Reconstructing de novo silencing of an active plant retrotransposon

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

Transitive RNA silencing signals induce cytosine methylation of a transgenic but not an endogenous target

(2013) Leen Vermeersch et al.   PLANT JOURNAL

Interplay among RNA polymerases II, IV and V in RNA-directed DNA methylation at a low copy transgene locus in Arabidopsis thaliana

(2013) Wanhui You et al.   PLANT MOLECULAR BIOLOGY

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs

(2013) S. Nuthikattu et al.   PLANT PHYSIOLOGY

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

(2013) A. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential effects of viral silencing suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1

(2012) Gregory Schott et al.   EMBO JOURNAL

Ago Hook and RNA Helicase Motifs Underpin Dual Roles for SDE3 in Antiviral Defense and Silencing of Nonconserved Intergenic Regions

(2012) Damien Garcia et al.   MOLECULAR CELL

NERD, a Plant-Specific GW Protein, Defines an Additional RNAi-Dependent Chromatin-Based Pathway in Arabidopsis

(2012) Dominique Pontier et al.   MOLECULAR CELL

RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

(2012) Qi Zheng et al.   PLANT JOURNAL

RDR2 Partially Antagonizes the Production of RDR6-Dependent siRNA in Sense Transgene-Mediated PTGS

(2012) Vincent Jauvion et al.   PLoS One

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

The 21-Nucleotide, but Not 22-Nucleotide, Viral Secondary Small Interfering RNAs Direct Potent Antiviral Defense by Two Cooperative Argonautes inArabidopsis thaliana

(2011) Xian-Bing Wang et al.   PLANT CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Viral Suppressors of RNA-Based Viral Immunity: Host Targets

(2010) Qingfa Wu et al.   Cell Host & Microbe

Polar auxin transport together with AINTEGUMENTA and REVOLUTA coordinate early Arabidopsis gynoecium development

(2010) Staci Nole-Wilson et al.   DEVELOPMENTAL BIOLOGY

An endogenous, systemic RNAi pathway in plants

(2010) Patrice Dunoyer et al.   EMBO JOURNAL

Accurate sodium bisulfite sequencing in plants

(2010) Ian R. Henderson et al.   Epigenetics

Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein

(2010) J. Azevedo et al.   GENES & DEVELOPMENT

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

A Gain-of-Function Mutation in the Arabidopsis Disease Resistance Gene RPP4 Confers Sensitivity to Low Temperature

(2010) X. Huang et al.   PLANT PHYSIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

RNA-mediated chromatin-based silencing in plants

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

Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes

(2009) J. Reinders et al.   GENES & DEVELOPMENT

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana

(2009) X.-B. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for RNAi in the Selective Correction of DNA Methylation Defects

(2009) F. K. Teixeira et al.   SCIENCE

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

(2009) Frank Johannes et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

Kismeth: Analyzer of plant methylation states through bisulfite sequencing

(2008) Eyal Gruntman et al.   BMC BIOINFORMATICS

A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation

(2008) Lucia Daxinger et al.   EMBO JOURNAL

Improved northern blot method for enhanced detection of small RNA

(2008) Gurman S Pall et al.   Nature Protocols

Invasion of the Arabidopsis Genome by the Tobacco Retrotransposon Tnt1 Is Controlled by Reversible Transcriptional Gene Silencing

(2008) J. Perez-Hormaeche et al.   PLANT PHYSIOLOGY

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE

Use, tolerance and avoidance of amplified RNA silencing by plants

(2008) Olivier Voinnet   TRENDS IN PLANT SCIENCE