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

siRNA-mediated chromatin maintenance and its function in Arabidopsis thaliana

(2011) Tatsuo Kanno et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

Regulation and function of DNA methylation in plants and animals

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

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

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

Examination of transpositional activity of nDart1 at different stages of rice development

(2011) Mika Hayashi-Tsugane et al.   GENES & GENETIC SYSTEMS

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

Iwr1 Directs RNA Polymerase II Nuclear Import

(2011) Elmar Czeko et al.   MOLECULAR CELL

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

Epigenetic variation in the FWA gene within the genus Arabidopsis

(2011) Ryo Fujimoto et al.   PLANT JOURNAL

Iwr1 Protein Is Important for Preinitiation Complex Formation by All Three Nuclear RNA Polymerases in Saccharomyces cerevisiae

(2011) Anders Esberg et al.   PLoS One

A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

(2011) H. La et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

The SUVR4 Histone Lysine Methyltransferase Binds Ubiquitin and Converts H3K9me1 to H3K9me3 on Transposon Chromatin in Arabidopsis

(2011) Silje V. Veiseth 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

DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling

(2011) Wei Li et al.   PLoS Genetics

Mammalian methyl-binding proteins: What might they do?

(2010) Michael Joulie et al.   BIOESSAYS

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

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

Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome

(2010) Soichi Inagaki 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

The epigenetic control of the Athila family of retrotransposons in Arabidopsis

(2010) R. Keith Slotkin   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

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

(2010) Zhihuan Gao et al.   NATURE

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

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

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis

(2010) Zhimin Zheng et al.   PLANT JOURNAL

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

Epigenetic reprogramming during vegetative phase change in maize

(2010) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

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

The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect

(2009) Travis Thomson et al.   Annual Review of Cell and Developmental Biology

Active DNA Demethylation Mediated by DNA Glycosylases

(2009) Jian-Kang Zhu   Annual Review of Genetics

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

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

An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites

(2009) Asuka Miura et al.   EMBO JOURNAL

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

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

Many paths to one goal? The proteins that recognize methylated DNA in eukaryotes

(2009) Nobuhiro Sasai et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Characterization of autonomous Dart1 transposons belonging to the hAT superfamily in rice

(2009) Zenpei Shimatani et al.   MOLECULAR GENETICS AND GENOMICS

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

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

(2009) Ken Naito et al.   NATURE

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

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

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

AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation

(2009) Mahmoud W. F. Yaish et al.   PLANT JOURNAL

The Methyl-CpG Binding Proteins Mecp2, Mbd2 and Kaiso Are Dispensable for Mouse Embryogenesis, but Play a Redundant Function in Neural Differentiation

(2009) Isabel Martín Caballero et al.   PLoS One

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

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

What controls nucleosome positions?

(2009) Eran Segal et al.   TRENDS IN GENETICS

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

(2009) Sanzhen Liu et al.   PLoS Genetics

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant 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

Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin?

(2008) T. Clouaire et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription

(2008) Makoto Tachibana et al.   EMBO JOURNAL

Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading

(2008) I. R. Henderson et al.   GENES & DEVELOPMENT

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR 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

Cyclical DNA methylation of a transcriptionally active promoter

(2008) Raphaël Métivier et al.   NATURE

Transient cyclical methylation of promoter DNA

(2008) Sara Kangaspeska et al.   NATURE

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism

(2008) Kyohei Arita et al.   NATURE

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

(2008) Xianwu Zheng et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

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

(2008) Tatsuo Kanno et al.   NATURE GENETICS

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS 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

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

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

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

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

(2008) H. Saze et al.   SCIENCE

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE

Retinoblastoma and Its Binding Partner MSI1 Control Imprinting in Arabidopsis

(2008) Pauline E Jullien et al.   PLOS BIOLOGY

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