The Role of the Epigenome in Gene Expression Control and the Epimark Changes in Response to the Environment

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

The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis

(2013) Cui-Jun Zhang et al.   EMBO JOURNAL

The DNA Repair Protein XRCC1 Functions in the Plant DNA Demethylation Pathway by Stimulating Cytosine Methylation (5-meC) Excision, Gap Tailoring, and DNA Ligation

(2013) María Isabel Martínez-Macías et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

The Arabidopsis Elongator Complex Subunit2 Epigenetically Regulates Plant Immune Responses

(2013) Y. Wang et al.   PLANT CELL

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

Epigenetic Mechanisms Underlying Genomic Imprinting in Plants

(2012) Claudia Köhler et al.   Annual Review of Plant Biology

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

(2012) Jiamu Du et al.   CELL

Chromatin modification and remodelling: a regulatory landscape for the control of Arabidopsis defence responses upon pathogen attack

(2012) Alexandre Berr et al.   CELLULAR MICROBIOLOGY

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

(2012) Andreas Finke et al.   Epigenetics

The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis

(2012) Israel Ausin et al.   Epigenetics

Seeing the forest for the trees: a wide perspective on RNA-directed DNA methylation

(2012) H. Zhang et al.   GENES & DEVELOPMENT

Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis

(2012) F. Pontvianne et al.   GENES & DEVELOPMENT

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

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

(2012) Yongyou Zhu et al.   MOLECULAR CELL

Demethylation initiated by ROS1 glycosylase involves random sliding along DNA

(2012) María Isabel Ponferrada-Marín et al.   NUCLEIC ACIDS RESEARCH

IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis

(2012) Di Fan et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation in Plants: Relationship to Small RNAs and Histone Modifications, and Functions in Transposon Inactivation

(2012) H. Saze et al.   PLANT AND CELL PHYSIOLOGY

De novo DNA methylation activity of METHYLTRANSFERASE 1 (MET1) partially restores body methylation in Arabidopsis thaliana

(2012) Elena Zubko et al.   PLANT JOURNAL

RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1

(2012) Taku Sasaki et al.   PLANT JOURNAL

Histone H1 affects gene imprinting and DNA methylation in Arabidopsis

(2012) Matthew Rea 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

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

Loss of DNA methylation affects the recombination landscape in Arabidopsis

(2012) M. Mirouze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis

(2012) W. Qian et al.   SCIENCE

Epigenetic and epigenomic variation in Arabidopsis thaliana

(2012) Robert J. Schmitz et al.   TRENDS IN PLANT SCIENCE

Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1

(2012) Taisuke Nishimura et al.   PLoS Genetics

The SET-Domain Protein SUVR5 Mediates H3K9me2 Deposition and Silencing at Stimulus Response Genes in a DNA Methylation–Independent Manner

(2012) Elena Caro et al.   PLoS Genetics

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

(2012) Devin Coleman-Derr et al.   PLoS Genetics

The origin and effect of small RNA signaling in plants

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

Epigenetic control of gene regulation in plants

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

Transgenerational epigenetic inheritance in plants

(2011) Marie-Theres Hauser et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA regulation in plant abiotic stress responses

(2011) Kentaro Nakaminami et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Regulation and function of DNA methylation in plants and animals

(2011) Xin-Jian He et al.   CELL RESEARCH

RNA-directed DNA methylation

(2011) Huiming Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

Epigenetic reprogramming during plant reproduction and seed development

(2011) Heike Wollmann et al.   CURRENT OPINION IN PLANT BIOLOGY

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

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

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

The Pisum sativum psp54 gene requires ABI3 and a chromatin remodeller to switch from a poised to a transcriptionally active state

(2011) Andrés P. Gagete et al.   NEW PHYTOLOGIST

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene

(2011) Li Dong et al.   PLANT JOURNAL

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

(2011) Huan Wang et al.   PLANT JOURNAL

MIGS: miRNA-induced gene silencing

(2011) Felipe Fenselau de Felippes et al.   PLANT JOURNAL

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

(2011) X. Liu et al.   PLANT PHYSIOLOGY

RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription

(2011) C. Sonmez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

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

(2011) Taiko Kim To et al.   PLoS Genetics

Silencing signals in plants: a long journey for small RNAs

(2011) Attila Molnar et al.   GENOME BIOLOGY

Histone Methylation in Higher Plants

(2010) Chunyan Liu et al.   Annual Review of Plant Biology

Epigenetic chromatin modifiers in barley: IV. The study of barley Polycomb group (PcG) genes during seed development and in response to external ABA

