The SET Domain Proteins SUVH2 and SUVH9 Are Required for Pol V Occupancy at RNA-Directed DNA Methylation Loci

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

(2013) Hume Stroud et al.   CELL

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

The stochastic silencing phenotype of Arabidopsismorc6mutants reveals a role in efficientRNA-directedDNAmethylation

(2013) Thomas R. Brabbs et al.   PLANT JOURNAL

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

(2012) Jiamu Du et al.   CELL

Involvement of a GHKL ATPase in RNA-Directed DNA Methylation in Arabidopsis thaliana

(2012) Zdravko J. Lorković et al.   CURRENT BIOLOGY

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats

(2012) Tzuu-fen Lee et al.   Epigenetics

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

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

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing

(2012) Yongyou Zhu 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

The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation

(2012) Meng Xie et al.   PLANT JOURNAL

Developmentally non-redundant SET domain proteins SUVH2 and SUVH9 are required for transcriptional gene silencing in Arabidopsis thaliana

(2012) Markus Kuhlmann et al.   PLANT MOLECULAR BIOLOGY

INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

(2012) I. Ausin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

(2012) G. Moissiard et al.   SCIENCE

IDN2 and Its Paralogs Form a Complex Required for RNA–Directed DNA Methylation

(2012) Cui-Jun Zhang et al.   PLoS Genetics

An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing

(2011) Jun Liu et al.   CELL RESEARCH

A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo

(2011) E. Rajakumara et al.   GENES & DEVELOPMENT

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

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

Independent Chromatin Binding of ARGONAUTE4 and SPT5L/KTF1 Mediates Transcriptional Gene Silencing

(2011) M. Jordan Rowley et al.   PLoS Genetics

SHH1, a Homeodomain Protein Required for DNA Methylation, As Well As RDR2, RDM4, and Chromatin Remodeling Factors, Associate with RNA Polymerase IV

(2011) Julie A. Law et al.   PLoS Genetics

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

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

An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation

(2010) Zhihuan Gao et al.   NATURE

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

(2010) Vianey Olmedo-Monfil et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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

The De Novo Cytosine Methyltransferase DRM2 Requires Intact UBA Domains and a Catalytically Mutated Paralog DRM3 during RNA–Directed DNA Methylation in Arabidopsis thaliana

(2010) Ian R. Henderson et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

An Effector of RNA-Directed DNA Methylation in Arabidopsis Is an ARGONAUTE 4- and RNA-Binding Protein

(2009) Xin-Jian He et al.   CELL

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

RNA-directed DNA methylation and plant development require an IWR1-type transcription factor

(2009) Tatsuo Kanno et al.   EMBO REPORTS

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

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

A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development

(2009) X.-J. He et al.   GENES & DEVELOPMENT

NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation

(2009) X.-J. He et al.   GENES & DEVELOPMENT

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

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

(2009) Rebecca A. Mosher 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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Ryan Lister 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

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

A structural-maintenance-of-chromosomes hinge domain–containing protein is required for RNA-directed DNA methylation

(2008) Tatsuo Kanno et al.   NATURE GENETICS

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

SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation

(2008) Lianna M. Johnson et al.   PLoS Genetics