Classification and Comparison of Small RNAs from Plants

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis

(2012) Virginie Jouannet et al.   EMBO JOURNAL

Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

(2012) A. T. Wierzbicki et al.   GENES & DEVELOPMENT

Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

(2012) Xuehua Zhong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of new microRNA-regulated genes by conserved targeting in plant species

(2012) Uciel Chorostecki et al.   NUCLEIC ACIDS RESEARCH

Effective Small RNA Destruction by the Expression of a Short Tandem Target Mimic in Arabidopsis

(2012) J. Yan et al.   PLANT CELL

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

(2012) A. Carbonell et al.   PLANT CELL

A MicroRNA Superfamily Regulates Nucleotide Binding Site-Leucine-Rich Repeats and Other mRNAs

(2012) P. V. Shivaprasad et al.   PLANT CELL

Roles of DICER-LIKE and ARGONAUTE Proteins in TAS-Derived Small Interfering RNA-Triggered DNA Methylation

(2012) L. Wu et al.   PLANT PHYSIOLOGY

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant secondary siRNA production determined by microRNA-duplex structure

(2012) P. A. Manavella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay

(2012) S. Djuranovic et al.   SCIENCE

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

(2012) Andrea D. McCue et al.   PLoS Genetics

Functional Specialization of the Plant miR396 Regulatory Network through Distinct MicroRNA–Target Interactions

(2012) Juan M. Debernardi et al.   PLoS Genetics

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

(2012) Xiaoming Zhang et al.   GENOME BIOLOGY

Uniting Germline and Stem Cells: The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms

(2011) Celina Juliano et al.   Annual Review of Genetics

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

Mobile 24 nt Small RNAs Direct Transcriptional Gene Silencing in the Root Meristems of Arabidopsis thaliana

(2011) Charles W. Melnyk et al.   CURRENT BIOLOGY

Natural Variation in Biogenesis Efficiency of Individual Arabidopsis thaliana MicroRNAs

(2011) Marco Todesco et al.   CURRENT BIOLOGY

Transposable element origins of epigenetic gene regulation

(2011) Damon Lisch et al.   CURRENT OPINION IN PLANT BIOLOGY

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

(2011) N. W. Breakfield et al.   GENOME RESEARCH

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

(2011) Xianwei Song et al.   PLANT JOURNAL

MIGS: miRNA-induced gene silencing

(2011) Felipe Fenselau de Felippes et al.   PLANT JOURNAL

Conservation and divergence in plant microRNAs

(2011) Matthew W. Jones-Rhoades   PLANT MOLECULAR BIOLOGY

An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis

(2011) Qing-Jun Luo et al.   PLANT MOLECULAR BIOLOGY

An Atypical Epigenetic Mechanism Affects Uniparental Expression of Pol IV-Dependent siRNAs

(2011) Rebecca A. Mosher et al.   PLoS One

Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis

(2011) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

A Protein Complex Required for Polymerase V Transcripts and RNA- Directed DNA Methylation in Arabidopsis

(2010) Julie A. Law et al.   CURRENT BIOLOGY

An endogenous, systemic RNAi pathway in plants

(2010) Patrice Dunoyer et al.   EMBO JOURNAL

Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis

(2010) M. Ron et al.   GENES & DEVELOPMENT

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

Control of female gamete formation by a small RNA pathway in Arabidopsis

(2010) Vianey Olmedo-Monfil et al.   NATURE

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis

(2010) Josh T Cuperus et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

siRNAs from miRNA sites mediate DNA methylation of target genes

(2010) Padmanabhan Chellappan et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Gene Evolution inArabidopsis lyrataandArabidopsis thaliana

(2010) Noah Fahlgren et al.   PLANT CELL

Arabidopsis lyrataSmall RNAs: TransientMIRNAand Small Interfering RNA Loci within theArabidopsisGenus

(2010) Zhaorong Ma et al.   PLANT CELL

The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci

(2010) E. R. Havecker et al.   PLANT CELL

microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis

(2010) Linda Beauclair et al.   PLANT JOURNAL

Identification and characterization of a novel miR159 target not related to MYB in tomato

(2010) Kobi Buxdorf et al.   PLANTA

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

(2010) H.-M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

siRNAs and DNA methylation: seedy epigenetics

(2010) Rebecca A. Mosher et al.   TRENDS IN PLANT SCIENCE

A Collection of Target Mimics for Comprehensive Analysis of MicroRNA Function in Arabidopsis thaliana

(2010) Marco Todesco et al.   PLoS Genetics

Small RNAs and Their Roles in Plant Development

(2009) Xuemei Chen   Annual Review of Cell and Developmental Biology

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

RNA-mediated chromatin-based silencing in plants

(2009) Marjori Matzke et al.   CURRENT OPINION IN CELL BIOLOGY

SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies

(2009) Naoyoshi Kumakura et al.   FEBS LETTERS

Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups

(2009) Jie Zong et al.   GENE

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

(2009) Rebecca A. Mosher et al.   NATURE

Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana

(2009) Leonardo Alves-Junior et al.   NUCLEIC ACIDS RESEARCH

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Evolution of microRNAs and their targets: Are all microRNAs biologically relevant?

(2008) M AXTELL   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis

(2008) Hailing Jin et al.   BMC MOLECULAR BIOLOGY

Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation

(2008) Taiowa A. Montgomery et al.   CELL

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

(2008) R. D. Morin et al.   GENOME RESEARCH

Evolution of Arabidopsis MIR genes generates novel microRNA classes

(2008) Franck Vazquez et al.   NUCLEIC ACIDS RESEARCH

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL

Gene silencing in plants using artificial microRNAs and other small RNAs

(2008) Stephan Ossowski et al.   PLANT JOURNAL

Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases

(2008) Diana V. Dugas et al.   PLANT MOLECULAR BIOLOGY

PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis

(2008) R. A. Mosher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

(2008) K. Nobuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conifers have a unique small RNA silencing signature

(2008) E. V. Dolgosheina et al.   RNA

Dual coding of siRNAs and miRNAs by plant transposable elements

(2008) J. Piriyapongsa et al.   RNA

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

Plant ARGONAUTES

(2008) Hervé Vaucheret   TRENDS IN PLANT SCIENCE

Epigenomic Consequences of Immortalized Plant Cell Suspension Culture

(2008) Milos Tanurdzic et al.   PLOS BIOLOGY

Physcomitrella patens DCL3 Is Required for 22–24 nt siRNA Accumulation, Suppression of Retrotransposon-Derived Transcripts, and Normal Development

(2008) Sung Hyun Cho et al.   PLoS Genetics