Maintenance of pre-existing DNA methylation states through recurring excess-light stress

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis

(2017) Peter A. Crisp et al.   PLANT CELL

Araport11: a complete reannotation of theArabidopsis thalianareference genome

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

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

(2017) Diep R. Ganguly et al.   PLANT PHYSIOLOGY

Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant’s adaptation to drought condition

(2017) Xiaoguo Zheng et al.   Scientific Reports

Plant Growth under Natural Light Conditions Provides Highly Flexible Short-Term Acclimation Properties toward High Light Stress

(2017) Tobias Schumann et al.   Frontiers in Plant Science

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

(2016) Steven R. Eichten et al.   GENOME RESEARCH

Least-Squares Means: TheRPackagelsmeans

(2016) Russell V. Lenth   Journal of Statistical Software

A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis

(2016) Ruiqiang Ye et al.   MOLECULAR CELL

Regulation and Levels of the Thylakoid K+/H+Antiporter KEA3 Shape the Dynamic Response of Photosynthesis in Fluctuating Light

(2016) Ute Armbruster et al.   PLANT AND CELL PHYSIOLOGY

Uncoupling High Light Responses from Singlet Oxygen Retrograde Signaling and Spatial-Temporal Systemic Acquired Acclimation

(2016) Melanie Carmody et al.   PLANT PHYSIOLOGY

Mobile small RNAs regulate genome-wide DNA methylation

(2016) Mathew G. Lewsey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation mediates genetic variation for adaptive transgenerational plasticity

(2016) Jacob J. Herman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana

(2016) Dazhe Meng et al.   PLoS Genetics

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

(2016) Anjar Wibowo et al.   eLife

Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling

(2016) Krzysztof Brzezinka et al.   eLife

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

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

A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory

(2015) J. La mke et al.   EMBO JOURNAL

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

The Roles of ROS and ABA in Systemic Acquired Acclimation

(2015) Ron Mittler et al.   PLANT CELL

Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses – a review

(2015) Jan F Humplík et al.   Plant Methods

Methylome analysis reveals an important role for epigenetic changes in the regulation of theArabidopsisresponse to phosphate starvation

(2015) Lenin Yong-Villalobos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

(2015) Qing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

piecewiseSEM: Piecewise structural equation modelling inr for ecology, evolution, and systematics

(2015) Jonathan S. Lefcheck   Methods in Ecology and Evolution

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

(2015) Jörg Hagmann et al.   PLoS Genetics

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

(2015) David Secco et al.   eLife

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

(2015) Manu J Dubin 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

The Split-Apply-Combine Strategy for Data Analysis

(2015) Hadley Wickham   Journal of Statistical Software

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

(2014) Caifu Jiang et al.   GENOME RESEARCH

Photoprotection of photosystems in fluctuating light intensities

(2014) Yagut Allahverdiyeva et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

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

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

Photosynthetic responses of sun- and shade-grown barley leaves to high light: is the lower PSII connectivity in shade leaves associated with protection against excess of light?

(2014) Marek Zivcak et al.   PHOTOSYNTHESIS RESEARCH

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

(2014) S. R. Eichten et al.   PLANT PHYSIOLOGY

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

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

Four distinct types of dehydration stress memory genes in Arabidopsis thaliana

(2013) Yong Ding et al.   BMC PLANT BIOLOGY

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

(2013) Hume Stroud et al.   CELL

Chlorophyll fluorescence analysis: a guide to good practice and understanding some new applications

(2013) E.H. Murchie et al.   JOURNAL OF EXPERIMENTAL BOTANY

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

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

Temporal-Spatial Interaction between Reactive Oxygen Species and Abscisic Acid Regulates Rapid Systemic Acclimation in Plants

(2013) N. Suzuki et al.   PLANT CELL

Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light

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

Systemic and Local Responses to Repeated HL Stress-Induced Retrograde Signaling in Arabidopsis

(2013) Matthew J. Gordon et al.   Frontiers in Plant Science

Photosynthetic acclimation responses of maize seedlings grown under artificial laboratory light gradients mimicking natural canopy conditions

(2013) Matthias Hirth et al.   Frontiers in Plant Science

Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development

(2012) Penny J. Tricker et al.   JOURNAL OF EXPERIMENTAL BOTANY

Carotenoid oxidation products are stress signals that mediate gene responses to singlet oxygen in plants

(2012) F. Ramel 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

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

(2012) Yong Ding et al.   Nature Communications

Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis

(2012) Yukio Kurihara et al.   G3-Genes Genomes Genetics

The role of the xanthophyll cycle and of lutein in photoprotection of photosystem II

(2011) Peter Jahns et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Herbivory in the Previous Generation Primes Plants for Enhanced Insect Resistance

(2011) S. Rasmann et al.   PLANT PHYSIOLOGY

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

Adaptive Transgenerational Plasticity in Plants: Case Studies, Mechanisms, and Implications for Natural Populations

(2011) Jacob J. Herman et al.   Frontiers in Plant Science

Identification of a slowly inducible zeaxanthin-dependent component of non-photochemical quenching of chlorophyll fluorescence generated under steady-state conditions in Arabidopsis

(2010) Manuela Nilkens et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

State transitions—The molecular remodeling of photosynthetic supercomplexes that controls energy flow in the chloroplast

(2010) Jun Minagawa   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

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

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

Systemic low temperature signaling in Arabidopsis

(2010) P. A. Gorsuch et al.   PLANT AND CELL PHYSIOLOGY

Evidence for Light Wavelength-Specific Photoelectrophysiological Signaling and Memory of Excess Light Episodes in Arabidopsis

(2010) M. Szechynska-Hebda et al.   PLANT CELL

RNA-mediated chromatin-based silencing in plants

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

Epigenetic inheritance during the cell cycle

(2009) Aline V. Probst et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Arabidopsis STN7 Kinase Provides a Link between Short- and Long-Term Photosynthetic Acclimation

(2009) P. Pesaresi et al.   PLANT CELL

Quantitative Genetic Analysis of Thermal Dissipation in Arabidopsis

(2009) H.-S. Jung et al.   PLANT PHYSIOLOGY

The Plant NADPH Oxidase RBOHD Mediates Rapid Systemic Signaling in Response to Diverse Stimuli

(2009) G. Miller et al.   Science Signaling

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Chlorophyll Fluorescence: A Probe of Photosynthesis In Vivo

(2008) Neil R. Baker   Annual Review of Plant Biology

Sensing and Responding to Excess Light

(2008) Zhirong Li et al.   Annual Review of Plant Biology

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

Agriculture and the new challenges for photosynthesis research

(2008) E. H. Murchie et al.   NEW PHYTOLOGIST