Ancient Origin and Recent Innovations of RNA Polymerase IV and V

Evolution of the Telomere-Associated Protein POT1a in Arabidopsis thaliana Is Characterized by Positive Selection to Reinforce Protein–Protein Interaction

(2015) Mark A. Beilstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Deep Conservation of Human Protein Tandem Repeats within the Eukaryotes

(2014) Elke Schaper et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation

(2014) Koichi Hori et al.   Nature Communications

Functional Diversification of Maize RNA Polymerase IV and V Subtypes via Alternative Catalytic Subunits

(2014) Jeremy R. Haag et al.   Cell Reports

Molecular Mechanisms of RNA Interference

(2013) Ross C. Wilson et al.   Annual Review of Biophysics

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

A nuclear perspective on RNAi pathways in metazoans

(2013) Germano Cecere et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing

(2012) Li-Chuan Wan et al.   BMC PLANT BIOLOGY

In Vitro Transcription Activities of Pol IV, Pol V, and RDR2 Reveal Coupling of Pol IV and RDR2 for dsRNA Synthesis in Plant RNA Silencing

(2012) Jeremy R. Haag et al.   MOLECULAR CELL

Dynamic expression of small RNA populations in larch (Larix leptolepis)

(2012) Junhong Zhang et al.   PLANTA

Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness

(2012) T. Sikosek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Consequences of Subunit Diversity in RNA Polymerases II and V

(2012) Ek Han Tan et al.   Cell Reports

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

AGO6 Functions in RNA-Mediated Transcriptional Gene Silencing in Shoot and Root Meristems in Arabidopsis thaliana

(2011) Changho Eun et al.   PLoS One

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

The Evolution of a High Copy Gene Array in Arabidopsis

(2010) Joshua Kane et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2010) Vianey Olmedo-Monfil et al.   NATURE

Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm

(2010) Rebecca A. Mosher   NEW PHYTOLOGIST

Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis

(2010) Wojciech M. Karlowski 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

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences

(2009) Andrew F. Neuwald   BIOINFORMATICS

RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family

(2009) Natacha Bies-Etheve et al.   EMBO REPORTS

Two GW Repeat Proteins Interact with Tetrahymena thermophila Argonaute and Promote Genome Rearrangement

(2009) J. Bednenko et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2009) Rebecca A. Mosher et al.   NATURE

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

A three-dimensional view of the molecular machinery of RNA interference

(2009) Martin Jinek et al.   NATURE

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit

(2009) Sylvie Lahmy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes

(2009) Lyudmila Sidorenko et al.   PLoS Genetics

Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

(2009) Jennifer L. Stonaker et al.   PLoS Genetics

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL

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

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

Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

(2008) Thomas S. Ream et al.   MOLECULAR CELL

Escape from adaptive conflict after duplication in an anthocyanin pathway gene

(2008) David L. Des Marais et al.   NATURE

An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II

(2008) Linfeng Huang et al.   NATURE STRUCTURAL & 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

Conifers have a unique small RNA silencing signature

(2008) E. V. Dolgosheina et al.   RNA

Plant ARGONAUTES

(2008) Hervé Vaucheret   TRENDS IN PLANT SCIENCE

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