DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress

Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis

(2020) Linhua Sun et al.   Nature Communications

DNA methylation enables transposable element-driven genome expansion

(2020) Wanding Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Shujing Liu et al.   NEW PHYTOLOGIST

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

(2019) Jered M Wendte et al.   eLife

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   BIOINFORMATICS

Dynamics and function of DNA methylation in plants

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

Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing

(2018) Xiangsong Chen et al.   PLANT CELL

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

(2018) Shuiming Qian et al.   Nature Communications

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

(2018) Cuijun Zhang et al.   Nature Communications

A subclass of HSP70s regulate development and abiotic stress responses in Arabidopsis thaliana

(2016) Linna Leng et al.   JOURNAL OF PLANT RESEARCH

DNA Methylation Signatures of the Plant Chromomethyltransferases

(2016) Quentin Gouil et al.   PLoS Genetics

Silencing of active transposable elements in plants

(2015) Dalen Fultz et al.   CURRENT OPINION IN PLANT BIOLOGY

Stress-induced structural changes in plant chromatin

(2015) Aline V Probst et al.   CURRENT OPINION IN PLANT BIOLOGY

DNA methylation pathways and their crosstalk with histone methylation

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

High-temperature effect on genes engaged in DNA methylation and affected by DNA methylation in Arabidopsis

(2015) Mladen Naydenov et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

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

(2015) Manu J Dubin et al.   eLife

A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis

(2015) Wataru Matsunaga et al.   Frontiers in Plant Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

(2013) Hume Stroud et al.   CELL

The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

(2013) Olga V. Popova et al.   Molecular Plant

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

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

(2012) Jiamu Du et al.   CELL

Epigenetic control of transposon transcription and mobility in Arabidopsis

(2012) Etienne Bucher et al.   CURRENT OPINION IN PLANT BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Arabidopsis HsfA1 transcription factors function as the main positive regulators in heat shock-responsive gene expression

(2011) Takumi Yoshida et al.   MOLECULAR GENETICS AND GENOMICS

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis

(2011) HSIANG-CHIN LIU et al.   PLANT CELL AND ENVIRONMENT

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Ales Pecinka et al.   PLANT CELL

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

(2009) Ken Naito et al.   NATURE

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading

(2008) I. R. Henderson et al.   GENES & DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY