The Epigenome and Plant Development

Histone Methylation in Higher Plants

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

Small RNAs in angiosperm gametophytes: from epigenetics to gamete development

(2010) G. Le Trionnaire et al.   GENES & DEVELOPMENT

Histone Acetyltransferase AtGCN5/HAG1 Is a Versatile Regulator of Developmental and Inducible Gene Expression in Arabidopsis

(2010) Caroline Servet et al.   Molecular Plant

Control of female gamete formation by a small RNA pathway in Arabidopsis

(2010) Vianey Olmedo-Monfil et al.   NATURE

Zeroing in on DNA methylomes with no BS

(2010) Joseph R Ecker   NATURE METHODS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

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

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

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice

(2010) Huihuang Yan 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

Conservation and divergence in eukaryotic DNA methylation

(2010) T.-f. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Small RNA Makes Its Move

(2010) R. Martienssen   SCIENCE

Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells

(2010) P. Dunoyer et al.   SCIENCE

Phylogeny of Methylomes

(2010) A. Jeltsch   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

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

(2010) A. Molnar et al.   SCIENCE

siRNAs and DNA methylation: seedy epigenetics

(2010) Rebecca A. Mosher et al.   TRENDS IN PLANT SCIENCE

Small RNAs and Their Roles in Plant Development

(2009) Xuemei Chen   Annual Review of Cell and Developmental Biology

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

RNA-mediated chromatin-based silencing in plants

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

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

(2009) Ryan Lister et al.   CURRENT OPINION IN PLANT BIOLOGY

Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes

(2009) J. Reinders et al.   GENES & DEVELOPMENT

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

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

(2009) Rebecca A. Mosher et al.   NATURE

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Dynamic Histone Modifications in Light-Regulated Gene Expression

(2009) N. R. Hofmann   PLANT CELL

Deep Sequencing Maps the Maize Epigenomic Landscape

(2009) N. A. Eckardt   PLANT CELL

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

Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis

(2009) J.-B. F. Charron et al.   PLANT CELL

A transcriptomic analysis of superhybrid rice LYP9 and its parents

(2009) G. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more

(2009) François Roudier et al.   TRENDS IN GENETICS

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

(2009) Frank Johannes et al.   PLoS Genetics

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

Reprogramming the epigenome during germline and seed development

(2009) Mark A Johnson et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Epigenome Sequencing Comes of Age

(2008) Jian-Kang Zhu   CELL

Cellular Programming of Plant Gene Imprinting

(2008) Jin Hoe Huh et al.   CELL

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

(2008) Ryan Lister et al.   CELL

Chromatin state maps: new technologies, new insights

(2008) Eric M Mendenhall et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Population epigenetics

(2008) Eric J Richards   CURRENT OPINION IN GENETICS & DEVELOPMENT

Developmental and Environmental Signals Induce Distinct Histone Acetylation Profiles on Distal and Proximal Promoter Elements of the C4-Pepc Gene in Maize

(2008) S. Offermann et al.   GENETICS

Dominance, Overdominance and Epistasis Condition the Heterosis in Two Heterotic Rice Hybrids

(2008) Lanzhi Li et al.   GENETICS

Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion

(2008) J. Reinders et al.   GENOME RESEARCH

Mechanism of PHERES1 imprinting in Arabidopsis

(2008) G. Makarevich et al.   JOURNAL OF CELL SCIENCE

A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

(2008) Hui-Yong Zhang et al.   Molecular Plant

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE

A molecular framework for light and gibberellin control of cell elongation

(2008) Miguel de Lucas et al.   NATURE

Coordinated regulation of Arabidopsis thaliana development by light and gibberellins

(2008) Suhua Feng et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Genome-wide approaches to studying chromatin modifications

(2008) Dustin E. Schones et al.   NATURE REVIEWS GENETICS

Epigenome dynamics: a quantitative genetics perspective

(2008) Frank Johannes et al.   NATURE REVIEWS GENETICS

DNA methylation landscapes: provocative insights from epigenomics

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

MATERNALLY EXPRESSED PAB C-TERMINAL, a Novel Imprinted Gene in Arabidopsis, Encodes the Conserved C-Terminal Domain of Polyadenylate Binding Proteins

(2008) S. Tiwari et al.   PLANT CELL

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

(2008) X. Li et al.   PLANT CELL

Histone Modifications and Expression of Light-Regulated Genes in Arabidopsis Are Cooperatively Influenced by Changing Light Conditions

(2008) L. Guo 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

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

From Genotype to Phenotype: Systems Biology Meets Natural Variation

(2008) P. N. Benfey et al.   SCIENCE

The Epigenetic Landscape of Plants

(2008) X. Zhang   SCIENCE

The methylome: approaches for global DNA methylation profiling

(2008) Stephan Beck et al.   TRENDS IN GENETICS

Inputs and outputs for chromatin-targeted RNAi

(2008) Simon W-L. Chan   TRENDS IN PLANT SCIENCE

Epigenomic Consequences of Immortalized Plant Cell Suspension Culture

(2008) Milos Tanurdzic et al.   PLOS BIOLOGY

Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana

(2008) Jixian Zhai et al.   PLoS Genetics

Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays

(2008) Xu Zhang et al.   PLoS Genetics