RNA-directed DNA Methylation

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Plant microRNAs: Biogenesis, Homeostasis, and Degradation

(2019) Junli Wang et al.   Frontiers in Plant Science

Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

(2019) Ashot Papikian et al.   Nature Communications

Author Correction: Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis

(2019) Javier Gallego-Bartolomé et al.   CELL

Paternally acting canonical RNA-directed DNA methylation pathway genes sensitize Arabidopsis endosperm to paternal genome dosage

(2019) P.R. V. Satyaki et al.   PLANT CELL

Non-canonical RNA-directed DNA methylation participates in maternal and environmental control of seed dormancy

(2019) Mayumi Iwasaki et al.   eLife

Crosstalk between epigenetic silencing and infection by tobacco rattle virus in Arabidopsis

(2019) Laura Diezma‐Navas et al.   MOLECULAR PLANT PATHOLOGY

GMO-free RNAi: exogenous application of RNA molecules in plants.

(2019) Athanasios Dalakouras et al.   PLANT PHYSIOLOGY

RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs

(2019) Rafael Yaari et al.   Nature Communications

Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway

(2019) Jasleen Singh et al.   MOLECULAR CELL

Transposons: a blessing curse

(2018) Manu J Dubin et al.   CURRENT OPINION IN PLANT BIOLOGY

Specifications of Targeting Heterochromatin Modifications in Plants

(2018) Jered M. Wendte et al.   Molecular Plant

Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family

(2018) Ming Zhou et al.   NATURE GENETICS

Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa

(2018) Jeffrey W. Grover et al.   PLANT JOURNAL

Transposon-Derived Non-coding RNAs and Their Function in Plants

(2018) Jungnam Cho   Frontiers in Plant Science

Dynamic DNA Methylation in Plant Growth and Development

(2018) Arthur Bartels et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation

(2018) Xueqin Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Four putative SWI2/SNF2 chromatin remodelers have dual roles in regulating DNA methylation in Arabidopsis

(2018) Dong-Lei Yang et al.   Cell Discovery

Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation

(2018) Shuai Zhao et al.   CELL RESEARCH

A DNA methylation reader complex that enhances gene transcription

(2018) C. Jake Harris et al.   SCIENCE

A variably imprinted epiallele impacts seed development

(2018) Daniela Pignatta et al.   PLoS Genetics

Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes

(2017) Jing Wang et al.   GENES & DEVELOPMENT

Regulation of genome-wide DNA methylation by mobile small RNAs

(2017) Muluneh Tamiru et al.   NEW PHYTOLOGIST

Active DNA demethylation: mechanism and role in plant development

(2017) Yan Li et al.   PLANT CELL REPORTS

Dual control of ROS1-mediated active DNA demethylation by DNA damage-binding protein 2 (DDB2)

(2017) Dolores Córdoba-Cañero et al.   PLANT JOURNAL

Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit

(2017) Ben P. Williams et al.   Nature Communications

The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity

(2017) Christina Ernst et al.   Nature Communications

A Small RNA Pathway Mediates Allelic Dosage in Endosperm

(2017) Robert M. Erdmann et al.   Cell Reports

Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants

(2017) Ana M. Fortes et al.   Frontiers in Plant Science

Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple

(2017) Xinwei Guo et al.   Frontiers in Plant Science

Molecular movement in the Arabidopsis thaliana female gametophyte

(2017) Robert M. Erdmann et al.   Plant Reproduction

The evolutionary origin of plant and animal microRNAs

(2017) Yehu Moran et al.   Nature Ecology & Evolution

Evidence for ARGONAUTE4–DNA interactions in RNA-directed DNA methylation in plants

(2016) Sylvie Lahmy et al.   GENES & DEVELOPMENT

The function of small RNAs in plant biotic stress response

(2016) Juan Huang et al.   Journal of Integrative Plant Biology

Arabidopsis RNA Polymerases IV and V Are Required To Establish H3K9 Methylation, but Not Cytosine Methylation, on Geminivirus Chromatin

(2016) Jamie N. Jackel et al.   JOURNAL OF VIROLOGY

RNAi in Plants: An Argonaute-Centered View

(2016) Xiaofeng Fang et al.   PLANT CELL

Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae

(2016) Marcelinus R. Hatorangan et al.   PLANT CELL

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

Mobile small RNAs regulate genome-wide DNA methylation

(2016) Mathew G. Lewsey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Methylation Signatures of the Plant Chromomethyltransferases

