Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

(2016) P. A. Crisp et al.   Science Advances

Parental effects and the evolution of phenotypic memory

(2015) B. Kuijper et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Salt-induced transcription factorMYB74is regulated by the RNA-directed DNA methylation pathway inArabidopsis

(2015) Rui Xu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Salinity Is an Agent of Divergent Selection Driving Local Adaptation of Arabidopsis to Coastal Habitats

(2015) Silvia Busoms et al.   PLANT PHYSIOLOGY

Regulatory link between DNA methylation and active demethylation inArabidopsis

(2015) Mingguang Lei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

When is incomplete epigenetic resetting in germ cells favoured by natural selection?

(2015) Tobias Uller et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

(2015) Jörg Hagmann et al.   PLoS Genetics

Methylation-Sensitive Expression of a DNA Demethylase Gene Serves As an Epigenetic Rheostat

(2015) Ben P. Williams et al.   PLoS Genetics

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

(2015) David Secco et al.   eLife

Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress

(2015) Steven R. Eichten et al.   Frontiers in Plant Science

Inositol transporters AtINT2 and AtINT4 regulate arsenic accumulation in Arabidopsis seeds

(2015) Gui-Lan Duan et al.   Nature Plants

Paternal Diet Defines Offspring Chromatin State and Intergenerational Obesity

(2014) Anita Öst et al.   CELL

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

(2014) Edith Heard et al.   CELL

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

Environmentally responsive genome-wide accumulation of de novoArabidopsis thalianamutations and epimutations

(2014) Caifu Jiang et al.   GENOME RESEARCH

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

Genome-Wide Prediction of Highly Specific Guide RNA Spacers for CRISPR–Cas9-Mediated Genome Editing in Model Plants and Major Crops

(2014) Kabin Xie et al.   Molecular Plant

Epigenetic reprogramming in plant sexual reproduction

(2014) Tomokazu Kawashima et al.   NATURE REVIEWS GENETICS

Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering inArabidopsis thaliana

(2014) Friedrich Fauser et al.   PLANT JOURNAL

Protocol: a beginner’s guide to the analysis of RNA-directed DNA methylation in plants

(2014) Huiming Zhang et al.   Plant Methods

In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism

(2014) E. J. Radford et al.   SCIENCE

DNA methylation as a system of plant genomic immunity

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

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

(2014) Danelle K. Seymour et al.   PLoS Genetics

PLncDB: plant long non-coding RNA database

(2013) J. Jin et al.   BIOINFORMATICS

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

(2013) Hume Stroud et al.   CELL

HOW STABLE ‘SHOULD’ EPIGENETIC MODIFICATIONS BE? INSIGHTS FROM ADAPTIVE PLASTICITY AND BET HEDGING

(2013) Jacob J. Herman et al.   EVOLUTION

An Arabidopsis R2R3-MYB transcription factor, AtMYB20, negatively regulates type 2C serine/threonine protein phosphatases to enhance salt tolerance

(2013) Mei Hua Cui et al.   FEBS LETTERS

Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice

(2013) Kanako Yasuda et al.   MOLECULAR BREEDING

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

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs

(2013) S. Nuthikattu et al.   PLANT PHYSIOLOGY

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

Genetics of Climate Change Adaptation

(2012) Steven J. Franks et al.   Annual Review of Genetics

piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans

(2012) Alyson Ashe et al.   CELL

piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline

(2012) Masaki Shirayama et al.   CELL

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

(2012) Joseph P. Calarco et al.   CELL

Epigenetics and the environment: emerging patterns and implications

(2012) Robert Feil et al.   NATURE REVIEWS GENETICS

Stress-Induced Chromatin Changes: A Critical View on Their Heritability

(2012) A. Pecinka et al.   PLANT AND CELL PHYSIOLOGY

Epigenetic Reprogramming in Plant Reproductive Lineages

(2012) J. F. Gutierrez-Marcos et al.   PLANT AND CELL PHYSIOLOGY

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

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

(2012) Filipe Borges et al.   Plant Methods

The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression

(2012) Andriy Bilichak et al.   PLoS One

Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana

(2012) Ivan Baxter et al.   PLoS One

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

Transgenerational epigenetic inheritance in plants

(2011) Marie-Theres Hauser et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Selected aspects of transgenerational epigenetic inheritance and resetting in plants

(2011) Jerzy Paszkowski et al.   CURRENT OPINION IN PLANT BIOLOGY

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Descendants of Primed Arabidopsis Plants Exhibit Resistance to Biotic Stress

(2011) A. Slaughter et al.   PLANT PHYSIOLOGY

Next-Generation Systemic Acquired Resistance

(2011) E. Luna et al.   PLANT PHYSIOLOGY

Herbivory in the Previous Generation Primes Plants for Enhanced Insect Resistance

(2011) S. Rasmann et al.   PLANT PHYSIOLOGY

Modes of response to environmental change and the elusive empirical evidence for bet hedging

(2011) A. M. Simons   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin–Dependent Regulation of AGAMOUS-LIKE36

(2011) Reza Shirzadi et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response

(2010) Michal Jaskiewicz et al.   EMBO REPORTS

Transgenerational Inheritance and Resetting of Stress-Induced Loss of Epigenetic Gene Silencing in Arabidopsis

(2010) Christina Lang-Mladek et al.   Molecular Plant

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

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

Regulated AtHKT1 Gene Expression by a Distal Enhancer Element and DNA Methylation in the Promoter Plays an Important Role in Salt Tolerance

(2010) Dongwon Baek et al.   PLANT AND CELL PHYSIOLOGY

MicroRNA Gene Evolution inArabidopsis lyrataandArabidopsis thaliana

(2010) Noah Fahlgren et al.   PLANT CELL

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

(2010) Zhimin Zheng et al.   PLANT JOURNAL

Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins

(2010) Alex Boyko et al.   PLoS One

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Active DNA Demethylation Mediated by DNA Glycosylases

(2009) Jian-Kang Zhu   Annual Review of Genetics

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

(2009) Szymon Swiezewski et al.   NATURE

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

(2009) Ken Naito et al.   NATURE

CNI1/ATL31, a RING-type ubiquitin ligase that functions in the carbon/nitrogen response for growth phase transition in Arabidopsis seedlings

(2009) Takeo Sato et al.   PLANT JOURNAL

Stress-induced changes in theArabidopsis thalianatranscriptome analyzed using whole-genome tiling arrays

(2009) Georg Zeller et al.   PLANT JOURNAL

AtMyb41 Regulates Transcriptional and Metabolic Responses to Osmotic Stress in Arabidopsis

(2009) F. Lippold et al.   PLANT PHYSIOLOGY

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

(2008) A. Matsui et al.   PLANT AND CELL PHYSIOLOGY