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

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

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

(2014) Zhang-Wei Liu et al.   PLoS Genetics

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

RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis

(2013) T. M. Vu et al.   DEVELOPMENT

The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

(2013) Olga V. Popova et al.   Molecular Plant

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

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

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

PIWI-interacting RNAs: from generation to transgenerational epigenetics

(2013) Maartje J. Luteijn et al.   NATURE REVIEWS GENETICS

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) Thomas R. Brabbs 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

Environmental Heat and Salt Stress Induce Transgenerational Phenotypic Changes in Arabidopsis thaliana

(2013) Léonie Suter et al.   PLoS One

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

Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm

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

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

(2013) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thaliana

(2013) Maxim V. C. Greenberg et al.   PLoS Genetics

DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall Tumors

(2013) Jochen Gohlke et al.   PLoS 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

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

Regulation of small RNA stability: methylation and beyond

(2012) Lijuan Ji et al.   CELL RESEARCH

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

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

DNA Methylation Dynamics during Sexual Reproduction in Arabidopsis thaliana

(2012) Pauline E. Jullien et al.   CURRENT BIOLOGY

IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation

(2012) Andreas Finke et al.   Epigenetics

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

(2012) Tzuu-fen Lee et al.   Epigenetics

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

Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development

(2012) Penny J. Tricker et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

(2012) Dominique Pontier et al.   MOLECULAR CELL

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

(2012) Yongyou Zhu et al.   MOLECULAR CELL

RNAi triggered by specialized machinery silences developmental genes and retrotransposons

(2012) Soichiro Yamanaka et al.   NATURE

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

(2012) Xuehua Zhong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation

(2012) Meng Xie et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

(2012) H. Shen et al.   PLANT CELL

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

(2012) Qi Zheng et al.   PLANT JOURNAL

C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with beet severe curly top virus

(2012) Li-Ping Yang 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

Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection

(2012) Elisson Romanel et al.   PLANT MOLECULAR BIOLOGY

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

(2012) L. Wu et al.   PLANT PHYSIOLOGY

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

(2012) Junhong Zhang et al.   PLANTA

Transgenerational Inheritance of Modified DNA Methylation Patterns and Enhanced Tolerance Induced by Heavy Metal Stress in Rice (Oryza sativa L.)

(2012) Xiufang Ou et al.   PLoS One

The Inheritance Pattern of 24 nt siRNA Clusters in Arabidopsis Hybrids Is Influenced by Proximity to Transposable Elements

(2012) Ying Li 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

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

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

Trans Chromosomal Methylation in Arabidopsis hybrids

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

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeat associated small RNAs vary among parents and following hybridization in maize

(2012) W. T. Barber 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

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

Functional Consequences of Subunit Diversity in RNA Polymerases II and V

(2012) Ek Han Tan et al.   Cell Reports

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

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

Mobile 24 nt Small RNAs Direct Transcriptional Gene Silencing in the Root Meristems of Arabidopsis thaliana

(2011) Charles W. Melnyk et al.   CURRENT BIOLOGY

Paramutation: a process for acquiring trans-generational regulatory states

(2011) Karl F Erhard et al.   CURRENT OPINION IN PLANT BIOLOGY

Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs

(2011) Padubidri V Shivaprasad et al.   EMBO JOURNAL

Identification of genes required for de novo DNA methylation in Arabidopsis

(2011) Maxim V.C. Greenberg et al.   Epigenetics

Genetic Evidence That DNA Methyltransferase DRM2 Has a Direct Catalytic Role in RNA-Directed DNA Methylation in Arabidopsis thaliana

(2011) U. Naumann et al.   GENETICS

Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs

(2011) Michal Kenan-Eichler et al.   GENETICS

Iwr1 Directs RNA Polymerase II Nuclear Import

(2011) Elmar Czeko et al.   MOLECULAR CELL

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker 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

BSCTV C2 Attenuates the Degradation of SAMDC1 to Suppress DNA Methylation-Mediated Gene Silencing inArabidopsis

(2011) Zhonghui Zhang et al.   PLANT CELL

Production of Viable Gametes without Meiosis in Maize Deficient for an ARGONAUTE Protein

(2011) Manjit Singh et al.   PLANT CELL

HDA6 Directly Interacts with DNA Methyltransferase MET1 and Maintains Transposable Element Silencing in Arabidopsis

(2011) X. Liu et al.   PLANT PHYSIOLOGY

Next-Generation Systemic Acquired Resistance

(2011) E. Luna et al.   PLANT PHYSIOLOGY

An Atypical Epigenetic Mechanism Affects Uniparental Expression of Pol IV-Dependent siRNAs

(2011) Rebecca A. Mosher et al.   PLoS One

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

(2011) Changho Eun et al.   PLoS One

Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor

(2011) M. Groszmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are there symplastic connections between the endosperm and embryo in some angiosperms?—a lesson from the Crassulaceae family

(2011) Małgorzata Kozieradzka-Kiszkurno et al.   PROTOPLASMA

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

Small RNAs Prevent Transcription-Coupled Loss of Histone H3 Lysine 9 Methylation in Arabidopsis thaliana

(2011) Raymond A. Enke et al.   PLoS Genetics

Arabidopsis HDA6 Regulates Locus-Directed Heterochromatin Silencing in Cooperation with MET1

(2011) Taiko Kim To et al.   PLoS Genetics

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

(2011) Ana López 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

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

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

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

An endogenous, systemic RNAi pathway in plants

(2010) Patrice Dunoyer et al.   EMBO JOURNAL

Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation

(2010) Angelique Deleris et al.   EMBO REPORTS

Genomic imprinting in plants

(2010) Olivier Garnier et al.   Epigenetics

JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis

(2010) I. R. Searle et al.   GENES & DEVELOPMENT

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

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

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

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

Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm

(2010) Rebecca A. Mosher   NEW PHYTOLOGIST

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

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

Inactivation of a DNA Methylation Pathway in Maize Reproductive Organs Results in Apomixis-Like Phenotypes

(2010) Marcelina Garcia-Aguilar et al.   PLANT CELL

Differential sensitivity of Arabidopsis siRNA biogenesis mutants to genotoxic stress

(2010) Youli Yao et al.   PLANT CELL REPORTS

RNA-mediated trans-communication can establish paramutation at the b1 locus in maize

(2010) M. Arteaga-Vazquez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells

(2010) A. Molnar et al.   SCIENCE

siRNAs and DNA methylation: seedy epigenetics

(2010) Rebecca A. Mosher et al.   TRENDS IN PLANT SCIENCE

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

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-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

Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin

(2009) Vera K Schoft 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

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

Geminivirus AL2 and L2 Proteins Suppress Transcriptional Gene Silencing and Cause Genome-Wide Reductions in Cytosine Methylation

(2009) R. C. Buchmann et al.   JOURNAL OF VIROLOGY

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

(2009) Rebecca A. Mosher et al.   NATURE

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana

(2009) Israel Ausin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Stress-induced DNA methylation changes and their heritability in asexual dandelions

(2009) Koen J. F. Verhoeven et al.   NEW PHYTOLOGIST

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

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

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

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Functional Divergence in the Growing Family of RNA Polymerases

(2009) Robert Landick   STRUCTURE

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

(2008) Andrzej T. Wierzbicki et al.   CELL

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

(2008) Lucia Daxinger et al.   EMBO JOURNAL

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

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

(2008) Tatsuo Kanno et al.   NATURE GENETICS

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

(2008) Linfeng Huang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

(2008) Yana V. Bernatavichute et al.   PLoS One

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

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

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

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