The DNA Methylome and Association of Differentially Methylated Regions with Differential Gene Expression during Heat Stress in Brassica rapa

Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

(2018) Mahmoud W. Yaish et al.   BMC GENOMICS

Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa

(2018) Jeffrey W. Grover et al.   PLANT JOURNAL

Cold acclimation alters DNA methylation patterns and confers tolerance to heat and increases growth rate in Brassica rapa

(2017) Tongkun Liu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage

(2016) Xiaoming Song et al.   BMC GENOMICS

Abiotic Stress Signaling and Responses in Plants

(2016) Jian-Kang Zhu   CELL

Water-deficiency conditions differently modulate the methylome of roots and leaves in barley (Hordeum vulgareL.)

(2016) Karolina Chwialkowska et al.   JOURNAL OF EXPERIMENTAL BOTANY

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

(2016) Bo Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylome of the 20-gigabase Norway spruce genome

(2016) Israel Ausin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas

(2016) Jun Li et al.   Scientific Reports

Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

(2015) Wensheng Wang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

DNA methylation and gene expression in Mimulus guttatus

(2015) Jack M. Colicchio et al.   BMC GENOMICS

Epigenetic variation and environmental change: Fig. 1.

(2015) Peter Meyer   JOURNAL OF EXPERIMENTAL BOTANY

SKIP Confers Osmotic Tolerance during Salt Stress by Controlling Alternative Gene Splicing in Arabidopsis

(2015) Jinlin Feng et al.   Molecular Plant

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2015) Manu J Dubin et al.   eLife

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

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

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

(2015) Rohini Garg et al.   Scientific Reports

Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress

(2014) Dan Liang et al.   BMC GENETICS

Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings

(2014) Guizhen Gao et al.   BREEDING SCIENCE

The Dynamics of DNA Methylation in Maize Roots under Pb Stress

(2014) Haiping Ding et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes

(2014) M. Mirouze et al.   JOURNAL OF EXPERIMENTAL BOTANY

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis

(2014) Hongxing Yang et al.   PLANT JOURNAL

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

(2014) Alex Boyko et al.   PLoS One

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

(2014) Xia Shen et al.   PLoS Genetics

The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat

(2014) Kazuo Nakashima et al.   Frontiers in Plant Science

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

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

(2013) Assaf Zemach et al.   CELL

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

(2013) Hume Stroud et al.   CELL

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

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

Analysis of the DNA methylation of maize (Zea mays L.) in response to cold stress based on methylation-sensitive amplified polymorphisms

(2013) Xiaohui Shan et al.   JOURNAL OF PLANT BIOLOGY

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

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

Global Priority Conservation Areas in the Face of 21st Century Climate Change

(2013) Junsheng Li et al.   PLoS One

Arguments for standardizing transposable element annotation in plant genomes

(2013) Raja Ragupathy et al.   TRENDS IN PLANT SCIENCE

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

A Hypomethylated population of Brassica rapa for forward and reverse Epi-genetics

(2012) Stephen Amoah et al.   BMC PLANT BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

(2012) Jiamu Du et al.   CELL

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

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

Salt Stress Induced Variation in DNA Methylation Pattern and Its Influence on Gene Expression in Contrasting Rice Genotypes

(2012) Ratna Karan et al.   PLoS One

The Dynamic Changes of DNA Methylation and Histone Modifications of Salt Responsive Transcription Factor Genes in Soybean

(2012) Yuguang Song 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

The correlation of genome size and DNA methylation rate in metazoans

(2012) Marcus Lechner et al.   THEORY IN BIOSCIENCES

Calmodulin and calmodulin-like proteins in plant calcium signaling

(2011) Alexandre Perochon et al.   BIOCHIMIE

Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.)

(2011) H.P. Kou et al.   JOURNAL OF PLANT PHYSIOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

(2011) Fabienne Brenet et al.   PLoS One

Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.)

(2010) Wen-Sheng Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

(2010) Hui Xiang et al.   NATURE BIOTECHNOLOGY

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

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

Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress inArabidopsis

(2010) Ales Pecinka et al.   PLANT CELL

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Plant molecular stress responses face climate change

(2010) Ishita Ahuja et al.   TRENDS IN PLANT SCIENCE

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

(2010) Yingrui Li et al.   PLOS BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2009) R. Lister et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Analysis of DNA methylation of maize in response to osmotic and salt stress based on methylation-sensitive amplified polymorphism

(2009) Ming-pu Tan   PLANT PHYSIOLOGY AND BIOCHEMISTRY

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

DNA methylation landscapes: provocative insights from epigenomics

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

Epigenetic control of plant stress response

(2007) Alex Boyko et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS