Accessing epigenetic variation in the plant methylome

Genomic Imprinting: Insights From Plants

(2013) Mary Gehring   Annual Review of Genetics

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize

(2013) M. Zhang et al.   GENOME RESEARCH

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis

(2013) Guangming He et al.   Journal of Genetics and Genomics

Genome-Wide Analysis of DNA Methylation in Soybean

(2013) Qing-Xin Song et al.   Molecular Plant

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

(2013) S. R. Eichten et al.   PLANT CELL

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

(2013) S. Takuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

The role of epigenetics in hybrid vigour

(2013) Michael Groszmann et al.   TRENDS IN GENETICS

Epigenetic Mechanisms Underlying Genomic Imprinting in Plants

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

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

(2012) Kelly J Vining et al.   BMC GENOMICS

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

(2012) Xin Li et al.   BMC GENOMICS

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

Paramutation: a trans-homolog interaction affecting heritable gene regulation

(2012) Jay B Hollick   CURRENT OPINION IN PLANT BIOLOGY

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

(2012) H. Shen et al.   PLANT CELL

Advances in plant genome sequencing

(2012) John P. Hamilton et al.   PLANT JOURNAL

FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei

(2012) Filipe Borges et al.   Plant Methods

Trans Chromosomal Methylation in Arabidopsis hybrids

(2012) I. K. Greaves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

Epigenetic and epigenomic variation in Arabidopsis thaliana

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

High-throughput approaches for plant epigenomic studies

(2011) Robert J Schmitz et al.   CURRENT OPINION IN PLANT BIOLOGY

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

(2011) Sébastien A Smallwood et al.   NATURE GENETICS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm

(2011) A. J. Waters et al.   PLANT CELL

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

A comparative analysis of DNA methylation across human embryonic stem cell lines

(2011) Pao-Yang Chen et al.   GENOME BIOLOGY

Paramutation in maize: RNA mediated trans-generational gene silencing

(2010) Mario Alberto Arteaga-Vazquez et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Accurate sodium bisulfite sequencing in plants

(2010) Ian R. Henderson et al.   Epigenetics

Tissue Culture-Induced Novel Epialleles of a Myb Transcription Factor Encoded by pericarp color1 in Maize

(2010) Y. Rhee et al.   GENETICS

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

(2010) M. D. Robinson et al.   GENOME RESEARCH

Whole genome DNA methylation analysis based on high throughput sequencing technology

(2010) Ning Li et al.   METHODS

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Taking the measure of the methylome

(2010) Stephan Beck   NATURE BIOTECHNOLOGY

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

(2010) Hongcang Gu et al.   NATURE METHODS

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

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Genome-scale DNA methylation analysis

(2010) Shaun D Fouse et al.   Epigenomics

RNA-mediated chromatin-based silencing in plants

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

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

(2009) A. L. Brunner et al.   GENOME RESEARCH

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

(2009) R. Lister et al.   GENOME RESEARCH

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

(2009) Mayumi Oda et al.   NUCLEIC ACIDS RESEARCH

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

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-wide DNA methylation profiling

(2009) Marina Bibikova et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Genome-wide DNA methylation profiling using Infinium®assay

(2009) Marina Bibikova et al.   Epigenomics

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

(2008) Ryan Lister et al.   CELL

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

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

Global Characterization of Cell-Specific Gene Expression through Fluorescence-Activated Sorting of Nuclei

(2008) C. Zhang et al.   PLANT PHYSIOLOGY

Repeated big bangs and the expanding universe: Directionality in plant genome size evolution

(2008) Jennifer S. Hawkins et al.   PLANT SCIENCE

The methylome: approaches for global DNA methylation profiling

(2008) Stephan Beck et al.   TRENDS IN GENETICS

Epigenomic Consequences of Immortalized Plant Cell Suspension Culture

(2008) Milos Tanurdzic et al.   PLOS BIOLOGY

Brassica oleracea displays a high level of DNA methylation polymorphism

(2007) Armel Salmon et al.   PLANT SCIENCE