Epigenome plasticity in plants

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level

(2021) Andrew Farmer et al.   Molecular Plant

Parental nucleosome segregation and the inheritance of cellular identity

(2021) Thelma M. Escobar et al.   NATURE REVIEWS GENETICS

A single-cell analysis of the Arabidopsis vegetative shoot apex

(2021) Tian-Qi Zhang et al.   DEVELOPMENTAL CELL

Nurse cell­–derived small RNAs define paternal epigenetic inheritance in Arabidopsis

(2021) Jincheng Long et al.   SCIENCE

BPC transcription factors and a Polycomb Group protein confine the expression of the ovule identity gene SEEDSTICK in Arabidopsis

(2020) Rosanna Petrella et al.   PLANT JOURNAL

Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin

(2020) Michael Borg et al.   NATURE CELL BIOLOGY

Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns

(2020) Ruben Gutzat et al.   EMBO JOURNAL

Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress

(2020) Shujing Liu et al.   NEW PHYTOLOGIST

A DNA Methylation Reader-Chaperone Regulator-Transcription Factor Complex Activates OsHKT1;5 Expression during Salinity Stress

(2020) Jie Wang et al.   PLANT CELL

DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem

(2020) Asuka Higo et al.   Nature Communications

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

(2019) Leonardo Furci et al.   eLife

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

(2019) Ashot Papikian et al.   Nature Communications

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

(2019) Wai Lim Ku et al.   NATURE METHODS

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

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

(2019) Javier Gallego-Bartolomé et al.   CELL

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

Storing memories: the distinct phases of Polycomb-mediated silencing of Arabidopsis FLC

(2019) Silvia Costa et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

(2019) Jered M Wendte et al.   eLife

Excess Light Priming in Arabidopsis thaliana Genotypes with Altered DNA Methylomes

(2019) Diep R. Ganguly et al.   G3-Genes Genomes Genetics

Monitoring the interplay between transposable element families and DNA methylation in maize

(2019) Jaclyn M. Noshay et al.   PLoS Genetics

Establishment, maintenance, and biological roles of non-CG methylation in plants

(2019) Sunil K. Kenchanmane Raju et al.   Essays in Biochemistry

Cell-type–specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage

(2019) Laura R. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of 5-azacytidine induces DNA hypomethylation and accelerates dormancy release in buds of tree peony

(2019) Yuxi Zhang et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

(2018) Zhaoxue Han et al.   GENETICS

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

(2018) Christian Pflueger et al.   GENOME RESEARCH

Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana

(2018) Yuan-Ye Zhang et al.   HEREDITY

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family

(2018) Ming Zhou et al.   NATURE GENETICS

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development

(2018) Matthias Benoit et al.   NEW PHYTOLOGIST

KAP1 facilitates reinstatement of heterochromatin after DNA replication

(2018) Suk Min Jang et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Diep R. Ganguly et al.   PLANT CELL AND ENVIRONMENT

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

Genome-wide tracking of dCas9-methyltransferase footprints

(2018) Christina Galonska et al.   Nature Communications

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

(2018) Zhaoxue Han et al.   GENETICS

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

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice

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

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

(2017) Jun Xiao et al.   NATURE GENETICS

Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis

(2017) James Walker et al.   NATURE GENETICS

Associating cellular epigenetic models with human phenotypes

(2017) Tuuli Lappalainen et al.   NATURE REVIEWS GENETICS

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

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

Chilling-responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break

(2017) Daniel Conde et al.   PLANT CELL AND ENVIRONMENT

Cyst Nematode Parasitism Induces Dynamic Changes in the Root Epigenome

(2017) Tarek Hewezi et al.   PLANT PHYSIOLOGY

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

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

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

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

Distinct phases of Polycomb silencing to hold epigenetic memory of cold inArabidopsis

(2017) Hongchun Yang et al.   SCIENCE

DNA replication–coupled histone modification maintains Polycomb gene silencing in plants

(2017) Danhua Jiang et al.   SCIENCE

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

Epigenetics, cellular memory and gene regulation

(2016) Steven Henikoff et al.   CURRENT BIOLOGY

The age of multiplexity: recruitment and interactions of Polycomb complexes in plants

(2016) Alexander Förderer et al.   CURRENT OPINION IN PLANT BIOLOGY

The ADP-ribose polymerase Tankyrase regulates adult intestinal stem cell proliferation during homeostasis inDrosophila

