How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA

(2020) Federico Ariel et al.   MOLECULAR CELL

Natural variation in DNA methylation homeostasis and the emergence of epialleles

(2020) Yinwen Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systemic signaling during abiotic stress combination in plants

(2020) Sara I. Zandalinas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals

(2020) Ben P. Williams et al.   TRENDS IN GENETICS

How Plant Hormones Mediate Salt Stress Responses

(2020) Zipeng Yu et al.   TRENDS IN PLANT SCIENCE

ONSEN shows different transposition activities in RdDM pathway mutants

(2020) Yui Hayashi et al.   GENES & GENETIC SYSTEMS

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

(2020) Ariadna Picart-Picolo et al.   GENOME RESEARCH

Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis

(2019) Leonardo Furci et al.   eLife

The histone methyltransferase G9a regulates tolerance to oxidative stress–induced energy consumption

(2019) Human Riahi et al.   PLOS BIOLOGY

Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress

(2019) C. R. Catacchio et al.   Scientific Reports

Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress

(2019) Soraya Mousavi et al.   Scientific Reports

Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

(2019) Ashot Papikian et al.   Nature Communications

Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis

(2019) Javier Gallego-Bartolomé et al.   CELL

Evidence of developmental escape from transcriptional‐gene‐silencing in MESSI retrotransposons

(2019) Diego H. Sanchez et al.   NEW PHYTOLOGIST

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

(2019) Leandro Quadrana et al.   Nature Communications

Evolutionary flexibility in flooding response circuitry in angiosperms

(2019) Mauricio A. Reynoso et al.   SCIENCE

Environmental and epigenetic regulation of Rider retrotransposons in tomato

(2019) Matthias Benoit et al.   PLoS Genetics

A Role for PICKLE in the Regulation of Cold and Salt Stress Tolerance in Arabidopsis

(2019) Rong Yang et al.   Frontiers in Plant Science

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

(2019) Cristian Forestan et al.   PLANT CELL AND ENVIRONMENT

Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana

(2019) Eriko Sasaki et al.   PLoS Genetics

Transposable elements: all mobile, all different, some stress responsive, some adaptive?

(2018) Sophie Lanciano et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transposable elements, genome evolution and transgenerational epigenetic variation

(2018) Aoi Hosaka et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Targeted DNA demethylation of theArabidopsisgenome using the human TET1 catalytic domain

(2018) Javier Gallego-Bartolomé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational tools to unmask transposable elements

(2018) Patricia Goerner-Potvin et al.   NATURE REVIEWS GENETICS

Immune receptor genes and pericentromeric transposons as targets of common epigenetic regulatory elements

(2018) Damián A Cambiagno et al.   PLANT JOURNAL

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

Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation

(2018) Anjar Wibowo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of epigenetic variation to adaptation in Arabidopsis

(2018) Marc W. Schmid et al.   Nature Communications

A variably imprinted epiallele impacts seed development

(2018) Daniela Pignatta et al.   PLoS Genetics

Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function

(2018) J Grey Monroe et al.   eLife

Developmental Restriction of Retrotransposition Activated in Arabidopsis by Environmental Stress

(2017) Hervé Gaubert et al.   GENETICS

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice

(2017) Jae Young Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

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

Tracking the genome-wide outcomes of a transposable element burst over decades of amplification

(2017) Lu Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural variation identifies genes affecting drought-induced abscisic acid accumulation inArabidopsis thaliana

(2017) Rajesh Kalladan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybrid incompatibility caused by an epiallele

(2017) Todd Blevins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-frequency recombination between members of an LTR retrotransposon family during transposition bursts

(2017) Diego H. Sanchez et al.   Nature Communications

An Arabidopsis Natural Epiallele Maintained by a Feed-Forward Silencing Loop between Histone and DNA

(2017) Astrid Agorio et al.   PLoS Genetics

Developmental Restriction of Retrotransposition Activated in Arabidopsis by Environmental Stress

(2017) Hervé Gaubert et al.   GENETICS

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

(2017) Moises Exposito-Alonso et al.   Nature Ecology & Evolution

Recurrent water deficit causes epigenetic and hormonal changes in citrus plants

(2017) Diana Matos Neves et al.   Scientific Reports

Plant Transgenerational Epigenetics

(2016) Leandro Quadrana et al.   Annual Review of Genetics

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

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

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

Controlled activation of retrotransposition for plant breeding

(2015) Jerzy Paszkowski   CURRENT OPINION IN BIOTECHNOLOGY

New mechanistic links between sugar and hormone signalling networks

(2015) Karin Ljung et al.   CURRENT OPINION IN PLANT BIOLOGY

The inheritance of acquired epigenetic variations: Table 1.