(2016) Quentin Gouil et al.   PLoS Genetics

Epigenetic Control of Defense Signaling and Priming in Plants

(2016) Nino A. Espinas et al.   Frontiers in Plant Science

A Stress-Activated Transposon in Arabidopsis Induces Transgenerational Abscisic Acid Insensitivity

(2016) Hidetaka Ito et al.   Scientific Reports

Exploiting mobile RNA silencing for crop improvement

(2015) Jochen Gohlke et al.   AMERICAN JOURNAL OF BOTANY

RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants

(2015) Marjori A. Matzke et al.   Annual Review of Plant Biology

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

(2015) Jixian Zhai et al.   CELL

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

(2015) Ming Zhou et al.   CURRENT OPINION IN PLANT BIOLOGY

Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway

(2015) Lu Ma et al.   Genome Biology and Evolution

Salt-induced transcription factorMYB74is regulated by the RNA-directed DNA methylation pathway inArabidopsis

(2015) Rui Xu et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA silencing movement in plants

(2015) Glykeria Mermigka et al.   Journal of Integrative Plant Biology

Ancient Origin and Recent Innovations of RNA Polymerase IV and V

(2015) Yi Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic transitions leading to heritable, RNA-mediated de novo silencing inArabidopsis thaliana

(2015) Donna M. Bond et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory link between DNA methylation and active demethylation inArabidopsis

(2015) Mingguang Lei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methylation-Sensitive Expression of a DNA Demethylase Gene Serves As an Epigenetic Rheostat

(2015) Ben P. Williams et al.   PLoS Genetics

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

The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs inArabidopsis

(2014) Nicolas G. Bologna et al.   Annual Review of Plant Biology

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation

(2014) A. D. McCue et al.   EMBO JOURNAL

A Two-Step Process for Epigenetic Inheritance in Arabidopsis

(2014) Todd Blevins et al.   MOLECULAR CELL

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

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

Graft-transmissible movement of inverted-repeat-induced siRNA signals into flowers

(2014) Wenna Zhang et al.   PLANT JOURNAL

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

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

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

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

(2014) Daniela Pignatta et al.   eLife

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

Transgenes and their contributions to epigenetic research

(2013) Peter Meyer   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Arabidopsis Double-Stranded RNA Binding Protein DRB3 Participates in Methylation-Mediated Defense against Geminiviruses

(2013) P. Raja et al.   JOURNAL OF VIROLOGY

The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

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

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

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & 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

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

Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species

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

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

(2013) Jochen Gohlke et al.   PLoS Genetics

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

(2012) Jiamu Du et al.   CELL

Regulation of small RNA stability: methylation and beyond

(2012) Lijuan Ji et al.   CELL RESEARCH

DNA Methylation Dynamics during Sexual Reproduction in Arabidopsis thaliana

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

Epigenetic responses to stress: triple defense?

(2012) Ruben Gutzat et al.   CURRENT OPINION IN PLANT BIOLOGY

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

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

RNA Silencing and Plant Viral Diseases

(2012) Ming-Bo Wang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

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

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

The origin and effect of small RNA signaling in plants

(2012) Jean-Sébastien Parent et al.   Frontiers in Plant Science

Identification of genes required for de novo DNA methylation in Arabidopsis

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

A mobile signal transported over a long distance induces systemic transcriptional gene silencing in a grafted partner

(2011) Songling Bai et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II

(2011) Mikel Zaratiegui et al.   NATURE

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

PIWI-interacting small RNAs: the vanguard of genome defence

(2011) Mikiko C. Siomi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Herbivory in the Previous Generation Primes Plants for Enhanced Insect Resistance

(2011) S. Rasmann et al.   PLANT PHYSIOLOGY

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

(2011) Changho Eun et al.   PLoS One

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

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

Virus-mediated efficient induction of epigenetic modifications of endogenous genes with phenotypic changes in plants

(2010) Akira Kanazawa et al.   PLANT JOURNAL

Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins

(2010) Alex Boyko et al.   PLoS One

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

(2010) A. Molnar et al.   SCIENCE

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

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

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

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

A hairpin RNA construct residing in an intron efficiently triggered RNA-directed DNA methylation in tobacco

(2009) Athanasios Dalakouras et al.   PLANT JOURNAL

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

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

Use, tolerance and avoidance of amplified RNA silencing by plants

(2008) Olivier Voinnet   TRENDS IN PLANT SCIENCE