(2016) Zhenghan Wang et al.   DEVELOPMENT

Paramutation and related phenomena in diverse species

(2016) Jay B. Hollick   NATURE REVIEWS GENETICS

Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase

(2016) Peter Stepper et al.   NUCLEIC ACIDS RESEARCH

The role of DNA (de)methylation in immune responsiveness of Arabidopsis

(2016) Ana López Sánchez et al.   PLANT JOURNAL

On the origin and evolutionary consequences of gene body DNA methylation

(2016) Adam J. Bewick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression

(2016) Stefanie Rosa et al.   Nature Communications

Polycomb repressive complex’s evolutionary conserved function: the role of EZH2 status and cellular background

(2016) Koraljka Gall Trošelj et al.   Clinical Epigenetics

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

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

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

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

The Methylome of Soybean Roots during the Compatible Interaction with the Soybean Cyst Nematode

(2015) Aditi Rambani et al.   PLANT PHYSIOLOGY

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

(2015) Adriaan van der Graaf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach

(2015) Lorena de la Fuente et al.   Tree Genetics & Genomes

Comprehensive Catalog of Currently Documented Histone Modifications

(2015) Yingming Zhao et al.   Cold Spring Harbor Perspectives in Biology

Requirement of CHROMOMETHYLASE3 for somatic inheritance of the spontaneous tomato epimutation Colourless non-ripening

(2015) Weiwei Chen et al.   Scientific Reports

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

(2015) David Secco et al.   eLife

Somaclonal variation associated with oil palm (Elaeis guineensis Jacq.) clonal propagation: A review

(2014) C. Mgbeze G. et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

Antagonistic Roles for H3K36me3 and H3K27me3 in the Cold-Induced Epigenetic Switch at Arabidopsis FLC

(2014) Hongchun Yang et al.   CURRENT BIOLOGY

Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

(2014) Scott C. Stelpflug et al.   GENETICS

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

(2014) Caifu Jiang et al.   GENOME RESEARCH

Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE

(2014) Jiamu Du et al.   MOLECULAR CELL

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

Genetic Perturbation of the Maize Methylome

(2014) Qing Li et al.   PLANT CELL

Transmission of Epi-Alleles with MET1-Dependent Dense Methylation in Arabidopsis thaliana

(2014) Michael Watson et al.   PLoS One

Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation

(2014) Chizuko Yamamuro et al.   Nature Communications

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

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

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

(2013) Assaf Zemach et al.   CELL

Genome-Wide Analysis of DNA Methylation in Soybean

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

Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes

(2013) Chad E. Niederhuth 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

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants

(2013) German Martinez et al.   NUCLEIC ACIDS RESEARCH

Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

(2013) I. Makarevitch et al.   PLANT CELL

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

Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues

(2013) Steven R. Eichten et al.   Plant Genome

Plants regenerated from tissue culture contain stable epigenome changes in rice

(2013) Hume Stroud et al.   eLife

Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation

(2012) Stéphanie Durand et al.   CURRENT BIOLOGY

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

Assembling chromatin: The long and winding road

(2011) Anthony T. Annunziato   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Maintenance of Silent Chromatin through Replication Requires SWI/SNF-like Chromatin Remodeler SMARCAD1

(2011) Samuel P. Rowbotham et al.   MOLECULAR CELL

A Polycomb-based switch underlying quantitative epigenetic memory

(2011) Andrew Angel et al.   NATURE

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

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity

(2011) Ana López et al.   PLoS Genetics

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

Regulation of stem cell maintenance by the Polycomb protein FIE has been conserved during land plant evolution

(2009) A. Mosquna et al.   DEVELOPMENT

The HP1α–CAF1–SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin

(2009) Alejandra Loyola et al.   EMBO REPORTS

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

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

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

(2009) Szymon Swiezewski et al.   NATURE

MULTIPOLAR SPINDLE 1 (MPS1), a novel coiled-coil protein ofArabidopsis thaliana, is required for meiotic spindle organization

(2009) Hua Jiang et al.   PLANT JOURNAL

Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem

(2009) S. P. Gordon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A polycomb repressive complex 2 gene regulates apogamy and gives evolutionary insights into early land plant evolution

(2009) Y. Okano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

(2009) Frank Johannes et al.   PLoS Genetics

DNA methylation landscapes: provocative insights from epigenomics

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