(2015) Eva Jablonka et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Epigenetic mutations can both help and hinder adaptive evolution

(2015) Ilkka Kronholm et al.   MOLECULAR ECOLOGY

Environmental perception and epigenetic memory: mechanistic insight throughFLC

(2015) Scott Berry et al.   PLANT JOURNAL

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

(2015) Tasuku Ito et al.   PLoS Genetics

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

(2015) David Secco et al.   eLife

Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress

(2015) Liliana J. Ferreira et al.   PLoS One

Epigenetic memory in plants

(2014) M. Iwasaki et al.   EMBO JOURNAL

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

(2014) Federico Ariel et al.   MOLECULAR CELL

Identification of Maize Long Non-Coding RNAs Responsive to Drought Stress

(2014) Wei Zhang et al.   PLoS One

Identification of genes preventing transgenerational transmission of stress-induced epigenetic states

(2014) M. Iwasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sugar demand, not auxin, is the initial regulator of apical dominance

(2014) M. G. Mason et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Regulation in Plant Responses to the Environment

(2014) D. C. Baulcombe et al.   Cold Spring Harbor Perspectives in Biology

Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

(2014) Xia Shen et al.   PLoS Genetics

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

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

Soil salinity: A neglected factor in plant ecology and biogeography

(2013) E.N. Bui   JOURNAL OF ARID ENVIRONMENTS

Reconstructing de novo silencing of an active plant retrotransposon

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

The combined effect of salinity and heat reveals a specific physiological, biochemical and molecular response in tomato plants

(2013) ROSA M. RIVERO et al.   PLANT CELL AND ENVIRONMENT

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

(2013) A. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The adaptive invasion of epialleles in a heterogeneous environment

(2013) Jemma L. Geoghegan et al.   THEORETICAL POPULATION BIOLOGY

Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation

(2012) Stéphanie Durand et al.   CURRENT BIOLOGY

Loss of DNA methylation affects the recombination landscape in Arabidopsis

(2012) M. Mirouze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring epiallele stability in a population-epigenetic model

(2012) Jemma L. Geoghegan et al.   THEORETICAL POPULATION BIOLOGY

Epialleles in plant evolution

(2012) Detlef Weigel et al.   GENOME BIOLOGY

A Unified Approach to the Evolutionary Consequences of Genetic and Nongenetic Inheritance

(2011) Troy Day et al.   AMERICAN NATURALIST

Energy efficiency and energy homeostasis as genetic and epigenetic components of plant performance and crop productivity

(2011) Marc De Block et al.   CURRENT OPINION IN PLANT BIOLOGY

Epigenetic contribution to stress adaptation in plants

(2011) Marie Mirouze et al.   CURRENT OPINION IN PLANT BIOLOGY

Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs

(2011) Padubidri V Shivaprasad et al.   EMBO JOURNAL

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana

(2011) W. Matsunaga et al.   PLANT AND CELL PHYSIOLOGY

Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor

(2011) M. Groszmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic control of plant immunity

(2010) MARÍA E. ALVAREZ et al.   MOLECULAR PLANT PATHOLOGY

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

(2010) Catarina Fonseca Lira-Medeiros et al.   PLoS One

Local DNA hypomethylation activates genes in rice endosperm

(2010) A. Zemach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stress-Induced Activation of Heterochromatic Transcription

(2010) Mireille Tittel-Elmer et al.   PLoS Genetics

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

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

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield

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

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Convergent energy and stress signaling

(2008) Elena Baena-González et al.   TRENDS IN PLANT SCIENCE