Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

Using computational modelling to reveal mechanisms of epigenetic Polycomb control

(2021) Cecilia Lövkvist et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W

(2021) Akihisa Osakabe et al.   NATURE CELL BIOLOGY

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

(2021) Pierre Bourguet et al.   Nature Communications

Intertwined evolution of plant epigenomes and genomes

(2021) Eleanore J Ritter et al.   CURRENT OPINION IN PLANT BIOLOGY

Nurse cell­–derived small RNAs define paternal epigenetic inheritance in Arabidopsis

(2021) Jincheng Long et al.   SCIENCE

Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis

(2020) Linhao Xu et al.   Frontiers in Plant Science

Long-read cDNA Sequencing Enables a 'Gene-Like' Transcript Annotation of Transposable Elements

(2020) Kaushik Panda et al.   PLANT CELL

The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression

(2020) Yan Lai et al.   PLoS Genetics

RNA-directed DNA Methylation

(2020) Robert M. Erdmann et al.   PLoS Genetics

Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in Arabidopsis

(2020) Martin Rougée et al.   Life Science Alliance

Establishment, maintenance, and biological roles of non-CG methylation in plants

(2019) Sunil K. Kenchanmane Raju et al.   Essays in Biochemistry

DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts

(2019) Jaemyung Choi et al.   MOLECULAR CELL

CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation

(2019) Somsakul Pop Wongpalee et al.   Nature Communications

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

(2018) Ming Zhou et al.   NATURE GENETICS

Dynamics and function of DNA methylation in plants

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

DDM1 Represses Noncoding RNA Expression and RNA-Directed DNA Methylation in Heterochromatin

(2018) Feng Tan et al.   PLANT PHYSIOLOGY

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation inArabidopsis

(2018) Yu Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase

(2018) Caitlin I. Stoddard et al.   MOLECULAR CELL

Ten principles of heterochromatin formation and function

(2017) Robin C. Allshire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

(2017) Nicolae Radu Zabet et al.   NUCLEIC ACIDS RESEARCH

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes

(2017) David B Lyons et al.   eLife

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

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

DNA Methylation Signatures of the Plant Chromomethyltransferases

(2016) Quentin Gouil et al.   PLoS Genetics

Accessing the Inaccessible: The Organization, Transcription, Replication, and Repair of Heterochromatin in Plants

(2015) Wei Feng et al.   Annual Review of Genetics

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

(2015) Jixian Zhai et al.   CELL

Gene Body CG and CHG Methylation and Suppression of Centromeric CHH Methylation are Mediated by DECREASE IN DNA METHYLATION1 in Rice

(2015) Hisataka Numa et al.   Molecular Plant

Environmental perception and epigenetic memory: mechanistic insight throughFLC

(2015) Scott Berry et al.   PLANT JOURNAL

A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis

(2015) Kinga Rutowicz et al.   PLANT PHYSIOLOGY

Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis

(2015) Tasuku Ito 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

Replicating nucleosomes

(2015) S. Ramachandran et al.   Science Advances

Plant genome size variation: bloating and purging DNA

(2014) T. P. Michael   Briefings in Functional Genomics

Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE

(2014) Jiamu Du et al.   MOLECULAR CELL

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

(2014) Lianna M. Johnson et al.   NATURE

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

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

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

(2014) J. Sequeira-Mendes et al.   PLANT CELL

DNA methylation as a system of plant genomic immunity

(2014) M. Yvonne Kim et al.   TRENDS IN PLANT SCIENCE

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

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

(2013) Julie A. Law et al.   NATURE

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

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

High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells

(2013) Kaixiang Cao et al.   PLoS Genetics

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

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

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

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

Loss of the DNA Methyltransferase MET1 Induces H3K9 Hypermethylation at PcG Target Genes and Redistribution of H3K27 Trimethylation to Transposons in Arabidopsis thaliana

(2012) Angelique Deleris et al.   PLoS Genetics

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

A Polycomb-based switch underlying quantitative epigenetic memory

(2011) Andrew Angel et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome

(2010) Soichi Inagaki et al.   EMBO JOURNAL

High-Dimensional Variable Selection for Survival Data

(2010) Hemant Ishwaran et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

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

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

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

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

(2009) Asuka Miura et al.   EMBO JOURNAL

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

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

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

(2008) H. Saze et al.   SCIENCE