic control of the Athila family of retrotransposons in Arabidopsis , 2010, Epigenetics.

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

[23]  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.

[24]  P. Waterhouse,et al.  The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. , 2009, RNA.

[25]  Jörg D. Becker,et al.  Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen , 2009, Cell.

[26]  D. Purcell,et al.  Bmc Molecular Biology Characterization of the Trbp Domain Required for Dicer Interaction and Function in Rna Interference , 2022 .

[27]  Matthew W Vaughn,et al.  Epigenomic Consequences of Immortalized Plant Cell Suspension Culture , 2008, PLoS biology.

[28]  P. Waterhouse,et al.  The roles of plant dsRNA‐binding proteins in RNAi‐like pathways , 2008, FEBS letters.

[29]  C. Camilleri,et al.  Arabidopsis TONNEAU1 Proteins Are Essential for Preprophase Band Formation and Interact with Centrin[W] , 2008, The Plant Cell Online.

[30]  O. Gascuel,et al.  An improved general amino acid replacement matrix. , 2008, Molecular biology and evolution.

[31]  A. Gatignol,et al.  Interactions between the double-stranded RNA-binding proteins TRBP and PACT define the Medipal domain that mediates protein-protein interactions , 2008, RNA biology.

[32]  Yunje Cho,et al.  Crystal structure of human DGCR8 core , 2007, Nature Structural &Molecular Biology.

[33]  O. Voinnet,et al.  Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways , 2007, Nature Genetics.

[34]  L. Maquat,et al.  Staufen1 regulates diverse classes of mammalian transcripts , 2007, The EMBO journal.

[35]  G. Hannon,et al.  A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. , 2007, Genes & development.

[36]  Gurman Singh Pall,et al.  Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot , 2007, Nucleic acids research.

[37]  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.

[38]  T. Fukuhara,et al.  The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway , 2007, Plant Molecular Biology.

[39]  D. Bartel,et al.  A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. , 2006, Genes & development.

[40]  V. Narry Kim,et al.  Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing , 2006, Nucleic acids research.

[41]  O. Gascuel,et al.  Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. , 2006, Systematic biology.

[42]  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.

[43]  Byoung-Tak Zhang,et al.  Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex , 2006, Cell.

[44]  Nicolas Bouché,et al.  DRB4-Dependent TAS3 trans-Acting siRNAs Control Leaf Morphology through AGO7 , 2006, Current Biology.

[45]  V. Kim,et al.  The role of PACT in the RNA silencing pathway , 2006, The EMBO journal.

[46]  Yuasa Takashi,et al.  The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. , 2005, RNA.

[47]  O. Borsani,et al.  Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis , 2005, Cell.

[48]  A. Mouland,et al.  Interaction of Staufen1 with the 5′ end of mRNA facilitates translation of these RNAs , 2005, Nucleic acids research.

[49]  David P. Bartel,et al.  Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs , 2005, Current Biology.

[50]  R. Shiekhattar,et al.  TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing , 2005, Nature.

[51]  Kuniaki Saito,et al.  Processing of Pre-microRNAs by the Dicer-1–Loquacious Complex in Drosophila Cells , 2005, PLoS biology.

[52]  Andres Ramos,et al.  The double‐stranded RNA‐binding motif, a versatile macromolecular docking platform , 2005, The FEBS journal.

[53]  V. Kim,et al.  The Drosha-DGCR8 complex in primary microRNA processing. , 2004, Genes & development.

[54]  Michael B. Mathews,et al.  The double-stranded-RNA-binding motif: interference and much more , 2004, Nature Reviews Molecular Cell Biology.

[55]  P. Zamore,et al.  A Protein Sensor for siRNA Asymmetry , 2004, Science.

[56]  R. Shiekhattar,et al.  The Microprocessor complex mediates the genesis of microRNAs , 2004, Nature.

[57]  G. Hannon,et al.  Processing of primary microRNAs by the Microprocessor complex , 2004, Nature.

[58]  M. Jantsch,et al.  Oligomerization activity of a double‐stranded RNA‐binding domain , 2004, FEBS letters.

[59]  Yuichiro Watanabe,et al.  Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

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

[62]  Kazuo Shinozaki,et al.  Specific interactions between Dicer-like proteins and HYL1/DRB- family dsRNA-binding proteins in Arabidopsis thaliana , 2004, Plant Molecular Biology.

[63]  J. Deragon,et al.  Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. , 2004, Nucleic acids research.

[64]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[65]  V. Kim,et al.  The nuclear RNase III Drosha initiates microRNA processing , 2003, Nature.

[66]  D. Baulcombe,et al.  An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. , 2003, The Plant journal : for cell and molecular biology.

[67]  K. Hokamp,et al.  A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. , 2003, Genome research.

[68]  C. Mello,et al.  The dsRNA Binding Protein RDE-4 Interacts with RDE-1, DCR-1, and a DExH-Box Helicase to Direct RNAi in C. elegans , 2002, Cell.

[69]  Chang‐Deng Hu,et al.  Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. , 2002, Molecular cell.

[70]  A. Pasquinelli,et al.  A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA , 2001, Science.

[71]  A. Caudy,et al.  Role for a bidentate ribonuclease in the initiation step of RNA interference , 2001 .

[72]  S. Nanduri,et al.  A dynamically tuned double‐stranded RNA binding mechanism for the activation of antiviral kinase PKR , 2000, The EMBO journal.

[73]  J. Paszkowski,et al.  Endogenous Targets of Transcriptional Gene Silencing in Arabidopsis , 2000, Plant Cell.

[74]  M. Mathews,et al.  Proteins binding to duplexed RNA: one motif, multiple functions. , 2000, Trends in biochemical sciences.

[75]  D. St Johnston,et al.  Distinct roles of two conserved Staufen domains in oskar mRNA localization and translation , 2000, The EMBO journal.

[76]  J. Jeddeloh,et al.  Maintenance of genomic methylation requires a SWI2/SNF2-like protein , 1999, Nature Genetics.

[77]  D. St Johnston,et al.  Miranda mediates asymmetric protein and RNA localization in the developing nervous system. , 1998, Genes & development.

[78]  Dominique Ferrandon,et al.  Staufen protein associates with the 3′UTR of bicoid mRNA to form particles that move in a microtubule-dependent manner , 1994, Cell.

[79]  D. St Johnston,et al.  A conserved double-stranded RNA-binding domain. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[80]  Daniel St Johnston,et al.  staufen, a gene required to localize maternal RNAs in the Drosophila egg , 1991, Cell.