(2010) Aliki Kapazoglou et al.   BMC PLANT BIOLOGY

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

Histone variants and modifications in plant gene regulation

(2010) Roger B Deal et al.   CURRENT OPINION IN PLANT BIOLOGY

Methylation and demethylation of the Arabidopsis genome

(2010) Ian J Furner et al.   CURRENT OPINION IN PLANT BIOLOGY

Small RNA-mediated epigenetic modifications in plants

(2010) Stacey A Simon et al.   CURRENT OPINION IN PLANT BIOLOGY

Silencing: new faces of Morpheus’ molecule

(2010) Andrzej T Wierzbicki   EMBO JOURNAL

DNA methylation systems and targets in plants

(2010) Peter Meyer   FEBS LETTERS

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

Methylation-independent DNA Binding Modulates Specificity of Repressor of Silencing 1 (ROS1) and Facilitates Demethylation in Long Substrates

(2010) María Isabel Ponferrada-Marín et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

Transgenerational Inheritance and Resetting of Stress-Induced Loss of Epigenetic Gene Silencing in Arabidopsis

(2010) Christina Lang-Mladek et al.   Molecular Plant

Gene regulation: A chromatin thermostat

(2010) Roger B. Deal et al.   NATURE

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

(2010) Zhihuan Gao et al.   NATURE

Epigenetics as a unifying principle in the aetiology of complex traits and diseases

(2010) Arturas Petronis   NATURE

Histone variants — ancient wrap artists of the epigenome

(2010) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

siRNAs from miRNA sites mediate DNA methylation of target genes

(2010) Padmanabhan Chellappan et al.   NUCLEIC ACIDS RESEARCH

MicroRNA402 Affects Seed Germination of Arabidopsis thaliana Under Stress Conditions via Targeting DEMETER-LIKE Protein3 mRNA

(2010) J. Y. Kim et al.   PLANT AND CELL PHYSIOLOGY

Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation

(2010) LEXUAN GAO et al.   PLANT CELL AND ENVIRONMENT

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression

(2010) Junli Zhou et al.   PLANT MOLECULAR BIOLOGY

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

(2010) Alex Boyko et al.   PLoS One

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

(2010) Catarina Fonseca Lira-Medeiros et al.   PLoS One

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

Active DNA Demethylation Mediated by DNA Glycosylases

(2009) Jian-Kang Zhu   Annual Review of Genetics

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

H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis

(2009) S. Vinod Kumar et al.   CELL

RNA-mediated chromatin-based silencing in plants

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

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

Active DNA demethylation and DNA repair

(2009) Christof Niehrs   DIFFERENTIATION

Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana

(2009) Hisataka Numa et al.   EMBO JOURNAL

MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing

(2009) Chotika Yokthongwattana et al.   EMBO JOURNAL

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

(2009) Tatsuo Kanno et al.   EMBO REPORTS

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

A Truncated Arabidopsis NUCLEOSOME ASSEMBLY PROTEIN 1, AtNAP1;3T, Alters Plant Growth Responses to Abscisic Acid and Salt in the Atnap1;3-2 Mutant

(2009) Zi-Qiang Liu et al.   Molecular Plant

Arabidopsis MSI1 Is Required for Negative Regulation of the Response to Drought Stress

(2009) Cristina Alexandre et al.   Molecular Plant

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

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

(2009) Rebecca A. Mosher et al.   NATURE

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

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

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang et al.   PLANT CELL

Members of the GCN5 Histone Acetyltransferase Complex Regulate PLETHORA-Mediated Root Stem Cell Niche Maintenance and Transit Amplifying Cell Proliferation in Arabidopsis

(2009) N. Kornet et al.   PLANT CELL

Aurora1 phosphorylation activity on histone H3 and its cross-talk with other post-translational histone modifications in Arabidopsis

(2009) Dmitri Demidov et al.   PLANT JOURNAL

Elongator mediates ABA responses, oxidative stress resistance and anthocyanin biosynthesis in Arabidopsis

(2009) Xiaofeng Zhou et al.   PLANT JOURNAL

VERNALIZATION INSENSITIVE 3(VIN3) is required for the response ofArabidopsis thalianaseedlings exposed to low oxygen conditions

(2009) Donna M. Bond et al.   PLANT JOURNAL

Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis

(2009) Chang Seob Kwon et al.   PLANT JOURNAL

SET DOMAIN GROUP25 Encodes a Histone Methyltransferase and Is Involved in FLOWERING LOCUS C Activation and Repression of Flowering

