AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana

The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation

(2021) Pierre Bourguet et al.   Nature Communications

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

(2020) Wen-Biao Jiao et al.   Nature Communications

New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs

(2020) Shoudong Zhang et al.   NUCLEIC ACIDS RESEARCH

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance

(2020) Wenjie Zeng et al.   Journal of Integrative Plant Biology

Chromatin accessibility and the regulatory epigenome

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

Peroxisomal β-oxidation regulates histone acetylation and DNA methylation in Arabidopsis

(2019) Lishuan Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis

(2019) Changqing Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Enhanced JBrowse plugins for epigenomics data visualization

(2018) Brigitte T. Hofmeister et al.   BMC BIOINFORMATICS

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FACT complex is required for DNA demethylation at heterochromatin during reproduction inArabidopsis

(2018) Jennifer M. Frost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

(2018) Cuijun Zhang et al.   Nature Communications

HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing

(2017) Chun-Wei Yu et al.   PLANT CELL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Hume Stroud et al.   CELL

The Methyl-CpG-Binding Protein MBD7 Facilitates Active DNA Demethylation to Limit DNA Hyper-Methylation and Transcriptional Gene Silencing

(2015) Zhaobo Lang et al.   MOLECULAR CELL

HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing

(2015) Emilija Hristova et al.   PLANT PHYSIOLOGY

Methyl-CpG-Binding Domain Protein MBD7 Is Required for Active DNA Demethylation in Arabidopsis

(2015) Chunlei Wang et al.   PLANT PHYSIOLOGY

Two domain-disrupted hda6 alleles have opposite epigenetic effects on transgenes and some endogenous targets

(2015) Shoudong Zhang et al.   Scientific Reports

A Two-Step Process for Epigenetic Inheritance in Arabidopsis

(2014) Todd Blevins et al.   MOLECULAR CELL

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Hume Stroud et al.   CELL

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Jiamu Du et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis

(2012) W. Qian et al.   SCIENCE

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

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

(2011) X. Liu et al.   PLANT PHYSIOLOGY

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

(2011) Taiko Kim To et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation

(2010) K. W. Earley 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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants

(2008) Abdelaty Saleh et al.   Nature Protocols

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

(2008) H. Saze et al.   SCIENCE