Secondary siRNAs fromMedicago NB-LRRsmodulated via miRNA-target interactions and their abundances

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synergistic and Independent Actions of Multiple Terminal Nucleotidyl Transferases in the 3’ Tailing of Small RNAs in Arabidopsis

(2015) Xiaoyan Wang et al.   PLoS Genetics

Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis

(2015) Bin Tu et al.   PLoS Genetics

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation

(2014) A. D. McCue et al.   EMBO JOURNAL

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

(2014) Siwaret Arikit et al.   PLANT CELL

Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay

(2014) Q. Liu et al.   PLANT CELL

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs

(2014) Reina Komiya et al.   PLANT JOURNAL

Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development

(2014) Marcela C. Dotto et al.   PLoS Genetics

The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling

(2014) Jie Liu et al.   PLoS Genetics

Determinants beyond Both Complementarity and Cleavage Govern MicroR159 Efficacy in Arabidopsis

(2014) Junyan Li et al.   PLoS Genetics

The Arabidopsis miR472-RDR6 Silencing Pathway Modulates PAMP- and Effector-Triggered Immunity through the Post-transcriptional Control of Disease Resistance Genes

(2014) Martine Boccara et al.   PLoS Pathogens

Multiple RNA recognition patterns during microRNA biogenesis in plants

(2013) N. G. Bologna et al.   GENOME RESEARCH

Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing

(2013) Jixian Zhai et al.   METHODS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots

(2013) Rui Xia et al.   PLANT CELL

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

Plant MicroRNAs Display Differential 3' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species

(2013) J. Zhai et al.   PLANT CELL

3' fragment of miR173-programmed RISC-cleaved RNA is protected from degradation in a complex with RISC and SGS3

(2013) M. Yoshikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis

(2012) Guodong Ren et al.   CURRENT BIOLOGY

The Arabidopsis Nucleotidyl Transferase HESO1 Uridylates Unmethylated Small RNAs to Trigger Their Degradation

(2012) Yuanyuan Zhao et al.   CURRENT BIOLOGY

Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants

(2012) Wanjun Gu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

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

(2012) J. Yan et al.   PLANT CELL

miR156 and miR390 Regulate tasiRNA Accumulation and Developmental Timing in Physcomitrella patens

(2012) S. H. Cho 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

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

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

Apple miRNAs and tasiRNAs with novel regulatory networks

(2012) Rui Xia et al.   GENOME 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

Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes

(2011) Jia-Xing Yue et al.   NEW PHYTOLOGIST

Function and Evolution of a MicroRNA That Regulates a Ca2+-ATPase and Triggers the Formation of Phased Small Interfering RNAs in Tomato Reproductive Growth

(2011) Ying Wang et al.   PLANT CELL

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

(2011) Xianwei Song et al.   PLANT JOURNAL

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

(2011) Y.-L. Guo et al.   PLANT PHYSIOLOGY

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

(2011) A. Si-Ammour et al.   PLANT PHYSIOLOGY

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

A sensitive non-radioactive northern blot method to detect small RNAs

(2010) Sang Woo Kim et al.   NUCLEIC ACIDS RESEARCH

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

miR390,Arabidopsis TAS3tasiRNAs, and TheirAUXIN RESPONSE FACTORTargets Define an Autoregulatory Network Quantitatively Regulating Lateral Root Growth

(2010) Elena Marin et al.   PLANT CELL

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

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

(2010) Marco Todesco et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

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

(2009) C. Johnson et al.   GENOME RESEARCH

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

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

(2008) Taiowa A. Montgomery et al.   CELL

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Criteria for Annotation of Plant MicroRNAs

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