(2009) A. Berr et al.   PLANT PHYSIOLOGY

Epigenetic Regulation of Gene Programs by EMF1 and EMF2 in Arabidopsis

(2009) S. Y. Kim et al.   PLANT PHYSIOLOGY

Transgenerational Stress Memory Is Not a General Response in Arabidopsis

(2009) Ales Pecinka et al.   PLoS One

Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing

(2009) D. Manzano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted 3' Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing

(2009) F. Liu et al.   SCIENCE

RNA Polymerase IV Functions in Paramutation in Zea mays

(2009) K. F. Erhard et al.   SCIENCE

MOLECULAR BIOLOGY: Dynamic DNA Methylation

(2009) J. A. Law et al.   SCIENCE

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

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

RNA-directed DNA methylation and demethylation in plants

(2009) Viswanathan Chinnusamy et al.   Science in China. Series C, Life sciences / Chinese Academy of Sciences

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

Characterization of a Lysine-Specific Histone Demethylase from Arabidopsis thaliana†

(2008) Valentina Spedaletti et al.   BIOCHEMISTRY

Epigenome Sequencing Comes of Age

(2008) Jian-Kang Zhu   CELL

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

The evolving functions of DNA methylation

(2008) Daniel Zilberman   CURRENT OPINION IN PLANT BIOLOGY

Mutations in theArabidopsis SWC6gene, encoding a component of the SWR1 chromatin remodelling complex, accelerate flowering time and alter leaf and flower development

(2008) Ana Lázaro et al.   JOURNAL OF EXPERIMENTAL BOTANY

HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis

(2008) K. Wu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Histone Ubiquitination: Triggering Gene Activity

(2008) Vikki M. Weake et al.   MOLECULAR CELL

ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis

(2008) Xianwu Zheng et al.   NATURE

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

(2008) Daniel Zilberman et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Alterations of Lysine Modifications on the Histone H3 N-Tail under Drought Stress Conditions in Arabidopsis thaliana

(2008) Jong-Myong Kim et al.   PLANT AND CELL PHYSIOLOGY

HAB1-SWI3B Interaction Reveals a Link between Abscisic Acid Signaling and Putative SWI/SNF Chromatin-Remodeling Complexes in Arabidopsis

(2008) A. Saez et al.   PLANT CELL

ARABIDOPSIS TRITHORAX1 Dynamically Regulates FLOWERING LOCUS C Activation via Histone 3 Lysine 4 Trimethylation

(2008) S. Pien et al.   PLANT CELL

Histone Acetylation and Chromatin Remodeling Are Required for UV-B-Dependent Transcriptional Activation of Regulated Genes in Maize

(2008) P. Casati et al.   PLANT CELL

AtCopeg1, the unique gene originated from AtCopia95 retrotransposon family, is sensitive to external hormones and abiotic stresses

(2008) Ke Duan et al.   PLANT CELL REPORTS

Repression of the floral transition via histone H2B monoubiquitination

(2008) Xiaofeng Gu et al.   PLANT JOURNAL

Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks

(2008) Ana Pilar Ortega-Galisteo et al.   PLANT MOLECULAR BIOLOGY

Histone H2B Deubiquitination Is Required for Transcriptional Activation of FLOWERING LOCUS C and for Proper Control of Flowering in Arabidopsis

(2008) R. J. Schmitz et al.   PLANT PHYSIOLOGY

Resetting of FLOWERING LOCUS C expression after epigenetic repression by vernalization

(2008) C. C. Sheldon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana

(2008) R. J. Schmitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development

(2008) Q. Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

(2008) K. Nobuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance

(2008) J. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of Genic DNA Methylation by a jmjC Domain-Containing Protein in Arabidopsis thaliana

(2008) H. Saze et al.   SCIENCE

The Epigenetic Landscape of Plants

(2008) X. Zhang   SCIENCE

Programming of gene expression by Polycomb group proteins

(2008) Claudia Köhler et al.   TRENDS IN CELL BIOLOGY

Roles of RNA polymerase IV in gene silencing

(2008) Craig S. Pikaard et al.   TRENDS IN PLANT SCIENCE

Divergent Evolution of CHD3 Proteins Resulted in MOM1 Refining Epigenetic Control in Vascular Plants

(2008) Marian Čaikovski et al.   PLoS Genetics

Three SRA-Domain Methylcytosine-Binding Proteins Cooperate to Maintain Global CpG Methylation and Epigenetic Silencing in Arabidopsis

(2008) Hye Ryun Woo et al.   PLoS Genetics

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

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