Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

(2015) Todd Blevins et al.   eLife

Characterizing RNA–protein interaction using cross-linking and metabolite supplemented nuclear RNA-immunoprecipitation

(2014) Phil Chi Khang Au et al.   MOLECULAR BIOLOGY REPORTS

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

(2013) Hume Stroud et al.   CELL

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

Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq

(2012) Qian-Hao Zhu et al.   GENE

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

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

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

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

(2012) L. Wu et al.   PLANT PHYSIOLOGY

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

Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis

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

Epigenetic control of gene regulation in plants

(2011) Massimiliano Lauria et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

(2011) Jeremy R. Haag et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions

(2011) Huan Wang et al.   PLANT JOURNAL

The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity

(2011) Ana López et al.   PLoS Genetics

RNA silencing directed against geminiviruses: Post-transcriptional and epigenetic components

(2010) Priya Raja et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Control of genic DNA methylation in Arabidopsis

(2010) Soichi Inagaki et al.   JOURNAL OF PLANT RESEARCH

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

(2010) Hui Xiang et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du 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

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

SPT5-like, a new component in plant RdDM

(2009) Ming-Bo Wang et al.   EMBO REPORTS

Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis

(2009) B. Zheng et al.   GENES & DEVELOPMENT

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

(2009) Rebecca A. Mosher et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

Fusarium oxysporumhijacks COI1-mediated jasmonate signaling to promote disease development in Arabidopsis

(2009) Louise F. Thatcher et al.   PLANT JOURNAL

RNA-directed DNA methylation induces transcriptional activation in plants

(2009) K. Shibuya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis

(2008) Yukio Kurihara et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

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

(2008) Shijun Mi et al.   CELL

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

(2008) Andrzej T. Wierzbicki et al.   CELL

Synthesis of complementary RNA by RNA-dependent RNA polymerases in plant extracts is independent of an RNA primer

(2008) Lei Wang et al.   FUNCTIONAL PLANT 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

Hairpin RNAs derived from RNA polymerase II and polymerase III promoter-directed transgenes are processed differently in plants

(2008) M.-B. Wang et al.   RNA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY